From: tcofoegbu Date: Thu, 23 Jul 2015 10:31:22 +0000 (+0100) Subject: JAL-1819 Test cases for Identify file X-Git-Tag: Release_2_10_0~563^2~2 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=4de381907ba9fbd6b079aaf5f1d089680f0d9c6f;p=jalview.git JAL-1819 Test cases for Identify file --- diff --git a/examples/test.aln b/examples/test.aln new file mode 100644 index 0000000..08a7ac3 --- /dev/null +++ b/examples/test.aln @@ -0,0 +1,53 @@ +CLUSTAL + +FER_CAPAA/1-97 -----------------------------------------------------------A +FER_CAPAN/1-144 MA------SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALFGLKS-A--NGGKVTCMA +FER1_SOLLC/1-144 MA------SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA +Q93XJ9_SOLTU/1-144 MA------SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA +FER1_PEA/1-149 MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMA +Q7XA98_TRIPR/1-152 MATT---PALYGTAVSTSFMRRQPVPMSV-ATTTTTKAFPSGFGLKSVSTKRGDLAVAMA +FER1_MESCR/1-148 MAAT--TAALSGATMSTAFAPK--TPPMTAALPTNVGR--ALFGLKS-SASR-GRVTAMA +FER1_SPIOL/1-147 MAAT--TTTMMG--MATTFVPKPQAPPMMAALPSNTGR--SLFGLKT-GSR--GGRMTMA +FER3_RAPSA/1-96 -----------------------------------------------------------A +FER1_ARATH/1-148 MAST----ALSSAIVGTSFIRRSPAPISLRSLPSANTQ--SLFGLKS-GTARGGRVTAMA +FER_BRANA/1-96 -----------------------------------------------------------A +FER2_ARATH/1-148 MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMA +Q93Z60_ARATH/1-118 MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMA +FER1_MAIZE/1-150 MATVLGSPRAPAFFFSSSSLRAAPAPTAV--ALPAAKV--GIMGRSA-SSRR--RLRAQA +O80429_MAIZE/1-140 MAAT---------ALSMSILR---APPPCFSSPLRLRV--AVAKPLA-APMRRQLLRAQA +1A70|/1-97 -----------------------------------------------------------A + +FER_CAPAA/1-97 SYKVKLITPDGPIEFDCPDDVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDG +FER_CAPAN/1-144 SYKVKLITPDGPIEFDCPDNVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDG +FER1_SOLLC/1-144 SYKVKLITPEGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGSVDQSDG +Q93XJ9_SOLTU/1-144 SYKVKLITPDGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGTVDQSDG +FER1_PEA/1-149 SYKVKLVTPDGTQEFECPSDVYILDHAEEVGIDLPYSCRAGSCSSCAGKVVGGEVDQSDG +Q7XA98_TRIPR/1-152 TYKVKLITPEGPQEFDCPDDVYILDHAEEVGIELPYSCRAGSCSSCAGKVVNGNVNQEDG +FER1_MESCR/1-148 AYKVTLVTPEGKQELECPDDVYILDAAEEAGIDLPYSCRAGSCSSCAGKVTSGSVNQDDG +FER1_SPIOL/1-147 AYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQ +FER3_RAPSA/1-96 TYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQ +FER1_ARATH/1-148 TYKVKFITPEGELEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQ +FER_BRANA/1-96 TYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDE +FER2_ARATH/1-148 TYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQ +Q93Z60_ARATH/1-118 TYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQ +FER1_MAIZE/1-150 TYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQ +O80429_MAIZE/1-140 TYNVKLITPEGEVELQVPDDVYILDFAEEEGIDLPFSCRAGSCSSCAGKVVSGSVDQSDQ +1A70|/1-97 AYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQ + +FER_CAPAA/1-97 NFLDDDQLEEGWVLTCVAYPQSDVTIETHKEAELVG- +FER_CAPAN/1-144 NFLDDDQLEEGWVLTCVAYPQSDVTIETHKEAELVG- +FER1_SOLLC/1-144 NFLDEDQEAAGFVLTCVAYPKGDVTIETHKEEELTA- +Q93XJ9_SOLTU/1-144 KFLDDDQEAAGFVLTCVAYPKCDVTIETHKEEELTA- +FER1_PEA/1-149 SFLDDEQIEAGFVLTCVAYPTSDVVIETHKEEDLTA- +Q7XA98_TRIPR/1-152 SFLDDEQIEGGWVLTCVAFPTSDVTIETHKEEELTA- +FER1_MESCR/1-148 SFLDDDQIKEGWVLTCVAYPTGDVTIETHKEEELTA- +FER1_SPIOL/1-147 SFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEELTA- +FER3_RAPSA/1-96 SFLDDDQIAEGFVLTCAAYPTSDVTIETHREEDMV-- +FER1_ARATH/1-148 SFLDDEQIGEGFVLTCAAYPTSDVTIETHKEEDIV-- +FER_BRANA/1-96 SFLDDDQIAEGFVLTCAAYPTSDVTIETHKEEELV-- +FER2_ARATH/1-148 SFLDDEQMSEGYVLTCVAYPTSDVVIETHKEEAIM-- +Q93Z60_ARATH/1-118 SFLDD-------------------------------- +FER1_MAIZE/1-150 SYLDDGQIADGWVLTCHAYPTSDVVIETHKEEELTGA +O80429_MAIZE/1-140 SFLNDNQVADGWVLTCAAYPTSDVVIETHKEDDLL-- +1A70|/1-97 SFLDDDQIDEGWVLTCAAYPVSDVTIETHKKEELTA + diff --git a/examples/test.amsa b/examples/test.amsa new file mode 100644 index 0000000..be456bf --- /dev/null +++ b/examples/test.amsa @@ -0,0 +1,72 @@ +>FER_CAPAA Ferredoxin +-----------------------------------------------------------ASYKVKLITPDGP +IEFDCPDDVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDV +TIETHKEAELVG- +>FER_CAPAN Ferredoxin, chloroplast precursor +MA------SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALFGLKS-A--NGGKVTCMASYKVKLITPDGP +IEFDCPDNVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDV +TIETHKEAELVG- +>FER1_SOLLC Ferredoxin-1, chloroplast precursor +MA------SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMASYKVKLITPEGP +IEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGSVDQSDGNFLDEDQEAAGFVLTCVAYPKGDV +TIETHKEEELTA- +>Q93XJ9_SOLTU Ferredoxin I precursor +MA------SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMASYKVKLITPDGP +IEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGTVDQSDGKFLDDDQEAAGFVLTCVAYPKCDV +TIETHKEEELTA- +>FER1_PEA Ferredoxin-1, chloroplast precursor +MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMASYKVKLVTPDGT +QEFECPSDVYILDHAEEVGIDLPYSCRAGSCSSCAGKVVGGEVDQSDGSFLDDEQIEAGFVLTCVAYPTSDV +VIETHKEEDLTA- +>Q7XA98_TRIPR Ferredoxin I +MATT---PALYGTAVSTSFMRRQPVPMSV-ATTTTTKAFPSGFGLKSVSTKRGDLAVAMATYKVKLITPEGP +QEFDCPDDVYILDHAEEVGIELPYSCRAGSCSSCAGKVVNGNVNQEDGSFLDDEQIEGGWVLTCVAFPTSDV +TIETHKEEELTA- +>FER1_MESCR Ferredoxin-1, chloroplast precursor +MAAT--TAALSGATMSTAFAPK--TPPMTAALPTNVGR--ALFGLKS-SASR-GRVTAMAAYKVTLVTPEGK +QELECPDDVYILDAAEEAGIDLPYSCRAGSCSSCAGKVTSGSVNQDDGSFLDDDQIKEGWVLTCVAYPTGDV +TIETHKEEELTA- +>FER1_SPIOL Ferredoxin-1, chloroplast precursor +MAAT--TTTMMG--MATTFVPKPQAPPMMAALPSNTGR--SLFGLKT-GSR--GGRMTMAAYKVTLVTPTGN +VEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDV +TIETHKEEELTA- +>FER3_RAPSA Ferredoxin, leaf L-A +-----------------------------------------------------------ATYKVKFITPEGE +QEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDDQIAEGFVLTCAAYPTSDV +TIETHREEDMV-- +>FER1_ARATH Ferredoxin-1, chloroplast precursor +MAST----ALSSAIVGTSFIRRSPAPISLRSLPSANTQ--SLFGLKS-GTARGGRVTAMATYKVKFITPEGE +LEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDV +TIETHKEEDIV-- +>FER_BRANA Ferredoxin +-----------------------------------------------------------ATYKVKFITPEGE +QEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDV +TIETHKEEELV-- +>FER2_ARATH Ferredoxin-2, chloroplast precursor +MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGE +QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDV +VIETHKEEAIM-- +>Q93Z60_ARATH At1g10960/T19D16_12 +MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGE +QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD------------------- +------------- +>FER1_MAIZE Ferredoxin-1, chloroplast precursor +MATVLGSPRAPAFFFSSSSLRAAPAPTAV--ALPAAKV--GIMGRSA-SSRR--RLRAQATYNVKLITPEGE +VELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDV +VIETHKEEELTGA +>O80429_MAIZE Ferredoxin +MAAT---------ALSMSILR---APPPCFSSPLRLRV--AVAKPLA-APMRRQLLRAQATYNVKLITPEGE +VELQVPDDVYILDFAEEEGIDLPFSCRAGSCSSCAGKVVSGSVDQSDQSFLNDNQVADGWVLTCAAYPTSDV +VIETHKEDDLL-- +>1A70| +-----------------------------------------------------------AAYKVTLVTPTGN +VEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDV +TIETHKKEELTA +>#_Secondary Structure New description + 1 2 + 3 F F F 4 5 6 7 F 9 + +>#_Iron Sulphur Contacts New description + + F F F F + diff --git a/examples/test.blc b/examples/test.blc new file mode 100644 index 0000000..f419862 --- /dev/null +++ b/examples/test.blc @@ -0,0 +1,175 @@ +>FER_CAPAA/1-97 Ferredoxin +>FER_CAPAN/1-144 Ferredoxin, chloroplast precursor +>FER1_SOLLC/1-144 Ferredoxin-1, chloroplast precursor +>Q93XJ9_SOLTU/1-144 Ferredoxin I precursor +>FER1_PEA/1-149 Ferredoxin-1, chloroplast precursor +>Q7XA98_TRIPR/1-152 Ferredoxin I +>FER1_MESCR/1-148 Ferredoxin-1, chloroplast precursor +>FER1_SPIOL/1-147 Ferredoxin-1, chloroplast precursor +>FER3_RAPSA/1-96 Ferredoxin, leaf L-A +>FER1_ARATH/1-148 Ferredoxin-1, chloroplast precursor +>FER_BRANA/1-96 Ferredoxin +>FER2_ARATH/1-148 Ferredoxin-2, chloroplast precursor +>Q93Z60_ARATH/1-118 At1g10960/T19D16_12 +>FER1_MAIZE/1-150 Ferredoxin-1, chloroplast precursor +>O80429_MAIZE/1-140 Ferredoxin +>1A70|/1-97 +* iteration 1 +-MMMMMMM-M-MMMM- +-AAAAAAA-A-AAAA- +----TTAA-S-SSTA- +----TTTT-T-TTVT- +-------------L-- +-------------G-- +------TT-----S-- +----PPAT-----P-- +-SSSAAAT-A-AAR-- +-VIILLLM-L-LLA-- +-SSSYYSM-S-SSP-- +-AGGGGGG-S-SSA-- +-TTTTTA--A-AAF-- +-MMMAAT--I-IIFA- +-IIIVVMM-V-VVFL- +-SSSSSSA-G-SSSS- +-TTTTTTT-T-TTSM- +-SSSSSAT-S-SSSS- +-FFFFFFF-F-FFSI- +-MLLLMAV-I-LLLL- +-PPPRRPP-R-RRRR- +-RRRTRKK-R-RRA-- +-KKKQQ-P-S-QQA-- +-PPPPP-Q-P-QQP-- +-AAVMVTA-A-TTAA- +-VVVPPPP-P-PPPP- +-TTTMMPP-I-IITP- +-SSSSSMM-S-SSAP- +-LLLVVTM-L-LLVC- +------AA-R-RR-F- +-KKKTAAA-S-SS-S- +-PAATTLL-L-LLAS- +-IIITTPP-P-PPLP- +-PSSKTTS-S-FFPL- +-NNNATNN-A-AAAR- +-VVVFTVT-N-NNAL- +-GGGSKGG-T-TTKR- +-EEENARR-Q-QQVV- +-----F---------- +-----P---------- +-AAAGSAS-S-SSGA- +-LLLFGLL-L-LLIV- +-FFFLFFF-F-FFMA- +-GGGGGGG-G-GGGK- +-LLLLLLL-L-LLRP- +-KKKKKKK-K-KKSL- +-SSSTSST-S-SSAA- +-----V---------- +-AGGSSSG-G-SSSA- +----LTAS-T-TTSP- +----KKSR-A-AARM- +-NRRRRR--R-RRRR- +-GNNGG---G-GG-R- +-GGGDDGG-G-GG-Q- +-KRRLLRG-R-RRRL- +-VIIAAVR-V-VVLL- +-TTTVVTM-T-TTRR- +-CCCAAAT-A-AAAA- +-MMMMMMM-M-MMQQ- +AAAAAAAAAAAAAAAA +SSSSSTAATTTTTTTA +YYYYYYYYYYYYYYYY +KKKKKKKKKKKKKNNK +VVVVVVVVVVVVVVVV +KKKKKKTTKKKKKKKT +LLLLLLLLFFFFFLLL +IIIIVIVVIIIIIIIV +TTTTTTTTTTTTTTTT +PPPPPPPPPPPPPPPP +DDEDDEETEEEEEEET +GGGGGGGGGGGGGGGG +PPPPTPKNEEEEEEEN +IIIIQQQVQLQQQVVV +EEEEEEEEEEEEEEEE +FFFFFFLFVVVVVLLF +DDEEEDEQEEEEEQQQ +CCCCCCCCCCCCCVVC +PPPPPPPPDDDEEPPP +DDDDSDDDDDDEEDDD +DNDDDDDDDDDDDDDD +VVVVVVVVVVVVVVVV +YYYYYYYYYYYYYYYY +IIIIIIIIVVVVVIII +LLLLLLLLLLLLLLLL +DDDDDDDDDDDDDDDD +QQQQHHAAAAAAAQFA +AAAAAAAAAAAAAAAA +EEEEEEEEEEEEEEEE +EEEEEEEEEEEEEEEE +AAEEVVAEAAAAADEE +GGGGGGGGGGGGGGGG +HHHHIIIIIIILLIII +DDDDDEDDDDDDDDDD +LLLLLLLLLLLLLLLL +PPPPPPPPPPPPPPPP +YYYYYYYYYYYYYYFY +SSSSSSSSSSSSSSSS +CCCCCCCCCCCCCCCC +RRRRRRRRRRRRRRRR +AAAAAAAAAAAAAAAA +GGGGGGGGGGGGGGGG +SSSSSSSSSSSSSSSS +CCCCCCCCCCCCCCCC +SSSSSSSSSSSSSSSS +SSSSSSSSSSSSSSSS +CCCCCCCCCCCCCCCC +AAAAAAAAAAAAAAAA +GGGGGGGGGGGGGGGG +KKKKKKKKKKKKKKKK +IIVVVVVLVVVVVVVL +AATTVVTKVVVVVVVK +GGAAGNSTSSSSSSST +GGGGGGGGGGGGGGGG +AASTENSSSSFSSSSS +VVVVVVVLVVVIIVVL +DDDDDNNNDDDDDDDN +QQQQQQQQQQQQQQQQ +TTSSSEDDSSSSSSSD +DDDDDDDDDDDDDDDD +GGGGGGGQQQEQQQQQ +NNNKSSSSSSSSSSSS +FFFFFFFFFFFFFYFF +LLLLLLLLLLLLLLLL +DDDDDDDDDDDDDDND +DDEDDDDDDDDDDDDD +DDDDEEDDDEDE-GND +QQQQQQQQQQQQ-QQQ +LLEEIIIIIIIM-IVI +EEAAEEKDAGAS-AAD +EEAAAGEEEEEE-DDE +GGGGGGGGGGGG-GGG +WWFFFWWWFFFY-WWW +VVVVVVVVVVVV-VVV +LLLLLLLLLLLL-LLL +TTTTTTTTTTTT-TTT +CCCCCCCCCCCC-CCC +VVVVVVVAAAAV-HAA +AAAAAAAAAAAA-AAA +YYYYYFYYYYYY-YYY +PPPPPPPPPPPP-PPP +QQKKTTTVTTTT-TTV +SSGCSSGSSSSS-SSS +DDDDDDDDDDDD-DDD +VVVVVVVVVVVV-VVV +TTTTVTTTTTTV-VVT +IIIIIIIIIIII-III +EEEEEEEEEEEE-EEE +TTTTTTTTTTTT-TTT +HHHHHHHHHHHH-HHH +KKKKKKKKRKKK-KKK +EEEEEEEEEEEE-EEK +AAEEEEEEEEEE-EDE +EEEEDEEEDDEA-EDE +LLLLLLLLMILI-LLL +VVTTTTTTVVVM-TLT +GGAAAAAA-----G-A +-------------A-- +* diff --git a/examples/test.html b/examples/test.html new file mode 100644 index 0000000..229596c --- /dev/null +++ b/examples/test.html @@ -0,0 +1,29 @@ + + +
+ + + + +
+ + + +
+ + + + +
+ + \ No newline at end of file diff --git a/examples/test.jvp b/examples/test.jvp new file mode 100644 index 0000000..f4eecc5 Binary files /dev/null and b/examples/test.jvp differ diff --git a/examples/test.msf b/examples/test.msf new file mode 100644 index 0000000..8a476aa --- /dev/null +++ b/examples/test.msf @@ -0,0 +1,93 @@ +!!AA_MULTIPLE_ALIGNMENT 1.0 + + MSF: 157 Type: P Check: 4683 .. + + + Name: FER_CAPAA/1-157 Len: 157 Check: 3320 Weight: 1.00 + Name: FER_CAPAN/1-145 Len: 157 Check: 2597 Weight: 1.00 + Name: FER1_SOLLC/1-145 Len: 157 Check: 3815 Weight: 1.00 + Name: Q93XJ9_SOLTU/1-145 Len: 157 Check: 4240 Weight: 1.00 + Name: FER1_PEA/1-150 Len: 157 Check: 9547 Weight: 1.00 + Name: Q7XA98_TRIPR/1-153 Len: 157 Check: 4969 Weight: 1.00 + Name: FER1_MESCR/1-149 Len: 157 Check: 7664 Weight: 1.00 + Name: FER1_SPIOL/1-148 Len: 157 Check: 5892 Weight: 1.00 + Name: FER3_RAPSA/1-157 Len: 157 Check: 8715 Weight: 1.00 + Name: FER1_ARATH/1-150 Len: 157 Check: 3201 Weight: 1.00 + Name: FER_BRANA/1-157 Len: 157 Check: 7649 Weight: 1.00 + Name: FER2_ARATH/1-150 Len: 157 Check: 4904 Weight: 1.00 + Name: Q93Z60_ARATH/1-150 Len: 157 Check: 4436 Weight: 1.00 + Name: FER1_MAIZE/1-150 Len: 157 Check: 4392 Weight: 1.00 + Name: O80429_MAIZE/1-142 Len: 157 Check: 8858 Weight: 1.00 + Name: 1A70|/1-156 Len: 156 Check: 484 Weight: 1.00 + + +// + +FER_CAPAA/1-157 ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ +FER_CAPAN/1-145 MA......SV SATMISTSFM PRKPAVTSL. KPIPNVGE.. ALFGLKS.A. +FER1_SOLLC/1-145 MA......SI SGTMISTSFL PRKPAVTSL. KAISNVGE.. ALFGLKS.G. +Q93XJ9_SOLTU/1-145 MA......SI SGTMISTSFL PRKPVVTSL. KAISNVGE.. ALFGLKS.G. +FER1_PEA/1-150 MATT...PAL YGTAVSTSFL RTQPMPMSV. TTTKAFSN.. GFLGLKT.SL +Q7XA98_TRIPR/1-153 MATT...PAL YGTAVSTSFM RRQPVPMSV. ATTTTTKAFP SGFGLKSVST +FER1_MESCR/1-149 MAAT..TAAL SGATMSTAFA PK..TPPMTA ALPTNVGR.. ALFGLKS.SA +FER1_SPIOL/1-148 MAAT..TTTM MG..MATTFV PKPQAPPMMA ALPSNTGR.. SLFGLKT.GS +FER3_RAPSA/1-157 ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ +FER1_ARATH/1-150 MAST....AL SSAIVGTSFI RRSPAPISLR SLPSANTQ.. SLFGLKS.GT +FER_BRANA/1-157 ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ +FER2_ARATH/1-150 MAST....AL SSAIVSTSFL RRQQTPISLR SLPFANTQ.. SLFGLKS.ST +Q93Z60_ARATH/1-150 MAST....AL SSAIVSTSFL RRQQTPISLR SLPFANTQ.. SLFGLKS.ST +FER1_MAIZE/1-150 MATVLGSPRA PAFFFSSSSL RAAPAPTAV. .ALPAAKV.. GIMGRSA.SS +O80429_MAIZE/1-142 MAAT...... ...ALSMSIL R...APPPCF SSPLRLRV.. AVAKPLA.AP +1A70|/1-156 ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ + +FER_CAPAA/1-157 ~~~~~~~~~A SYKVKLITPD GPIEFDCPDD VYILDQAEEA GHDLPYSCRA +FER_CAPAN/1-145 .NGGKVTCMA SYKVKLITPD GPIEFDCPDN VYILDQAEEA GHDLPYSCRA +FER1_SOLLC/1-145 .RNGRITCMA SYKVKLITPE GPIEFECPDD VYILDQAEEE GHDLPYSCRA +Q93XJ9_SOLTU/1-145 .RNGRITCMA SYKVKLITPD GPIEFECPDD VYILDQAEEE GHDLPYSCRA +FER1_PEA/1-150 KRGDLAVAMA SYKVKLVTPD GTQEFECPSD VYILDHAEEV GIDLPYSCRA +Q7XA98_TRIPR/1-153 KRGDLAVAMA TYKVKLITPE GPQEFDCPDD VYILDHAEEV GIELPYSCRA +FER1_MESCR/1-149 SR.GRVTAMA AYKVTLVTPE GKQELECPDD VYILDAAEEA GIDLPYSCRA +FER1_SPIOL/1-148 R..GGRMTMA AYKVTLVTPT GNVEFQCPDD VYILDAAEEE GIDLPYSCRA +FER3_RAPSA/1-157 ~~~~~~~~~A TYKVKFITPE GEQEVECDDD VYVLDAAEEA GIDLPYSCRA +FER1_ARATH/1-150 ARGGRVTAMA TYKVKFITPE GELEVECDDD VYVLDAAEEA GIDLPYSCRA +FER_BRANA/1-157 ~~~~~~~~~A TYKVKFITPE GEQEVECDDD VYVLDAAEEA GIDLPYSCRA +FER2_ARATH/1-150 ARGGRVTAMA TYKVKFITPE GEQEVECEED VYVLDAAEEA GLDLPYSCRA +Q93Z60_ARATH/1-150 ARGGRVTAMA TYKVKFITPE GEQEVECEED VYVLDAAEEA GLDLPYSCRA +FER1_MAIZE/1-150 RR..RLRAQA TYNVKLITPE GEVELQVPDD VYILDQAEED GIDLPYSCRA +O80429_MAIZE/1-142 MRRQLLRAQA TYNVKLITPE GEVELQVPDD VYILDFAEEE GIDLPFSCRA +1A70|/1-156 ~~~~~~~~~A AYKVTLVTPT GNVEFQCPDD VYILDAAEEE GIDLPYSCRA + +FER_CAPAA/1-157 GSCSSCAGKI AGGAVDQTDG NFLDDDQLEE GWVLTCVAYP QSDVTIETHK +FER_CAPAN/1-145 GSCSSCAGKI AGGAVDQTDG NFLDDDQLEE GWVLTCVAYP QSDVTIETHK +FER1_SOLLC/1-145 GSCSSCAGKV TAGSVDQSDG NFLDEDQEAA GFVLTCVAYP KGDVTIETHK +Q93XJ9_SOLTU/1-145 GSCSSCAGKV TAGTVDQSDG KFLDDDQEAA GFVLTCVAYP KCDVTIETHK +FER1_PEA/1-150 GSCSSCAGKV VGGEVDQSDG SFLDDEQIEA GFVLTCVAYP TSDVVIETHK +Q7XA98_TRIPR/1-153 GSCSSCAGKV VNGNVNQEDG SFLDDEQIEG GWVLTCVAFP TSDVTIETHK +FER1_MESCR/1-149 GSCSSCAGKV TSGSVNQDDG SFLDDDQIKE GWVLTCVAYP TGDVTIETHK +FER1_SPIOL/1-148 GSCSSCAGKL KTGSLNQDDQ SFLDDDQIDE GWVLTCAAYP VSDVTIETHK +FER3_RAPSA/1-157 GSCSSCAGKV VSGSVDQSDQ SFLDDDQIAE GFVLTCAAYP TSDVTIETHR +FER1_ARATH/1-150 GSCSSCAGKV VSGSVDQSDQ SFLDDEQIGE GFVLTCAAYP TSDVTIETHK +FER_BRANA/1-157 GSCSSCAGKV VSGFVDQSDE SFLDDDQIAE GFVLTCAAYP TSDVTIETHK +FER2_ARATH/1-150 GSCSSCAGKV VSGSIDQSDQ SFLDDEQMSE GYVLTCVAYP TSDVVIETHK +Q93Z60_ARATH/1-150 GSCSSCAGKV VSGSIDQSDQ SFLDD~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ +FER1_MAIZE/1-150 GSCSSCAGKV VSGSVDQSDQ SYLDDGQIAD GWVLTCHAYP TSDVVIETHK +O80429_MAIZE/1-142 GSCSSCAGKV VSGSVDQSDQ SFLNDNQVAD GWVLTCAAYP TSDVVIETHK +1A70|/1-156 GSCSSCAGKL KTGSLNQDDQ SFLDDDQIDE GWVLTCAAYP VSDVTIETHK + +FER_CAPAA/1-157 EAELVG~ +FER_CAPAN/1-145 EAELVG~ +FER1_SOLLC/1-145 EEELTA~ +Q93XJ9_SOLTU/1-145 EEELTA~ +FER1_PEA/1-150 EEDLTA~ +Q7XA98_TRIPR/1-153 EEELTA~ +FER1_MESCR/1-149 EEELTA~ +FER1_SPIOL/1-148 EEELTA~ +FER3_RAPSA/1-157 EEDMV~~ +FER1_ARATH/1-150 EEDIV~~ +FER_BRANA/1-157 EEELV~~ +FER2_ARATH/1-150 EEAIM~~ +Q93Z60_ARATH/1-150 ~~~~~~~ +FER1_MAIZE/1-150 EEELTGA +O80429_MAIZE/1-142 EDDLL~~ +1A70|/1-156 KEELTA + diff --git a/examples/test.pfam b/examples/test.pfam new file mode 100644 index 0000000..dfaadf7 --- /dev/null +++ b/examples/test.pfam @@ -0,0 +1,17 @@ +FER_CAPAA/1-97 -----------------------------------------------------------ASYKVKLITPDGPIEFDCPDDVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDVTIETHKEAELVG- +FER_CAPAN/1-144 MA------SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALFGLKS-A--NGGKVTCMASYKVKLITPDGPIEFDCPDNVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDVTIETHKEAELVG- +FER1_SOLLC/1-144 MA------SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMASYKVKLITPEGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGSVDQSDGNFLDEDQEAAGFVLTCVAYPKGDVTIETHKEEELTA- +Q93XJ9_SOLTU/1-144 MA------SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMASYKVKLITPDGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGTVDQSDGKFLDDDQEAAGFVLTCVAYPKCDVTIETHKEEELTA- +FER1_PEA/1-149 MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMASYKVKLVTPDGTQEFECPSDVYILDHAEEVGIDLPYSCRAGSCSSCAGKVVGGEVDQSDGSFLDDEQIEAGFVLTCVAYPTSDVVIETHKEEDLTA- +Q7XA98_TRIPR/1-152 MATT---PALYGTAVSTSFMRRQPVPMSV-ATTTTTKAFPSGFGLKSVSTKRGDLAVAMATYKVKLITPEGPQEFDCPDDVYILDHAEEVGIELPYSCRAGSCSSCAGKVVNGNVNQEDGSFLDDEQIEGGWVLTCVAFPTSDVTIETHKEEELTA- +FER1_MESCR/1-148 MAAT--TAALSGATMSTAFAPK--TPPMTAALPTNVGR--ALFGLKS-SASR-GRVTAMAAYKVTLVTPEGKQELECPDDVYILDAAEEAGIDLPYSCRAGSCSSCAGKVTSGSVNQDDGSFLDDDQIKEGWVLTCVAYPTGDVTIETHKEEELTA- +FER1_SPIOL/1-147 MAAT--TTTMMG--MATTFVPKPQAPPMMAALPSNTGR--SLFGLKT-GSR--GGRMTMAAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEELTA- +FER3_RAPSA/1-96 -----------------------------------------------------------ATYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDDQIAEGFVLTCAAYPTSDVTIETHREEDMV-- +FER1_ARATH/1-148 MAST----ALSSAIVGTSFIRRSPAPISLRSLPSANTQ--SLFGLKS-GTARGGRVTAMATYKVKFITPEGELEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDVTIETHKEEDIV-- +FER_BRANA/1-96 -----------------------------------------------------------ATYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDVTIETHKEEELV-- +FER2_ARATH/1-148 MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDVVIETHKEEAIM-- +Q93Z60_ARATH/1-118 MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD-------------------------------- +FER1_MAIZE/1-150 MATVLGSPRAPAFFFSSSSLRAAPAPTAV--ALPAAKV--GIMGRSA-SSRR--RLRAQATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVVIETHKEEELTGA +O80429_MAIZE/1-140 MAAT---------ALSMSILR---APPPCFSSPLRLRV--AVAKPLA-APMRRQLLRAQATYNVKLITPEGEVELQVPDDVYILDFAEEEGIDLPFSCRAGSCSSCAGKVVSGSVDQSDQSFLNDNQVADGWVLTCAAYPTSDVVIETHKEDDLL-- +1A70|/1-97 -----------------------------------------------------------AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDVTIETHKKEELTA + diff --git a/examples/test.pileup b/examples/test.pileup new file mode 100644 index 0000000..d191e4b --- /dev/null +++ b/examples/test.pileup @@ -0,0 +1,93 @@ +PileUp + + MSF: 157 Type: P Check: 1935 .. + + + Name: FER_CAPAA/1-97 oo Len: 157 Check: 5701 Weight: 1.00 + Name: FER_CAPAN/1-144 oo Len: 157 Check: 8823 Weight: 1.00 + Name: FER1_SOLLC/1-144 oo Len: 157 Check: 41 Weight: 1.00 + Name: Q93XJ9_SOLTU/1-144 oo Len: 157 Check: 466 Weight: 1.00 + Name: FER1_PEA/1-149 oo Len: 157 Check: 5889 Weight: 1.00 + Name: Q7XA98_TRIPR/1-152 oo Len: 157 Check: 1438 Weight: 1.00 + Name: FER1_MESCR/1-148 oo Len: 157 Check: 3943 Weight: 1.00 + Name: FER1_SPIOL/1-147 oo Len: 157 Check: 2139 Weight: 1.00 + Name: FER3_RAPSA/1-96 oo Len: 157 Check: 7694 Weight: 1.00 + Name: FER1_ARATH/1-148 oo Len: 157 Check: 6163 Weight: 1.00 + Name: FER_BRANA/1-96 oo Len: 157 Check: 6628 Weight: 1.00 + Name: FER2_ARATH/1-148 oo Len: 157 Check: 7866 Weight: 1.00 + Name: Q93Z60_ARATH/1-118 oo Len: 157 Check: 3003 Weight: 1.00 + Name: FER1_MAIZE/1-150 oo Len: 157 Check: 4097 Weight: 1.00 + Name: O80429_MAIZE/1-140 oo Len: 157 Check: 1696 Weight: 1.00 + Name: 1A70|/1-97 oo Len: 156 Check: 6348 Weight: 1.00 + + +// + +FER_CAPAA/1-97 ---------- ---------- ---------- ---------- ---------- +FER_CAPAN/1-144 MA------SV SATMISTSFM PRKPAVTSL- KPIPNVGE-- ALFGLKS-A- +FER1_SOLLC/1-144 MA------SI SGTMISTSFL PRKPAVTSL- KAISNVGE-- ALFGLKS-G- +Q93XJ9_SOLTU/1-144 MA------SI SGTMISTSFL PRKPVVTSL- KAISNVGE-- ALFGLKS-G- +FER1_PEA/1-149 MATT---PAL YGTAVSTSFL RTQPMPMSV- TTTKAFSN-- GFLGLKT-SL +Q7XA98_TRIPR/1-152 MATT---PAL YGTAVSTSFM RRQPVPMSV- ATTTTTKAFP SGFGLKSVST +FER1_MESCR/1-148 MAAT--TAAL SGATMSTAFA PK--TPPMTA ALPTNVGR-- ALFGLKS-SA +FER1_SPIOL/1-147 MAAT--TTTM MG--MATTFV PKPQAPPMMA ALPSNTGR-- SLFGLKT-GS +FER3_RAPSA/1-96 ---------- ---------- ---------- ---------- ---------- +FER1_ARATH/1-148 MAST----AL SSAIVGTSFI RRSPAPISLR SLPSANTQ-- SLFGLKS-GT +FER_BRANA/1-96 ---------- ---------- ---------- ---------- ---------- +FER2_ARATH/1-148 MAST----AL SSAIVSTSFL RRQQTPISLR SLPFANTQ-- SLFGLKS-ST +Q93Z60_ARATH/1-118 MAST----AL SSAIVSTSFL RRQQTPISLR SLPFANTQ-- SLFGLKS-ST +FER1_MAIZE/1-150 MATVLGSPRA PAFFFSSSSL RAAPAPTAV- -ALPAAKV-- GIMGRSA-SS +O80429_MAIZE/1-140 MAAT------ ---ALSMSIL R---APPPCF SSPLRLRV-- AVAKPLA-AP +1A70|/1-97 ---------- ---------- ---------- ---------- ---------- + +FER_CAPAA/1-97 ---------A SYKVKLITPD GPIEFDCPDD VYILDQAEEA GHDLPYSCRA +FER_CAPAN/1-144 -NGGKVTCMA SYKVKLITPD GPIEFDCPDN VYILDQAEEA GHDLPYSCRA +FER1_SOLLC/1-144 -RNGRITCMA SYKVKLITPE GPIEFECPDD VYILDQAEEE GHDLPYSCRA +Q93XJ9_SOLTU/1-144 -RNGRITCMA SYKVKLITPD GPIEFECPDD VYILDQAEEE GHDLPYSCRA +FER1_PEA/1-149 KRGDLAVAMA SYKVKLVTPD GTQEFECPSD VYILDHAEEV GIDLPYSCRA +Q7XA98_TRIPR/1-152 KRGDLAVAMA TYKVKLITPE GPQEFDCPDD VYILDHAEEV GIELPYSCRA +FER1_MESCR/1-148 SR-GRVTAMA AYKVTLVTPE GKQELECPDD VYILDAAEEA GIDLPYSCRA +FER1_SPIOL/1-147 R--GGRMTMA AYKVTLVTPT GNVEFQCPDD VYILDAAEEE GIDLPYSCRA +FER3_RAPSA/1-96 ---------A TYKVKFITPE GEQEVECDDD VYVLDAAEEA GIDLPYSCRA +FER1_ARATH/1-148 ARGGRVTAMA TYKVKFITPE GELEVECDDD VYVLDAAEEA GIDLPYSCRA +FER_BRANA/1-96 ---------A TYKVKFITPE GEQEVECDDD VYVLDAAEEA GIDLPYSCRA +FER2_ARATH/1-148 ARGGRVTAMA TYKVKFITPE GEQEVECEED VYVLDAAEEA GLDLPYSCRA +Q93Z60_ARATH/1-118 ARGGRVTAMA TYKVKFITPE GEQEVECEED VYVLDAAEEA GLDLPYSCRA +FER1_MAIZE/1-150 RR--RLRAQA TYNVKLITPE GEVELQVPDD VYILDQAEED GIDLPYSCRA +O80429_MAIZE/1-140 MRRQLLRAQA TYNVKLITPE GEVELQVPDD VYILDFAEEE GIDLPFSCRA +1A70|/1-97 ---------A AYKVTLVTPT GNVEFQCPDD VYILDAAEEE GIDLPYSCRA + +FER_CAPAA/1-97 GSCSSCAGKI AGGAVDQTDG NFLDDDQLEE GWVLTCVAYP QSDVTIETHK +FER_CAPAN/1-144 GSCSSCAGKI AGGAVDQTDG NFLDDDQLEE GWVLTCVAYP QSDVTIETHK +FER1_SOLLC/1-144 GSCSSCAGKV TAGSVDQSDG NFLDEDQEAA GFVLTCVAYP KGDVTIETHK +Q93XJ9_SOLTU/1-144 GSCSSCAGKV TAGTVDQSDG KFLDDDQEAA GFVLTCVAYP KCDVTIETHK +FER1_PEA/1-149 GSCSSCAGKV VGGEVDQSDG SFLDDEQIEA GFVLTCVAYP TSDVVIETHK +Q7XA98_TRIPR/1-152 GSCSSCAGKV VNGNVNQEDG SFLDDEQIEG GWVLTCVAFP TSDVTIETHK +FER1_MESCR/1-148 GSCSSCAGKV TSGSVNQDDG SFLDDDQIKE GWVLTCVAYP TGDVTIETHK +FER1_SPIOL/1-147 GSCSSCAGKL KTGSLNQDDQ SFLDDDQIDE GWVLTCAAYP VSDVTIETHK +FER3_RAPSA/1-96 GSCSSCAGKV VSGSVDQSDQ SFLDDDQIAE GFVLTCAAYP TSDVTIETHR +FER1_ARATH/1-148 GSCSSCAGKV VSGSVDQSDQ SFLDDEQIGE GFVLTCAAYP TSDVTIETHK +FER_BRANA/1-96 GSCSSCAGKV VSGFVDQSDE SFLDDDQIAE GFVLTCAAYP TSDVTIETHK +FER2_ARATH/1-148 GSCSSCAGKV VSGSIDQSDQ SFLDDEQMSE GYVLTCVAYP TSDVVIETHK +Q93Z60_ARATH/1-118 GSCSSCAGKV VSGSIDQSDQ SFLDD----- ---------- ---------- +FER1_MAIZE/1-150 GSCSSCAGKV VSGSVDQSDQ SYLDDGQIAD GWVLTCHAYP TSDVVIETHK +O80429_MAIZE/1-140 GSCSSCAGKV VSGSVDQSDQ SFLNDNQVAD GWVLTCAAYP TSDVVIETHK +1A70|/1-97 GSCSSCAGKL KTGSLNQDDQ SFLDDDQIDE GWVLTCAAYP VSDVTIETHK + +FER_CAPAA/1-97 EAELVG- +FER_CAPAN/1-144 EAELVG- +FER1_SOLLC/1-144 EEELTA- +Q93XJ9_SOLTU/1-144 EEELTA- +FER1_PEA/1-149 EEDLTA- +Q7XA98_TRIPR/1-152 EEELTA- +FER1_MESCR/1-148 EEELTA- +FER1_SPIOL/1-147 EEELTA- +FER3_RAPSA/1-96 EEDMV-- +FER1_ARATH/1-148 EEDIV-- +FER_BRANA/1-96 EEELV-- +FER2_ARATH/1-148 EEAIM-- +Q93Z60_ARATH/1-118 ------- +FER1_MAIZE/1-150 EEELTGA +O80429_MAIZE/1-140 EDDLL-- +1A70|/1-97 KEELTA + diff --git a/examples/test.pir b/examples/test.pir new file mode 100644 index 0000000..689561f --- /dev/null +++ b/examples/test.pir @@ -0,0 +1,80 @@ +>P1;FER_CAPAA/1-97 +Ferredoxin +-----------------------------------------------------------ASYKVKLITPDGP +IEFDCPDDVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDV +TIETHKEAELVG-* +>P1;FER_CAPAN/1-144 +Ferredoxin, chloroplast precursor +MA------SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALFGLKS-A--NGGKVTCMASYKVKLITPDGP +IEFDCPDNVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDV +TIETHKEAELVG-* +>P1;FER1_SOLLC/1-144 +Ferredoxin-1, chloroplast precursor +MA------SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMASYKVKLITPEGP +IEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGSVDQSDGNFLDEDQEAAGFVLTCVAYPKGDV +TIETHKEEELTA-* +>P1;Q93XJ9_SOLTU/1-144 +Ferredoxin I precursor +MA------SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMASYKVKLITPDGP +IEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGTVDQSDGKFLDDDQEAAGFVLTCVAYPKCDV +TIETHKEEELTA-* +>P1;FER1_PEA/1-149 +Ferredoxin-1, chloroplast precursor +MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMASYKVKLVTPDGT +QEFECPSDVYILDHAEEVGIDLPYSCRAGSCSSCAGKVVGGEVDQSDGSFLDDEQIEAGFVLTCVAYPTSDV +VIETHKEEDLTA-* +>P1;Q7XA98_TRIPR/1-152 +Ferredoxin I +MATT---PALYGTAVSTSFMRRQPVPMSV-ATTTTTKAFPSGFGLKSVSTKRGDLAVAMATYKVKLITPEGP +QEFDCPDDVYILDHAEEVGIELPYSCRAGSCSSCAGKVVNGNVNQEDGSFLDDEQIEGGWVLTCVAFPTSDV +TIETHKEEELTA-* +>P1;FER1_MESCR/1-148 +Ferredoxin-1, chloroplast precursor +MAAT--TAALSGATMSTAFAPK--TPPMTAALPTNVGR--ALFGLKS-SASR-GRVTAMAAYKVTLVTPEGK +QELECPDDVYILDAAEEAGIDLPYSCRAGSCSSCAGKVTSGSVNQDDGSFLDDDQIKEGWVLTCVAYPTGDV +TIETHKEEELTA-* +>P1;FER1_SPIOL/1-147 +Ferredoxin-1, chloroplast precursor +MAAT--TTTMMG--MATTFVPKPQAPPMMAALPSNTGR--SLFGLKT-GSR--GGRMTMAAYKVTLVTPTGN +VEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDV +TIETHKEEELTA-* +>P1;FER3_RAPSA/1-96 +Ferredoxin, leaf L-A +-----------------------------------------------------------ATYKVKFITPEGE +QEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDDQIAEGFVLTCAAYPTSDV +TIETHREEDMV--* +>P1;FER1_ARATH/1-148 +Ferredoxin-1, chloroplast precursor +MAST----ALSSAIVGTSFIRRSPAPISLRSLPSANTQ--SLFGLKS-GTARGGRVTAMATYKVKFITPEGE +LEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDV +TIETHKEEDIV--* +>P1;FER_BRANA/1-96 +Ferredoxin +-----------------------------------------------------------ATYKVKFITPEGE +QEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDV +TIETHKEEELV--* +>P1;FER2_ARATH/1-148 +Ferredoxin-2, chloroplast precursor +MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGE +QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDV +VIETHKEEAIM--* +>P1;Q93Z60_ARATH/1-118 +At1g10960/T19D16_12 +MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGE +QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD------------------- +-------------* +>P1;FER1_MAIZE/1-150 +Ferredoxin-1, chloroplast precursor +MATVLGSPRAPAFFFSSSSLRAAPAPTAV--ALPAAKV--GIMGRSA-SSRR--RLRAQATYNVKLITPEGE +VELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDV +VIETHKEEELTGA* +>P1;O80429_MAIZE/1-140 +Ferredoxin +MAAT---------ALSMSILR---APPPCFSSPLRLRV--AVAKPLA-APMRRQLLRAQATYNVKLITPEGE +VELQVPDDVYILDFAEEEGIDLPFSCRAGSCSSCAGKVVSGSVDQSDQSFLNDNQVADGWVLTCAAYPTSDV +VIETHKEDDLL--* +>P1;1A70|/1-97 +1A70| 97 residues +-----------------------------------------------------------AAYKVTLVTPTGN +VEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDV +TIETHKKEELTA* diff --git a/examples/test.rnaml b/examples/test.rnaml new file mode 100644 index 0000000..0c716f9 --- /dev/null +++ b/examples/test.rnaml @@ -0,0 +1,2200 @@ + + + + + + + + + + 1 + 89 + + + + 1 2 3 4 5 6 7 8 9 10 + 11 12 13 14 15 16 17 18 19 20 + 21 22 23 24 25 26 27 28 29 30 + 31 32 33 34 35 36 37 38 39 40 + 41 42 43 44 45 46 47 48 49 50 + 51 52 53 54 55 56 57 58 59 60 + 61 62 63 64 65 66 67 68 69 70 + 71 72 73 74 75 76 77 78 79 80 + 81 82 83 84 85 86 87 88 89 + + + GGAGAGUAGA UGAUUCGCGU UAAGCGUGUG UGAAUGGGAU GUCGUCACAC AACGAAGCGA + GAGCGCGGUG AAUCAUUGCA UCCGCUCCA + + + + LOOP1 + 60 + 61 + + + + + + + Crystallography ? + ? Angstroms + + + 1 + G + + P + 39.406 -40.727 -8.772 + + + O3' + 35.728 -40.286 -12.682 + + + + 2 + G + + P + 34.946 -38.900 -12.475 + + + O3' + 30.080 -38.122 -13.566 + + + + 3 + A + + P + 29.830 -36.592 -13.144 + + + O3' + 25.299 -34.832 -11.157 + + + + 4 + G + + P + 25.525 -33.291 -10.748 + + + O3' + 22.725 -31.357 -6.447 + + + + 5 + A + + P + 23.004 -29.821 -6.080 + + + O3' + 21.811 -28.069 -1.298 + + + + 6 + G + + P + 21.792 -26.530 -1.767 + + + O3' + 24.489 -23.234 1.411 + + + + 7 + U + + P + 24.494 -21.833 0.618 + + + O3' + 26.796 -17.886 2.729 + + + + 8 + A + + P + 25.940 -16.593 2.288 + + + O3' + 27.995 -11.947 1.918 + + + + 9 + G + + P + 26.631 -11.127 1.714 + + + O3' + 25.187 -8.816 -3.450 + + + + 10 + A + + P + 23.765 -8.232 -3.892 + + + O3' + 22.114 -8.019 -8.607 + + + + 11 + U + + P + 20.793 -7.127 -8.411 + + + O3' + 16.589 -7.608 -11.167 + + + + 12 + G + + P + 15.563 -6.541 -10.537 + + + O3' + 10.446 -7.534 -10.495 + + + + 13 + A + + P + 9.719 -6.369 -9.662 + + + O3' + 5.301 -7.413 -7.169 + + + + 14 + U + + P + 4.913 -6.043 -6.428 + + + O3' + 2.471 -6.216 -1.841 + + + + 15 + U + + P + 2.306 -4.695 -1.355 + + + O3' + 2.523 -3.519 3.678 + + + + 16 + C + + P + 2.410 -1.916 3.716 + + + O3' + 4.861 0.478 7.750 + + + + 17 + G + + P + 5.097 2.068 7.705 + + + O3' + 9.837 5.342 8.056 + + + + 18 + C + + P + 9.957 6.906 7.713 + + + O3' + 14.285 9.278 6.633 + + + + 19 + G + + P + 13.701 10.760 6.394 + + + O3' + 16.027 13.756 2.831 + + + + 20 + U + + P + 15.167 15.091 3.070 + + + O3' + 13.625 17.842 -0.910 + + + + 21 + U + + P + 12.758 18.952 -0.136 + + + O3' + 18.055 19.867 1.942 + + + + 22 + A + + P + 19.169 19.634 0.806 + + + O3' + 21.578 14.723 -0.062 + + + + 23 + A + + P + 23.185 14.817 -0.069 + + + O3' + 24.197 10.234 2.787 + + + + 24 + G + + P + 25.187 9.332 1.904 + + + O3' + 23.533 4.428 0.543 + + + + 25 + C + + P + 24.698 3.762 -0.344 + + + O3' + 23.832 1.164 -4.830 + + + + 26 + G + + P + 25.358 0.687 -5.012 + + + O3' + 27.639 1.163 -9.624 + + + + 27 + U 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MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMA +Q7XA98_TRIPR/1-152 MATT---PALYGTAVSTSFMRRQPVPMSV-ATTTTTKAFPSGFGLKSVSTKRGDLAVAMA +FER1_MESCR/1-148 MAAT--TAALSGATMSTAFAPK--TPPMTAALPTNVGR--ALFGLKS-SASR-GRVTAMA +FER1_SPIOL/1-147 MAAT--TTTMMG--MATTFVPKPQAPPMMAALPSNTGR--SLFGLKT-GSR--GGRMTMA +FER3_RAPSA/1-96 -----------------------------------------------------------A +FER1_ARATH/1-148 MAST----ALSSAIVGTSFIRRSPAPISLRSLPSANTQ--SLFGLKS-GTARGGRVTAMA +FER_BRANA/1-96 -----------------------------------------------------------A +FER2_ARATH/1-148 MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMA +Q93Z60_ARATH/1-118 MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMA +FER1_MAIZE/1-150 MATVLGSPRAPAFFFSSSSLRAAPAPTAV--ALPAAKV--GIMGRSA-SSRR--RLRAQA +O80429_MAIZE/1-140 MAAT---------ALSMSILR---APPPCFSSPLRLRV--AVAKPLA-APMRRQLLRAQA +1A70|/1-97 -----------------------------------------------------------A + +FER_CAPAA/1-97 SYKVKLITPDGPIEFDCPDDVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDG +FER_CAPAN/1-144 SYKVKLITPDGPIEFDCPDNVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDG +FER1_SOLLC/1-144 SYKVKLITPEGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGSVDQSDG +Q93XJ9_SOLTU/1-144 SYKVKLITPDGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGTVDQSDG +FER1_PEA/1-149 SYKVKLVTPDGTQEFECPSDVYILDHAEEVGIDLPYSCRAGSCSSCAGKVVGGEVDQSDG +Q7XA98_TRIPR/1-152 TYKVKLITPEGPQEFDCPDDVYILDHAEEVGIELPYSCRAGSCSSCAGKVVNGNVNQEDG +FER1_MESCR/1-148 AYKVTLVTPEGKQELECPDDVYILDAAEEAGIDLPYSCRAGSCSSCAGKVTSGSVNQDDG +FER1_SPIOL/1-147 AYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQ +FER3_RAPSA/1-96 TYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQ +FER1_ARATH/1-148 TYKVKFITPEGELEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQ +FER_BRANA/1-96 TYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDE +FER2_ARATH/1-148 TYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQ +Q93Z60_ARATH/1-118 TYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQ +FER1_MAIZE/1-150 TYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQ +O80429_MAIZE/1-140 TYNVKLITPEGEVELQVPDDVYILDFAEEEGIDLPFSCRAGSCSSCAGKVVSGSVDQSDQ +1A70|/1-97 AYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQ + +FER_CAPAA/1-97 NFLDDDQLEEGWVLTCVAYPQSDVTIETHKEAELVG- +FER_CAPAN/1-144 NFLDDDQLEEGWVLTCVAYPQSDVTIETHKEAELVG- +FER1_SOLLC/1-144 NFLDEDQEAAGFVLTCVAYPKGDVTIETHKEEELTA- +Q93XJ9_SOLTU/1-144 KFLDDDQEAAGFVLTCVAYPKCDVTIETHKEEELTA- +FER1_PEA/1-149 SFLDDEQIEAGFVLTCVAYPTSDVVIETHKEEDLTA- +Q7XA98_TRIPR/1-152 SFLDDEQIEGGWVLTCVAFPTSDVTIETHKEEELTA- +FER1_MESCR/1-148 SFLDDDQIKEGWVLTCVAYPTGDVTIETHKEEELTA- +FER1_SPIOL/1-147 SFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEELTA- +FER3_RAPSA/1-96 SFLDDDQIAEGFVLTCAAYPTSDVTIETHREEDMV-- +FER1_ARATH/1-148 SFLDDEQIGEGFVLTCAAYPTSDVTIETHKEEDIV-- +FER_BRANA/1-96 SFLDDDQIAEGFVLTCAAYPTSDVTIETHKEEELV-- +FER2_ARATH/1-148 SFLDDEQMSEGYVLTCVAYPTSDVVIETHKEEAIM-- +Q93Z60_ARATH/1-118 SFLDD-------------------------------- +FER1_MAIZE/1-150 SYLDDGQIADGWVLTCHAYPTSDVVIETHKEEELTGA +O80429_MAIZE/1-140 SFLNDNQVADGWVLTCAAYPTSDVVIETHKEDDLL-- +1A70|/1-97 SFLDDDQIDEGWVLTCAAYPVSDVTIETHKKEELTA + diff --git a/examples/testdata/test.amsa b/examples/testdata/test.amsa new file mode 100644 index 0000000..be456bf --- /dev/null +++ b/examples/testdata/test.amsa @@ -0,0 +1,72 @@ +>FER_CAPAA Ferredoxin +-----------------------------------------------------------ASYKVKLITPDGP +IEFDCPDDVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDV +TIETHKEAELVG- +>FER_CAPAN Ferredoxin, chloroplast precursor +MA------SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALFGLKS-A--NGGKVTCMASYKVKLITPDGP +IEFDCPDNVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDV +TIETHKEAELVG- +>FER1_SOLLC Ferredoxin-1, chloroplast precursor +MA------SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMASYKVKLITPEGP +IEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGSVDQSDGNFLDEDQEAAGFVLTCVAYPKGDV +TIETHKEEELTA- +>Q93XJ9_SOLTU Ferredoxin I precursor +MA------SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMASYKVKLITPDGP +IEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGTVDQSDGKFLDDDQEAAGFVLTCVAYPKCDV +TIETHKEEELTA- +>FER1_PEA Ferredoxin-1, chloroplast precursor +MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMASYKVKLVTPDGT +QEFECPSDVYILDHAEEVGIDLPYSCRAGSCSSCAGKVVGGEVDQSDGSFLDDEQIEAGFVLTCVAYPTSDV +VIETHKEEDLTA- +>Q7XA98_TRIPR Ferredoxin I +MATT---PALYGTAVSTSFMRRQPVPMSV-ATTTTTKAFPSGFGLKSVSTKRGDLAVAMATYKVKLITPEGP +QEFDCPDDVYILDHAEEVGIELPYSCRAGSCSSCAGKVVNGNVNQEDGSFLDDEQIEGGWVLTCVAFPTSDV +TIETHKEEELTA- +>FER1_MESCR Ferredoxin-1, chloroplast precursor +MAAT--TAALSGATMSTAFAPK--TPPMTAALPTNVGR--ALFGLKS-SASR-GRVTAMAAYKVTLVTPEGK +QELECPDDVYILDAAEEAGIDLPYSCRAGSCSSCAGKVTSGSVNQDDGSFLDDDQIKEGWVLTCVAYPTGDV +TIETHKEEELTA- +>FER1_SPIOL Ferredoxin-1, chloroplast precursor +MAAT--TTTMMG--MATTFVPKPQAPPMMAALPSNTGR--SLFGLKT-GSR--GGRMTMAAYKVTLVTPTGN +VEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDV +TIETHKEEELTA- +>FER3_RAPSA Ferredoxin, leaf L-A +-----------------------------------------------------------ATYKVKFITPEGE +QEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDDQIAEGFVLTCAAYPTSDV +TIETHREEDMV-- +>FER1_ARATH Ferredoxin-1, chloroplast precursor +MAST----ALSSAIVGTSFIRRSPAPISLRSLPSANTQ--SLFGLKS-GTARGGRVTAMATYKVKFITPEGE +LEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDV +TIETHKEEDIV-- +>FER_BRANA Ferredoxin +-----------------------------------------------------------ATYKVKFITPEGE +QEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDV +TIETHKEEELV-- +>FER2_ARATH Ferredoxin-2, chloroplast precursor +MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGE +QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDV +VIETHKEEAIM-- +>Q93Z60_ARATH At1g10960/T19D16_12 +MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGE +QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD------------------- +------------- +>FER1_MAIZE Ferredoxin-1, chloroplast precursor +MATVLGSPRAPAFFFSSSSLRAAPAPTAV--ALPAAKV--GIMGRSA-SSRR--RLRAQATYNVKLITPEGE +VELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDV +VIETHKEEELTGA +>O80429_MAIZE Ferredoxin +MAAT---------ALSMSILR---APPPCFSSPLRLRV--AVAKPLA-APMRRQLLRAQATYNVKLITPEGE +VELQVPDDVYILDFAEEEGIDLPFSCRAGSCSSCAGKVVSGSVDQSDQSFLNDNQVADGWVLTCAAYPTSDV +VIETHKEDDLL-- +>1A70| +-----------------------------------------------------------AAYKVTLVTPTGN +VEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDV +TIETHKKEELTA +>#_Secondary Structure New description + 1 2 + 3 F F F 4 5 6 7 F 9 + +>#_Iron Sulphur Contacts New description + + F F F F + diff --git a/examples/testdata/test.blc b/examples/testdata/test.blc new file mode 100644 index 0000000..f419862 --- /dev/null +++ b/examples/testdata/test.blc @@ -0,0 +1,175 @@ +>FER_CAPAA/1-97 Ferredoxin +>FER_CAPAN/1-144 Ferredoxin, chloroplast precursor +>FER1_SOLLC/1-144 Ferredoxin-1, chloroplast precursor +>Q93XJ9_SOLTU/1-144 Ferredoxin I precursor +>FER1_PEA/1-149 Ferredoxin-1, chloroplast precursor +>Q7XA98_TRIPR/1-152 Ferredoxin I +>FER1_MESCR/1-148 Ferredoxin-1, chloroplast precursor +>FER1_SPIOL/1-147 Ferredoxin-1, chloroplast precursor +>FER3_RAPSA/1-96 Ferredoxin, leaf L-A +>FER1_ARATH/1-148 Ferredoxin-1, chloroplast precursor +>FER_BRANA/1-96 Ferredoxin +>FER2_ARATH/1-148 Ferredoxin-2, chloroplast precursor +>Q93Z60_ARATH/1-118 At1g10960/T19D16_12 +>FER1_MAIZE/1-150 Ferredoxin-1, chloroplast precursor +>O80429_MAIZE/1-140 Ferredoxin +>1A70|/1-97 +* iteration 1 +-MMMMMMM-M-MMMM- +-AAAAAAA-A-AAAA- +----TTAA-S-SSTA- +----TTTT-T-TTVT- +-------------L-- +-------------G-- +------TT-----S-- +----PPAT-----P-- +-SSSAAAT-A-AAR-- +-VIILLLM-L-LLA-- +-SSSYYSM-S-SSP-- +-AGGGGGG-S-SSA-- +-TTTTTA--A-AAF-- +-MMMAAT--I-IIFA- +-IIIVVMM-V-VVFL- +-SSSSSSA-G-SSSS- +-TTTTTTT-T-TTSM- +-SSSSSAT-S-SSSS- +-FFFFFFF-F-FFSI- +-MLLLMAV-I-LLLL- +-PPPRRPP-R-RRRR- +-RRRTRKK-R-RRA-- +-KKKQQ-P-S-QQA-- +-PPPPP-Q-P-QQP-- +-AAVMVTA-A-TTAA- +-VVVPPPP-P-PPPP- +-TTTMMPP-I-IITP- +-SSSSSMM-S-SSAP- +-LLLVVTM-L-LLVC- +------AA-R-RR-F- +-KKKTAAA-S-SS-S- +-PAATTLL-L-LLAS- +-IIITTPP-P-PPLP- +-PSSKTTS-S-FFPL- +-NNNATNN-A-AAAR- +-VVVFTVT-N-NNAL- +-GGGSKGG-T-TTKR- +-EEENARR-Q-QQVV- +-----F---------- +-----P---------- +-AAAGSAS-S-SSGA- +-LLLFGLL-L-LLIV- +-FFFLFFF-F-FFMA- +-GGGGGGG-G-GGGK- +-LLLLLLL-L-LLRP- +-KKKKKKK-K-KKSL- +-SSSTSST-S-SSAA- +-----V---------- +-AGGSSSG-G-SSSA- +----LTAS-T-TTSP- +----KKSR-A-AARM- +-NRRRRR--R-RRRR- +-GNNGG---G-GG-R- +-GGGDDGG-G-GG-Q- +-KRRLLRG-R-RRRL- +-VIIAAVR-V-VVLL- +-TTTVVTM-T-TTRR- +-CCCAAAT-A-AAAA- +-MMMMMMM-M-MMQQ- +AAAAAAAAAAAAAAAA +SSSSSTAATTTTTTTA +YYYYYYYYYYYYYYYY +KKKKKKKKKKKKKNNK +VVVVVVVVVVVVVVVV +KKKKKKTTKKKKKKKT +LLLLLLLLFFFFFLLL +IIIIVIVVIIIIIIIV +TTTTTTTTTTTTTTTT +PPPPPPPPPPPPPPPP +DDEDDEETEEEEEEET +GGGGGGGGGGGGGGGG +PPPPTPKNEEEEEEEN +IIIIQQQVQLQQQVVV +EEEEEEEEEEEEEEEE +FFFFFFLFVVVVVLLF +DDEEEDEQEEEEEQQQ +CCCCCCCCCCCCCVVC +PPPPPPPPDDDEEPPP +DDDDSDDDDDDEEDDD +DNDDDDDDDDDDDDDD +VVVVVVVVVVVVVVVV +YYYYYYYYYYYYYYYY +IIIIIIIIVVVVVIII +LLLLLLLLLLLLLLLL +DDDDDDDDDDDDDDDD +QQQQHHAAAAAAAQFA +AAAAAAAAAAAAAAAA +EEEEEEEEEEEEEEEE +EEEEEEEEEEEEEEEE +AAEEVVAEAAAAADEE +GGGGGGGGGGGGGGGG +HHHHIIIIIIILLIII +DDDDDEDDDDDDDDDD +LLLLLLLLLLLLLLLL +PPPPPPPPPPPPPPPP +YYYYYYYYYYYYYYFY +SSSSSSSSSSSSSSSS +CCCCCCCCCCCCCCCC +RRRRRRRRRRRRRRRR +AAAAAAAAAAAAAAAA +GGGGGGGGGGGGGGGG +SSSSSSSSSSSSSSSS +CCCCCCCCCCCCCCCC +SSSSSSSSSSSSSSSS +SSSSSSSSSSSSSSSS +CCCCCCCCCCCCCCCC +AAAAAAAAAAAAAAAA +GGGGGGGGGGGGGGGG +KKKKKKKKKKKKKKKK +IIVVVVVLVVVVVVVL +AATTVVTKVVVVVVVK +GGAAGNSTSSSSSSST +GGGGGGGGGGGGGGGG +AASTENSSSSFSSSSS +VVVVVVVLVVVIIVVL +DDDDDNNNDDDDDDDN +QQQQQQQQQQQQQQQQ +TTSSSEDDSSSSSSSD +DDDDDDDDDDDDDDDD +GGGGGGGQQQEQQQQQ +NNNKSSSSSSSSSSSS +FFFFFFFFFFFFFYFF +LLLLLLLLLLLLLLLL +DDDDDDDDDDDDDDND +DDEDDDDDDDDDDDDD +DDDDEEDDDEDE-GND +QQQQQQQQQQQQ-QQQ +LLEEIIIIIIIM-IVI +EEAAEEKDAGAS-AAD +EEAAAGEEEEEE-DDE +GGGGGGGGGGGG-GGG +WWFFFWWWFFFY-WWW +VVVVVVVVVVVV-VVV +LLLLLLLLLLLL-LLL +TTTTTTTTTTTT-TTT +CCCCCCCCCCCC-CCC +VVVVVVVAAAAV-HAA +AAAAAAAAAAAA-AAA +YYYYYFYYYYYY-YYY +PPPPPPPPPPPP-PPP +QQKKTTTVTTTT-TTV +SSGCSSGSSSSS-SSS +DDDDDDDDDDDD-DDD +VVVVVVVVVVVV-VVV +TTTTVTTTTTTV-VVT +IIIIIIIIIIII-III +EEEEEEEEEEEE-EEE +TTTTTTTTTTTT-TTT +HHHHHHHHHHHH-HHH +KKKKKKKKRKKK-KKK +EEEEEEEEEEEE-EEK +AAEEEEEEEEEE-EDE +EEEEDEEEDDEA-EDE +LLLLLLLLMILI-LLL +VVTTTTTTVVVM-TLT +GGAAAAAA-----G-A +-------------A-- +* diff --git a/examples/testdata/test.html b/examples/testdata/test.html new file mode 100644 index 0000000..229596c --- /dev/null +++ b/examples/testdata/test.html @@ -0,0 +1,29 @@ + + +
+ + + + +
+ + + +
+ + + + +
+ + \ No newline at end of file diff --git a/examples/testdata/test.jvp b/examples/testdata/test.jvp new file mode 100644 index 0000000..f4eecc5 Binary files /dev/null and b/examples/testdata/test.jvp differ diff --git a/examples/testdata/test.msf b/examples/testdata/test.msf new file mode 100644 index 0000000..8a476aa --- /dev/null +++ b/examples/testdata/test.msf @@ -0,0 +1,93 @@ +!!AA_MULTIPLE_ALIGNMENT 1.0 + + MSF: 157 Type: P Check: 4683 .. + + + Name: FER_CAPAA/1-157 Len: 157 Check: 3320 Weight: 1.00 + Name: FER_CAPAN/1-145 Len: 157 Check: 2597 Weight: 1.00 + Name: FER1_SOLLC/1-145 Len: 157 Check: 3815 Weight: 1.00 + Name: Q93XJ9_SOLTU/1-145 Len: 157 Check: 4240 Weight: 1.00 + Name: FER1_PEA/1-150 Len: 157 Check: 9547 Weight: 1.00 + Name: Q7XA98_TRIPR/1-153 Len: 157 Check: 4969 Weight: 1.00 + Name: FER1_MESCR/1-149 Len: 157 Check: 7664 Weight: 1.00 + Name: FER1_SPIOL/1-148 Len: 157 Check: 5892 Weight: 1.00 + Name: FER3_RAPSA/1-157 Len: 157 Check: 8715 Weight: 1.00 + Name: FER1_ARATH/1-150 Len: 157 Check: 3201 Weight: 1.00 + Name: FER_BRANA/1-157 Len: 157 Check: 7649 Weight: 1.00 + Name: FER2_ARATH/1-150 Len: 157 Check: 4904 Weight: 1.00 + Name: Q93Z60_ARATH/1-150 Len: 157 Check: 4436 Weight: 1.00 + Name: FER1_MAIZE/1-150 Len: 157 Check: 4392 Weight: 1.00 + Name: O80429_MAIZE/1-142 Len: 157 Check: 8858 Weight: 1.00 + Name: 1A70|/1-156 Len: 156 Check: 484 Weight: 1.00 + + +// + +FER_CAPAA/1-157 ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ +FER_CAPAN/1-145 MA......SV SATMISTSFM PRKPAVTSL. KPIPNVGE.. ALFGLKS.A. +FER1_SOLLC/1-145 MA......SI SGTMISTSFL PRKPAVTSL. KAISNVGE.. ALFGLKS.G. +Q93XJ9_SOLTU/1-145 MA......SI SGTMISTSFL PRKPVVTSL. KAISNVGE.. ALFGLKS.G. +FER1_PEA/1-150 MATT...PAL YGTAVSTSFL RTQPMPMSV. TTTKAFSN.. GFLGLKT.SL +Q7XA98_TRIPR/1-153 MATT...PAL YGTAVSTSFM RRQPVPMSV. ATTTTTKAFP SGFGLKSVST +FER1_MESCR/1-149 MAAT..TAAL SGATMSTAFA PK..TPPMTA ALPTNVGR.. ALFGLKS.SA +FER1_SPIOL/1-148 MAAT..TTTM MG..MATTFV PKPQAPPMMA ALPSNTGR.. SLFGLKT.GS +FER3_RAPSA/1-157 ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ +FER1_ARATH/1-150 MAST....AL SSAIVGTSFI RRSPAPISLR SLPSANTQ.. SLFGLKS.GT +FER_BRANA/1-157 ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ +FER2_ARATH/1-150 MAST....AL SSAIVSTSFL RRQQTPISLR SLPFANTQ.. SLFGLKS.ST +Q93Z60_ARATH/1-150 MAST....AL SSAIVSTSFL RRQQTPISLR SLPFANTQ.. SLFGLKS.ST +FER1_MAIZE/1-150 MATVLGSPRA PAFFFSSSSL RAAPAPTAV. .ALPAAKV.. GIMGRSA.SS +O80429_MAIZE/1-142 MAAT...... ...ALSMSIL R...APPPCF SSPLRLRV.. AVAKPLA.AP +1A70|/1-156 ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ + +FER_CAPAA/1-157 ~~~~~~~~~A SYKVKLITPD GPIEFDCPDD VYILDQAEEA GHDLPYSCRA +FER_CAPAN/1-145 .NGGKVTCMA SYKVKLITPD GPIEFDCPDN VYILDQAEEA GHDLPYSCRA +FER1_SOLLC/1-145 .RNGRITCMA SYKVKLITPE GPIEFECPDD VYILDQAEEE GHDLPYSCRA +Q93XJ9_SOLTU/1-145 .RNGRITCMA SYKVKLITPD GPIEFECPDD VYILDQAEEE GHDLPYSCRA +FER1_PEA/1-150 KRGDLAVAMA SYKVKLVTPD GTQEFECPSD VYILDHAEEV GIDLPYSCRA +Q7XA98_TRIPR/1-153 KRGDLAVAMA TYKVKLITPE GPQEFDCPDD VYILDHAEEV GIELPYSCRA +FER1_MESCR/1-149 SR.GRVTAMA AYKVTLVTPE GKQELECPDD VYILDAAEEA GIDLPYSCRA +FER1_SPIOL/1-148 R..GGRMTMA AYKVTLVTPT GNVEFQCPDD VYILDAAEEE GIDLPYSCRA +FER3_RAPSA/1-157 ~~~~~~~~~A TYKVKFITPE GEQEVECDDD VYVLDAAEEA GIDLPYSCRA +FER1_ARATH/1-150 ARGGRVTAMA TYKVKFITPE GELEVECDDD VYVLDAAEEA GIDLPYSCRA +FER_BRANA/1-157 ~~~~~~~~~A TYKVKFITPE GEQEVECDDD VYVLDAAEEA GIDLPYSCRA +FER2_ARATH/1-150 ARGGRVTAMA TYKVKFITPE GEQEVECEED VYVLDAAEEA GLDLPYSCRA +Q93Z60_ARATH/1-150 ARGGRVTAMA TYKVKFITPE GEQEVECEED VYVLDAAEEA GLDLPYSCRA +FER1_MAIZE/1-150 RR..RLRAQA TYNVKLITPE GEVELQVPDD VYILDQAEED GIDLPYSCRA +O80429_MAIZE/1-142 MRRQLLRAQA TYNVKLITPE GEVELQVPDD VYILDFAEEE GIDLPFSCRA +1A70|/1-156 ~~~~~~~~~A AYKVTLVTPT GNVEFQCPDD VYILDAAEEE GIDLPYSCRA + +FER_CAPAA/1-157 GSCSSCAGKI AGGAVDQTDG NFLDDDQLEE GWVLTCVAYP QSDVTIETHK +FER_CAPAN/1-145 GSCSSCAGKI AGGAVDQTDG NFLDDDQLEE GWVLTCVAYP QSDVTIETHK +FER1_SOLLC/1-145 GSCSSCAGKV TAGSVDQSDG NFLDEDQEAA GFVLTCVAYP KGDVTIETHK +Q93XJ9_SOLTU/1-145 GSCSSCAGKV TAGTVDQSDG KFLDDDQEAA GFVLTCVAYP KCDVTIETHK +FER1_PEA/1-150 GSCSSCAGKV VGGEVDQSDG SFLDDEQIEA GFVLTCVAYP TSDVVIETHK +Q7XA98_TRIPR/1-153 GSCSSCAGKV VNGNVNQEDG SFLDDEQIEG GWVLTCVAFP TSDVTIETHK +FER1_MESCR/1-149 GSCSSCAGKV TSGSVNQDDG SFLDDDQIKE GWVLTCVAYP TGDVTIETHK +FER1_SPIOL/1-148 GSCSSCAGKL KTGSLNQDDQ SFLDDDQIDE GWVLTCAAYP VSDVTIETHK +FER3_RAPSA/1-157 GSCSSCAGKV VSGSVDQSDQ SFLDDDQIAE GFVLTCAAYP TSDVTIETHR +FER1_ARATH/1-150 GSCSSCAGKV VSGSVDQSDQ SFLDDEQIGE GFVLTCAAYP TSDVTIETHK +FER_BRANA/1-157 GSCSSCAGKV VSGFVDQSDE SFLDDDQIAE GFVLTCAAYP TSDVTIETHK +FER2_ARATH/1-150 GSCSSCAGKV VSGSIDQSDQ SFLDDEQMSE GYVLTCVAYP TSDVVIETHK +Q93Z60_ARATH/1-150 GSCSSCAGKV VSGSIDQSDQ SFLDD~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ +FER1_MAIZE/1-150 GSCSSCAGKV VSGSVDQSDQ SYLDDGQIAD GWVLTCHAYP TSDVVIETHK +O80429_MAIZE/1-142 GSCSSCAGKV VSGSVDQSDQ SFLNDNQVAD GWVLTCAAYP TSDVVIETHK +1A70|/1-156 GSCSSCAGKL KTGSLNQDDQ SFLDDDQIDE GWVLTCAAYP VSDVTIETHK + +FER_CAPAA/1-157 EAELVG~ +FER_CAPAN/1-145 EAELVG~ +FER1_SOLLC/1-145 EEELTA~ +Q93XJ9_SOLTU/1-145 EEELTA~ +FER1_PEA/1-150 EEDLTA~ +Q7XA98_TRIPR/1-153 EEELTA~ +FER1_MESCR/1-149 EEELTA~ +FER1_SPIOL/1-148 EEELTA~ +FER3_RAPSA/1-157 EEDMV~~ +FER1_ARATH/1-150 EEDIV~~ +FER_BRANA/1-157 EEELV~~ +FER2_ARATH/1-150 EEAIM~~ +Q93Z60_ARATH/1-150 ~~~~~~~ +FER1_MAIZE/1-150 EEELTGA +O80429_MAIZE/1-142 EDDLL~~ +1A70|/1-156 KEELTA + diff --git a/examples/testdata/test.pfam b/examples/testdata/test.pfam new file mode 100644 index 0000000..dfaadf7 --- /dev/null +++ b/examples/testdata/test.pfam @@ -0,0 +1,17 @@ +FER_CAPAA/1-97 -----------------------------------------------------------ASYKVKLITPDGPIEFDCPDDVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDVTIETHKEAELVG- +FER_CAPAN/1-144 MA------SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALFGLKS-A--NGGKVTCMASYKVKLITPDGPIEFDCPDNVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDVTIETHKEAELVG- +FER1_SOLLC/1-144 MA------SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMASYKVKLITPEGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGSVDQSDGNFLDEDQEAAGFVLTCVAYPKGDVTIETHKEEELTA- +Q93XJ9_SOLTU/1-144 MA------SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMASYKVKLITPDGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGTVDQSDGKFLDDDQEAAGFVLTCVAYPKCDVTIETHKEEELTA- +FER1_PEA/1-149 MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMASYKVKLVTPDGTQEFECPSDVYILDHAEEVGIDLPYSCRAGSCSSCAGKVVGGEVDQSDGSFLDDEQIEAGFVLTCVAYPTSDVVIETHKEEDLTA- +Q7XA98_TRIPR/1-152 MATT---PALYGTAVSTSFMRRQPVPMSV-ATTTTTKAFPSGFGLKSVSTKRGDLAVAMATYKVKLITPEGPQEFDCPDDVYILDHAEEVGIELPYSCRAGSCSSCAGKVVNGNVNQEDGSFLDDEQIEGGWVLTCVAFPTSDVTIETHKEEELTA- +FER1_MESCR/1-148 MAAT--TAALSGATMSTAFAPK--TPPMTAALPTNVGR--ALFGLKS-SASR-GRVTAMAAYKVTLVTPEGKQELECPDDVYILDAAEEAGIDLPYSCRAGSCSSCAGKVTSGSVNQDDGSFLDDDQIKEGWVLTCVAYPTGDVTIETHKEEELTA- +FER1_SPIOL/1-147 MAAT--TTTMMG--MATTFVPKPQAPPMMAALPSNTGR--SLFGLKT-GSR--GGRMTMAAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEELTA- +FER3_RAPSA/1-96 -----------------------------------------------------------ATYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDDQIAEGFVLTCAAYPTSDVTIETHREEDMV-- +FER1_ARATH/1-148 MAST----ALSSAIVGTSFIRRSPAPISLRSLPSANTQ--SLFGLKS-GTARGGRVTAMATYKVKFITPEGELEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDVTIETHKEEDIV-- +FER_BRANA/1-96 -----------------------------------------------------------ATYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDVTIETHKEEELV-- +FER2_ARATH/1-148 MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDVVIETHKEEAIM-- +Q93Z60_ARATH/1-118 MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD-------------------------------- +FER1_MAIZE/1-150 MATVLGSPRAPAFFFSSSSLRAAPAPTAV--ALPAAKV--GIMGRSA-SSRR--RLRAQATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVVIETHKEEELTGA +O80429_MAIZE/1-140 MAAT---------ALSMSILR---APPPCFSSPLRLRV--AVAKPLA-APMRRQLLRAQATYNVKLITPEGEVELQVPDDVYILDFAEEEGIDLPFSCRAGSCSSCAGKVVSGSVDQSDQSFLNDNQVADGWVLTCAAYPTSDVVIETHKEDDLL-- +1A70|/1-97 -----------------------------------------------------------AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDVTIETHKKEELTA + diff --git a/examples/testdata/test.pileup b/examples/testdata/test.pileup new file mode 100644 index 0000000..d191e4b --- /dev/null +++ b/examples/testdata/test.pileup @@ -0,0 +1,93 @@ +PileUp + + MSF: 157 Type: P Check: 1935 .. + + + Name: FER_CAPAA/1-97 oo Len: 157 Check: 5701 Weight: 1.00 + Name: FER_CAPAN/1-144 oo Len: 157 Check: 8823 Weight: 1.00 + Name: FER1_SOLLC/1-144 oo Len: 157 Check: 41 Weight: 1.00 + Name: Q93XJ9_SOLTU/1-144 oo Len: 157 Check: 466 Weight: 1.00 + Name: FER1_PEA/1-149 oo Len: 157 Check: 5889 Weight: 1.00 + Name: Q7XA98_TRIPR/1-152 oo Len: 157 Check: 1438 Weight: 1.00 + Name: FER1_MESCR/1-148 oo Len: 157 Check: 3943 Weight: 1.00 + Name: FER1_SPIOL/1-147 oo Len: 157 Check: 2139 Weight: 1.00 + Name: FER3_RAPSA/1-96 oo Len: 157 Check: 7694 Weight: 1.00 + Name: FER1_ARATH/1-148 oo Len: 157 Check: 6163 Weight: 1.00 + Name: FER_BRANA/1-96 oo Len: 157 Check: 6628 Weight: 1.00 + Name: FER2_ARATH/1-148 oo Len: 157 Check: 7866 Weight: 1.00 + Name: Q93Z60_ARATH/1-118 oo Len: 157 Check: 3003 Weight: 1.00 + Name: FER1_MAIZE/1-150 oo Len: 157 Check: 4097 Weight: 1.00 + Name: O80429_MAIZE/1-140 oo Len: 157 Check: 1696 Weight: 1.00 + Name: 1A70|/1-97 oo Len: 156 Check: 6348 Weight: 1.00 + + +// + +FER_CAPAA/1-97 ---------- ---------- ---------- ---------- ---------- +FER_CAPAN/1-144 MA------SV SATMISTSFM PRKPAVTSL- KPIPNVGE-- ALFGLKS-A- +FER1_SOLLC/1-144 MA------SI SGTMISTSFL PRKPAVTSL- KAISNVGE-- ALFGLKS-G- +Q93XJ9_SOLTU/1-144 MA------SI SGTMISTSFL PRKPVVTSL- KAISNVGE-- ALFGLKS-G- +FER1_PEA/1-149 MATT---PAL YGTAVSTSFL RTQPMPMSV- TTTKAFSN-- GFLGLKT-SL +Q7XA98_TRIPR/1-152 MATT---PAL YGTAVSTSFM RRQPVPMSV- ATTTTTKAFP SGFGLKSVST +FER1_MESCR/1-148 MAAT--TAAL SGATMSTAFA PK--TPPMTA ALPTNVGR-- ALFGLKS-SA +FER1_SPIOL/1-147 MAAT--TTTM MG--MATTFV PKPQAPPMMA ALPSNTGR-- SLFGLKT-GS +FER3_RAPSA/1-96 ---------- ---------- ---------- ---------- ---------- +FER1_ARATH/1-148 MAST----AL SSAIVGTSFI RRSPAPISLR SLPSANTQ-- SLFGLKS-GT +FER_BRANA/1-96 ---------- ---------- ---------- ---------- ---------- +FER2_ARATH/1-148 MAST----AL SSAIVSTSFL RRQQTPISLR SLPFANTQ-- SLFGLKS-ST +Q93Z60_ARATH/1-118 MAST----AL SSAIVSTSFL RRQQTPISLR SLPFANTQ-- SLFGLKS-ST +FER1_MAIZE/1-150 MATVLGSPRA PAFFFSSSSL RAAPAPTAV- -ALPAAKV-- GIMGRSA-SS +O80429_MAIZE/1-140 MAAT------ ---ALSMSIL R---APPPCF SSPLRLRV-- AVAKPLA-AP +1A70|/1-97 ---------- ---------- ---------- ---------- ---------- + +FER_CAPAA/1-97 ---------A SYKVKLITPD GPIEFDCPDD VYILDQAEEA GHDLPYSCRA +FER_CAPAN/1-144 -NGGKVTCMA SYKVKLITPD GPIEFDCPDN VYILDQAEEA GHDLPYSCRA +FER1_SOLLC/1-144 -RNGRITCMA SYKVKLITPE GPIEFECPDD VYILDQAEEE GHDLPYSCRA +Q93XJ9_SOLTU/1-144 -RNGRITCMA SYKVKLITPD GPIEFECPDD VYILDQAEEE GHDLPYSCRA +FER1_PEA/1-149 KRGDLAVAMA SYKVKLVTPD GTQEFECPSD VYILDHAEEV GIDLPYSCRA +Q7XA98_TRIPR/1-152 KRGDLAVAMA TYKVKLITPE GPQEFDCPDD VYILDHAEEV GIELPYSCRA +FER1_MESCR/1-148 SR-GRVTAMA AYKVTLVTPE GKQELECPDD VYILDAAEEA GIDLPYSCRA +FER1_SPIOL/1-147 R--GGRMTMA AYKVTLVTPT GNVEFQCPDD VYILDAAEEE GIDLPYSCRA +FER3_RAPSA/1-96 ---------A TYKVKFITPE GEQEVECDDD VYVLDAAEEA GIDLPYSCRA +FER1_ARATH/1-148 ARGGRVTAMA TYKVKFITPE GELEVECDDD VYVLDAAEEA GIDLPYSCRA +FER_BRANA/1-96 ---------A TYKVKFITPE GEQEVECDDD VYVLDAAEEA GIDLPYSCRA +FER2_ARATH/1-148 ARGGRVTAMA TYKVKFITPE GEQEVECEED VYVLDAAEEA GLDLPYSCRA +Q93Z60_ARATH/1-118 ARGGRVTAMA TYKVKFITPE GEQEVECEED VYVLDAAEEA GLDLPYSCRA +FER1_MAIZE/1-150 RR--RLRAQA TYNVKLITPE GEVELQVPDD VYILDQAEED GIDLPYSCRA +O80429_MAIZE/1-140 MRRQLLRAQA TYNVKLITPE GEVELQVPDD VYILDFAEEE GIDLPFSCRA +1A70|/1-97 ---------A AYKVTLVTPT GNVEFQCPDD VYILDAAEEE GIDLPYSCRA + +FER_CAPAA/1-97 GSCSSCAGKI AGGAVDQTDG NFLDDDQLEE GWVLTCVAYP QSDVTIETHK +FER_CAPAN/1-144 GSCSSCAGKI AGGAVDQTDG NFLDDDQLEE GWVLTCVAYP QSDVTIETHK +FER1_SOLLC/1-144 GSCSSCAGKV TAGSVDQSDG NFLDEDQEAA GFVLTCVAYP KGDVTIETHK +Q93XJ9_SOLTU/1-144 GSCSSCAGKV TAGTVDQSDG KFLDDDQEAA GFVLTCVAYP KCDVTIETHK +FER1_PEA/1-149 GSCSSCAGKV VGGEVDQSDG SFLDDEQIEA GFVLTCVAYP TSDVVIETHK +Q7XA98_TRIPR/1-152 GSCSSCAGKV VNGNVNQEDG SFLDDEQIEG GWVLTCVAFP TSDVTIETHK +FER1_MESCR/1-148 GSCSSCAGKV TSGSVNQDDG SFLDDDQIKE GWVLTCVAYP TGDVTIETHK +FER1_SPIOL/1-147 GSCSSCAGKL KTGSLNQDDQ SFLDDDQIDE GWVLTCAAYP VSDVTIETHK +FER3_RAPSA/1-96 GSCSSCAGKV VSGSVDQSDQ SFLDDDQIAE GFVLTCAAYP TSDVTIETHR +FER1_ARATH/1-148 GSCSSCAGKV VSGSVDQSDQ SFLDDEQIGE GFVLTCAAYP TSDVTIETHK +FER_BRANA/1-96 GSCSSCAGKV VSGFVDQSDE SFLDDDQIAE GFVLTCAAYP TSDVTIETHK +FER2_ARATH/1-148 GSCSSCAGKV VSGSIDQSDQ SFLDDEQMSE GYVLTCVAYP TSDVVIETHK +Q93Z60_ARATH/1-118 GSCSSCAGKV VSGSIDQSDQ SFLDD----- ---------- ---------- +FER1_MAIZE/1-150 GSCSSCAGKV VSGSVDQSDQ SYLDDGQIAD GWVLTCHAYP TSDVVIETHK +O80429_MAIZE/1-140 GSCSSCAGKV VSGSVDQSDQ SFLNDNQVAD GWVLTCAAYP TSDVVIETHK +1A70|/1-97 GSCSSCAGKL KTGSLNQDDQ SFLDDDQIDE GWVLTCAAYP VSDVTIETHK + +FER_CAPAA/1-97 EAELVG- +FER_CAPAN/1-144 EAELVG- +FER1_SOLLC/1-144 EEELTA- +Q93XJ9_SOLTU/1-144 EEELTA- +FER1_PEA/1-149 EEDLTA- +Q7XA98_TRIPR/1-152 EEELTA- +FER1_MESCR/1-148 EEELTA- +FER1_SPIOL/1-147 EEELTA- +FER3_RAPSA/1-96 EEDMV-- +FER1_ARATH/1-148 EEDIV-- +FER_BRANA/1-96 EEELV-- +FER2_ARATH/1-148 EEAIM-- +Q93Z60_ARATH/1-118 ------- +FER1_MAIZE/1-150 EEELTGA +O80429_MAIZE/1-140 EDDLL-- +1A70|/1-97 KEELTA + diff --git a/examples/testdata/test.pir b/examples/testdata/test.pir new file mode 100644 index 0000000..689561f --- /dev/null +++ b/examples/testdata/test.pir @@ -0,0 +1,80 @@ +>P1;FER_CAPAA/1-97 +Ferredoxin +-----------------------------------------------------------ASYKVKLITPDGP +IEFDCPDDVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDV +TIETHKEAELVG-* +>P1;FER_CAPAN/1-144 +Ferredoxin, chloroplast precursor +MA------SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALFGLKS-A--NGGKVTCMASYKVKLITPDGP +IEFDCPDNVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDV +TIETHKEAELVG-* +>P1;FER1_SOLLC/1-144 +Ferredoxin-1, chloroplast precursor +MA------SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMASYKVKLITPEGP +IEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGSVDQSDGNFLDEDQEAAGFVLTCVAYPKGDV +TIETHKEEELTA-* +>P1;Q93XJ9_SOLTU/1-144 +Ferredoxin I precursor +MA------SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMASYKVKLITPDGP +IEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGTVDQSDGKFLDDDQEAAGFVLTCVAYPKCDV +TIETHKEEELTA-* +>P1;FER1_PEA/1-149 +Ferredoxin-1, chloroplast precursor +MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMASYKVKLVTPDGT +QEFECPSDVYILDHAEEVGIDLPYSCRAGSCSSCAGKVVGGEVDQSDGSFLDDEQIEAGFVLTCVAYPTSDV +VIETHKEEDLTA-* +>P1;Q7XA98_TRIPR/1-152 +Ferredoxin I +MATT---PALYGTAVSTSFMRRQPVPMSV-ATTTTTKAFPSGFGLKSVSTKRGDLAVAMATYKVKLITPEGP +QEFDCPDDVYILDHAEEVGIELPYSCRAGSCSSCAGKVVNGNVNQEDGSFLDDEQIEGGWVLTCVAFPTSDV +TIETHKEEELTA-* +>P1;FER1_MESCR/1-148 +Ferredoxin-1, chloroplast precursor +MAAT--TAALSGATMSTAFAPK--TPPMTAALPTNVGR--ALFGLKS-SASR-GRVTAMAAYKVTLVTPEGK +QELECPDDVYILDAAEEAGIDLPYSCRAGSCSSCAGKVTSGSVNQDDGSFLDDDQIKEGWVLTCVAYPTGDV +TIETHKEEELTA-* +>P1;FER1_SPIOL/1-147 +Ferredoxin-1, chloroplast precursor +MAAT--TTTMMG--MATTFVPKPQAPPMMAALPSNTGR--SLFGLKT-GSR--GGRMTMAAYKVTLVTPTGN +VEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDV +TIETHKEEELTA-* +>P1;FER3_RAPSA/1-96 +Ferredoxin, leaf L-A +-----------------------------------------------------------ATYKVKFITPEGE +QEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDDQIAEGFVLTCAAYPTSDV +TIETHREEDMV--* +>P1;FER1_ARATH/1-148 +Ferredoxin-1, chloroplast precursor +MAST----ALSSAIVGTSFIRRSPAPISLRSLPSANTQ--SLFGLKS-GTARGGRVTAMATYKVKFITPEGE +LEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDV +TIETHKEEDIV--* +>P1;FER_BRANA/1-96 +Ferredoxin +-----------------------------------------------------------ATYKVKFITPEGE +QEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDV +TIETHKEEELV--* +>P1;FER2_ARATH/1-148 +Ferredoxin-2, chloroplast precursor +MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGE +QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDV +VIETHKEEAIM--* +>P1;Q93Z60_ARATH/1-118 +At1g10960/T19D16_12 +MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGE +QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD------------------- +-------------* +>P1;FER1_MAIZE/1-150 +Ferredoxin-1, chloroplast precursor +MATVLGSPRAPAFFFSSSSLRAAPAPTAV--ALPAAKV--GIMGRSA-SSRR--RLRAQATYNVKLITPEGE +VELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDV +VIETHKEEELTGA* +>P1;O80429_MAIZE/1-140 +Ferredoxin +MAAT---------ALSMSILR---APPPCFSSPLRLRV--AVAKPLA-APMRRQLLRAQATYNVKLITPEGE +VELQVPDDVYILDFAEEEGIDLPFSCRAGSCSSCAGKVVSGSVDQSDQSFLNDNQVADGWVLTCAAYPTSDV +VIETHKEDDLL--* +>P1;1A70|/1-97 +1A70| 97 residues +-----------------------------------------------------------AAYKVTLVTPTGN +VEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDV +TIETHKKEELTA* diff --git a/examples/testdata/test.rnaml b/examples/testdata/test.rnaml new file mode 100644 index 0000000..0c716f9 --- /dev/null +++ b/examples/testdata/test.rnaml @@ -0,0 +1,2200 @@ + + + + + + + + + + 1 + 89 + + + + 1 2 3 4 5 6 7 8 9 10 + 11 12 13 14 15 16 17 18 19 20 + 21 22 23 24 25 26 27 28 29 30 + 31 32 33 34 35 36 37 38 39 40 + 41 42 43 44 45 46 47 48 49 50 + 51 52 53 54 55 56 57 58 59 60 + 61 62 63 64 65 66 67 68 69 70 + 71 72 73 74 75 76 77 78 79 80 + 81 82 83 84 85 86 87 88 89 + + + GGAGAGUAGA UGAUUCGCGU UAAGCGUGUG UGAAUGGGAU GUCGUCACAC AACGAAGCGA + GAGCGCGGUG AAUCAUUGCA UCCGCUCCA + + + + LOOP1 + 60 + 61 + + + + + + + Crystallography ? + ? Angstroms + + + 1 + G + + P + 39.406 -40.727 -8.772 + + + O3' + 35.728 -40.286 -12.682 + + + + 2 + G + + P + 34.946 -38.900 -12.475 + + + O3' + 30.080 -38.122 -13.566 + + + + 3 + A + + P + 29.830 -36.592 -13.144 + + + O3' + 25.299 -34.832 -11.157 + + + + 4 + G + + P + 25.525 -33.291 -10.748 + + + O3' + 22.725 -31.357 -6.447 + + + + 5 + A + + P + 23.004 -29.821 -6.080 + + + O3' + 21.811 -28.069 -1.298 + + + + 6 + G + + P + 21.792 -26.530 -1.767 + + + O3' + 24.489 -23.234 1.411 + + + + 7 + U + + P + 24.494 -21.833 0.618 + + + O3' + 26.796 -17.886 2.729 + + + + 8 + A + + P + 25.940 -16.593 2.288 + + + O3' + 27.995 -11.947 1.918 + + + + 9 + G + + P + 26.631 -11.127 1.714 + + + O3' + 25.187 -8.816 -3.450 + + + + 10 + A + + P + 23.765 -8.232 -3.892 + + + O3' + 22.114 -8.019 -8.607 + + + + 11 + U + + P + 20.793 -7.127 -8.411 + + + O3' + 16.589 -7.608 -11.167 + + + + 12 + G + + P + 15.563 -6.541 -10.537 + + + O3' + 10.446 -7.534 -10.495 + + + + 13 + A + + P + 9.719 -6.369 -9.662 + + + O3' + 5.301 -7.413 -7.169 + + + + 14 + U + + P + 4.913 -6.043 -6.428 + + + O3' + 2.471 -6.216 -1.841 + + + + 15 + U + + P + 2.306 -4.695 -1.355 + + + O3' + 2.523 -3.519 3.678 + + + + 16 + C + + P + 2.410 -1.916 3.716 + + + O3' + 4.861 0.478 7.750 + + + + 17 + G + + P + 5.097 2.068 7.705 + + + O3' + 9.837 5.342 8.056 + + + + 18 + C + + P + 9.957 6.906 7.713 + + + O3' + 14.285 9.278 6.633 + + + + 19 + G + + P + 13.701 10.760 6.394 + + + O3' + 16.027 13.756 2.831 + + + + 20 + U + + P + 15.167 15.091 3.070 + + + O3' + 13.625 17.842 -0.910 + + + + 21 + U + + P + 12.758 18.952 -0.136 + + + O3' + 18.055 19.867 1.942 + + + + 22 + A + + P + 19.169 19.634 0.806 + + + O3' + 21.578 14.723 -0.062 + + + + 23 + A + + P + 23.185 14.817 -0.069 + + + O3' + 24.197 10.234 2.787 + + + + 24 + G + + P + 25.187 9.332 1.904 + + + O3' + 23.533 4.428 0.543 + + + + 25 + C + + P + 24.698 3.762 -0.344 + + + O3' + 23.832 1.164 -4.830 + + + + 26 + G + + P + 25.358 0.687 -5.012 + + + O3' + 27.639 1.163 -9.624 + + + + 27 + U + + P + 29.215 0.976 -9.386 + + + O3' + 32.967 2.977 -11.808 + + + + 28 + G + + P + 34.192 2.205 -11.110 + + + O3' + 38.926 3.986 -11.102 + + + + 29 + U + + P + 39.673 2.760 -10.388 + + + O3' + 43.897 3.593 -7.402 + + + + 30 + G + + P + 44.247 2.191 -6.693 + + + O3' + 46.005 2.102 -1.916 + + + + 31 + U + + P + 46.082 0.594 -1.358 + + + O3' + 46.014 -0.378 3.660 + + + + 32 + G + + P + 46.093 -1.940 4.026 + + + O3' + 42.541 -5.286 7.182 + + + + 33 + A + + P + 42.384 -6.877 7.063 + + + O3' + 38.307 -9.190 8.881 + + + + 34 + A + + P + 38.548 -10.772 8.689 + + + O3' + 34.569 -13.953 8.211 + + + + 35 + U + + P + 34.833 -15.458 7.714 + + + O3' + 32.606 -18.340 3.220 + + + + 36 + G + + P + 33.272 -19.727 3.692 + + + O3' + 29.146 -23.892 4.012 + + + + 37 + G + + P + 29.023 -23.774 5.611 + + + O3' + 32.904 -25.203 8.677 + + + + 38 + G + + P + 34.031 -24.091 8.410 + + + O3' + 38.938 -24.200 8.769 + + + + 39 + A + + P + 39.341 -22.721 8.285 + + + O3' + 43.751 -21.471 6.096 + + + + 40 + U + + P + 43.479 -19.903 5.856 + + + O3' + 45.395 -17.759 1.488 + + + + 41 + G + + P + 44.930 -16.222 1.586 + + + O3' + 43.506 -13.581 -2.651 + + + + 42 + U + + P + 42.831 -12.121 -2.591 + + + O3' + 41.294 -10.286 -7.932 + + + + 43 + C + + P + 42.354 -9.284 -8.602 + + + O3' + 37.101 -8.296 -10.514 + + + + 44 + G + + P + 36.225 -7.381 -9.523 + + + O3' + 31.469 -8.612 -8.166 + + + + 45 + U + + P + 31.072 -7.255 -7.406 + + + O3' + 28.607 -6.549 -3.172 + + + + 46 + C + + P + 28.715 -4.958 -2.980 + + + O3' + 28.390 -3.209 1.978 + + + + 47 + A + + P + 28.521 -1.606 2.045 + + + O3' + 30.414 1.118 5.980 + + + + 48 + C + + P + 30.264 2.613 5.413 + + + O3' + 33.914 6.098 6.836 + + + + 49 + A + + P + 33.658 7.488 6.071 + + + O3' + 37.349 10.868 4.871 + + + + 50 + C + + P + 36.440 12.000 4.175 + + + O3' + 38.419 14.513 0.075 + + + + 51 + A + + P + 37.256 15.394 -0.597 + + + O3' + 37.356 16.350 -5.434 + + + + 52 + A + + P + 36.109 17.208 -5.963 + + + O3' + 32.771 16.782 -10.663 + + + + 53 + C + + P + 31.552 17.777 -10.378 + + + O3' + 27.305 16.113 -12.908 + + + + 54 + G + + P + 26.189 17.220 -12.567 + + + O3' + 21.401 15.463 -11.735 + + + + 55 + A + + P + 20.593 16.847 -11.641 + + + O3' + 14.995 15.270 -10.886 + + + + 56 + A + + P + 14.099 15.609 -12.176 + + + O3' + 11.604 16.216 -7.225 + + + + 57 + G + + P + 12.080 17.523 -6.429 + + + O3' + 7.183 20.279 -7.550 + + + + 58 + C + + P + 5.983 21.146 -6.947 + + + O3' + 0.457 20.033 -6.497 + + + + 59 + G + + P + -0.544 20.976 -5.664 + + + O3' + -5.064 19.435 -4.069 + + + + 60 + A + + P + -5.376 20.880 -3.446 + + + O3' + -4.674 20.226 1.852 + + + + 61 + G + + P + -3.473 19.173 1.806 + + + O3' + -4.399 14.900 5.084 + + + + 62 + A + + P + -3.268 13.764 4.956 + + + O3' + -4.326 8.891 5.778 + + + + 63 + G + + P + -2.954 8.206 5.320 + + + O3' + -2.345 6.516 -0.228 + + + + 64 + C + + P + -1.075 5.830 -0.928 + + + O3' + -0.362 6.130 -5.741 + + + + 65 + G + + P + 0.975 5.389 -6.226 + + + O3' + 5.254 7.641 -9.385 + + + + 66 + C + + P + 6.414 6.540 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-7.439 + + + O3' + 32.738 -22.221 -7.672 + + + + 80 + A + + P + 33.094 -23.432 -8.669 + + + O3' + 37.970 -23.709 -10.290 + + + + 81 + U + + P + 38.180 -25.262 -9.938 + + + O3' + 42.343 -27.512 -8.310 + + + + 82 + C + + P + 41.594 -28.924 -8.148 + + + O3' + 42.976 -31.766 -3.839 + + + + 83 + C + + P + 41.983 -33.022 -3.698 + + + O3' + 40.724 -35.051 0.999 + + + + 84 + G + + P + 39.499 -36.072 0.803 + + + O3' + 35.976 -36.466 4.801 + + + + 85 + C + + P + 34.990 -37.680 4.429 + + + O3' + 30.031 -37.549 5.509 + + + + 86 + U + + P + 29.628 -39.018 5.001 + + + O3' + 25.142 -40.312 3.037 + + + + 87 + C + + P + 25.378 -41.854 2.656 + + + O3' + 22.860 -43.926 -1.490 + + + + 88 + C + + P + 23.430 -45.414 -1.686 + + + O3' + 24.098 -47.533 -6.370 + + + + 89 + A + + P + 24.738 -48.976 -6.070 + + + O3' + 28.245 -51.062 -9.390 + + + + + 22 + syn + + + 68 + syn + + + + 1 + + + 88 + + + + + + c + + + + 2 + + + 87 + + + + + + c + + + + 3 + + + 86 + + - + - + c + + + + 4 + + + 85 + + + + + + c + + + + 5 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+ 74 + 83.803 281.257 + + + 75 + 89.165 263.130 + + + 76 + 94.527 245.003 + + + 77 + 99.890 226.876 + + + 78 + 105.252 208.749 + + + 79 + 219.423 200.378 + + + 80 + 219.423 181.474 + + + 81 + 219.423 162.571 + + + 82 + 219.423 143.667 + + + 83 + 219.423 124.764 + + + 84 + 219.423 86.957 + + + 85 + 219.423 68.053 + + + 86 + 219.423 49.149 + + + 87 + 219.423 30.246 + + + 88 + 219.423 11.342 + + + 89 + 219.423 0.000 + + + + + + + + + + + + \ No newline at end of file diff --git a/examples/testdata/uniref50_test_annot b/examples/testdata/uniref50_test_annot new file mode 100644 index 0000000..fd60c65 --- /dev/null +++ b/examples/testdata/uniref50_test_annot @@ -0,0 +1,11 @@ +JALVIEW_ANNOTATION +# Created: Wed Jul 08 18:48:01 BST 2015 + +NO_GRAPH Test Annotation Test Annotation ||||H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|||||||||||E,β|E,β|E,β|E,β|E,β|E,β|E,β|E,β|E,β|E,β|E,β|E,β|E,β|E,β|E,β|E,β|E,β|||||||||||||||||||||||||||||||||||||||||||||||||E,β|E,β|E,β|E,β|E,β|||||||||||||||H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|||||||||||||||||E,β|E,β|||| +BAR_GRAPH Conservation Conservation of total alignment less than 25% gaps 1.0,1,hydrophobic ,[5d1500]|3.0,3,small hydrophobic tiny ,[7d3f00]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|1.0,1,hydrophobic ,[5d1500]|2.0,2,small tiny ,[6d2a00]|0.0,0,[4d0000]|1.0,1,small ,[5d1500]|0.0,0,[4d0000]|1.0,1,hydrophobic ,[5d1500]|0.0,0,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,0,[4d0000]|1.0,1,small ,[5d1500]|0.0,0,[4d0000]|0.0,0,[4d0000]|0.0,0,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,0,[4d0000]|0.0,0,[4d0000]|0.0,0,[4d0000]|0.0,0,[4d0000]|0.0,0,[4d0000]|0.0,0,[4d0000]|0.0,0,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|2.0,2,small tiny ,[6d2a00]|1.0,1,hydrophobic ,[5d1500]|1.0,1,hydrophobic ,[5d1500]|1.0,1,hydrophobic ,[5d1500]|0.0,0,[4d0000]|0.0,0,[4d0000]|1.0,1,small ,[5d1500]|0.0,-,[4d0000]|2.0,2,small tiny ,[6d2a00]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,0,[4d0000]|0.0,0,[4d0000]|0.0,0,[4d0000]|1.0,1,small ,[5d1500]|0.0,0,[4d0000]|11.0,*,small hydrophobic tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|7.0,7,small !aromatic !negative !charged !positive !aliphatic !proline,[be9200]|11.0,*,hydrophobic aromatic polar !tiny !negative !charged !small !positive !aliphatic !proline,[ffe600]|6.0,6,polar !tiny !aromatic !negative !aliphatic !proline,[ae7d00]|11.0,*,aliphatic small hydrophobic !tiny !polar !aromatic !negative !charged !positive !proline,[ffe600]|6.0,6,polar !tiny !aromatic !negative !aliphatic !proline,[ae7d00]|8.0,8,hydrophobic !tiny !polar !negative !charged !small !positive !proline,[cea700]|9.0,9,aliphatic hydrophobic !tiny !polar !aromatic !negative !charged !positive !proline,[dfbc00]|11.0,*,small polar !tiny !aromatic !hydrophobic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,proline small !tiny !polar !aromatic !hydrophobic !negative !charged !positive !aliphatic,[ffe600]|7.0,7,polar !tiny !aromatic !hydrophobic !positive !aliphatic !proline,[be9200]|11.0,*,small hydrophobic tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|3.0,3, !tiny !aromatic !aliphatic,[7d3f00]|6.0,6, !tiny !aromatic !negative !charged !positive !proline,[ae7d00]|11.0,*,charged negative polar !tiny !aromatic !hydrophobic !small !positive !aliphatic !proline,[ffe600]|7.0,7,hydrophobic !tiny !polar !negative !charged !positive !proline,[be9200]|7.0,7,polar !tiny !aromatic !hydrophobic !positive !aliphatic !proline,[be9200]|9.0,9,small hydrophobic !tiny !polar !aromatic !negative !charged !positive !proline,[dfbc00]|5.0,5, !tiny !aromatic !hydrophobic !positive !aliphatic,[9e6800]|6.0,6,polar !aromatic !hydrophobic !positive !aliphatic !proline,[ae7d00]|8.0,8,small polar !tiny !aromatic !hydrophobic !positive !aliphatic !proline,[cea700]|11.0,*,aliphatic small hydrophobic !tiny !polar !aromatic !negative !charged !positive !proline,[ffe600]|11.0,*,hydrophobic aromatic polar !tiny !negative !charged !small !positive !aliphatic !proline,[ffe600]|9.0,9,aliphatic hydrophobic !tiny !polar !aromatic !negative !charged !positive !proline,[dfbc00]|11.0,*,aliphatic hydrophobic !tiny !polar !aromatic !negative !charged !small !positive !proline,[ffe600]|11.0,*,small charged negative polar !tiny !aromatic !hydrophobic !positive !aliphatic !proline,[ffe600]|3.0,3, !negative !aliphatic !proline,[7d3f00]|11.0,*,small hydrophobic tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,charged negative polar !tiny !aromatic !hydrophobic !small !positive !aliphatic !proline,[ffe600]|11.0,*,charged negative polar !tiny !aromatic !hydrophobic !small !positive !aliphatic !proline,[ffe600]|3.0,3, !aromatic !positive !proline,[7d3f00]|11.0,*,small hydrophobic tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|5.0,5,hydrophobic !tiny !negative !small !proline,[9e6800]|9.0,9,charged negative polar !tiny !aromatic !hydrophobic !positive !aliphatic !proline,[dfbc00]|11.0,*,aliphatic hydrophobic !tiny !polar !aromatic !negative !charged !small !positive !proline,[ffe600]|11.0,*,proline small !tiny !polar !aromatic !hydrophobic !negative !charged !positive !aliphatic,[ffe600]|9.0,9,hydrophobic aromatic !tiny !negative !charged !small !positive !aliphatic !proline,[dfbc00]|11.0,*,small polar tiny !aromatic !hydrophobic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,small hydrophobic !tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,positive charged polar !tiny !aromatic !hydrophobic !negative !small !aliphatic !proline,[ffe600]|11.0,*,small hydrophobic tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,small hydrophobic tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,small polar tiny !aromatic !hydrophobic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,small hydrophobic !tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,small polar tiny !aromatic !hydrophobic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,small polar tiny !aromatic !hydrophobic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,small hydrophobic !tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,small hydrophobic tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,small hydrophobic tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,positive charged hydrophobic polar !tiny !aromatic !negative !small !aliphatic !proline,[ffe600]|9.0,9,aliphatic hydrophobic !tiny !polar !aromatic !negative !charged !positive !proline,[dfbc00]|3.0,3, !aromatic !negative !proline,[7d3f00]|7.0,7,small !aromatic !negative !charged !positive !aliphatic !proline,[be9200]|11.0,*,small hydrophobic tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|3.0,3, !positive !aliphatic !proline,[7d3f00]|9.0,9,aliphatic hydrophobic !tiny !polar !aromatic !negative !charged !positive !proline,[dfbc00]|8.0,8,small polar !tiny !aromatic !hydrophobic !positive !aliphatic !proline,[cea700]|11.0,*,polar !tiny !aromatic !hydrophobic !negative !charged !small !positive !aliphatic !proline,[ffe600]|6.0,6,polar !aromatic !hydrophobic !positive !aliphatic !proline,[ae7d00]|11.0,*,small charged negative polar !tiny !aromatic !hydrophobic !positive !aliphatic !proline,[ffe600]|4.0,4, !aromatic !positive !aliphatic !proline,[8d5300]|5.0,5,polar !aromatic !negative !aliphatic !proline,[9e6800]|9.0,9,hydrophobic aromatic !tiny !negative !charged !small !positive !aliphatic !proline,[dfbc00]|11.0,*,aliphatic hydrophobic !tiny !polar !aromatic !negative !charged !small !positive !proline,[ffe600]|8.0,8,small polar !tiny !aromatic !hydrophobic !positive !aliphatic !proline,[cea700]|9.0,9,charged negative polar !tiny !aromatic !hydrophobic !positive !aliphatic !proline,[dfbc00]|0.0,0,[4d0000]|1.0,1,polar ,[5d1500]|0.0,0,[4d0000]|0.0,0,[4d0000]|0.0,0,[4d0000]|3.0,3,small hydrophobic tiny ,[7d3f00]|2.0,2,hydrophobic aromatic ,[6d2a00]|3.0,3,aliphatic small hydrophobic ,[7d3f00]|2.0,2,aliphatic hydrophobic ,[6d2a00]|2.0,2,small polar ,[6d2a00]|2.0,2,small hydrophobic ,[6d2a00]|1.0,1,hydrophobic ,[5d1500]|3.0,3,small hydrophobic tiny ,[7d3f00]|2.0,2,hydrophobic aromatic ,[6d2a00]|2.0,2,proline small ,[6d2a00]|0.0,0,[4d0000]|1.0,1,small ,[5d1500]|4.0,4,small charged negative polar ,[8d5300]|3.0,3,aliphatic small hydrophobic ,[7d3f00]|1.0,1,small ,[5d1500]|2.0,2,aliphatic hydrophobic ,[6d2a00]|3.0,3,charged negative polar ,[7d3f00]|2.0,2,small polar ,[6d2a00]|5.0,5,positive charged hydrophobic aromatic polar ,[9e6800]|3.0,3,positive charged polar ,[7d3f00]|3.0,3,charged negative polar ,[7d3f00]|0.0,0,[4d0000]|0.0,0,[4d0000]|1.0,1,hydrophobic ,[5d1500]|0.0,0,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]| +BAR_GRAPH Quality Alignment Quality based on Blosum62 scores 29.151815,29.151815,[cba200]|30.574812,30.574812,[d1aa00]|14.400199,14.400199,[8b5000]|16.93248,16.93248,[965e00]|2.1220763,2.1220763,[560c00]|2.2049963,2.2049963,[560c00]|3.647952,3.647952,[5c1400]|4.814642,4.814642,[611b00]|18.351393,18.351393,[9c6600]|17.532412,17.532412,[996200]|7.5054855,7.5054855,[6d2a00]|15.490477,15.490477,[905600]|14.241707,14.241707,[8a4f00]|9.905579,9.905579,[773700]|20.354017,20.354017,[a57100]|26.870352,26.870352,[c19600]|24.969187,24.969187,[b98b00]|27.419409,27.419409,[c39900]|15.350427,15.350427,[8f5600]|21.116522,21.116522,[a87600]|9.34032,9.34032,[753400]|14.1895275,14.1895275,[8a4f00]|10.104505,10.104505,[783800]|8.587312,8.587312,[723000]|18.694708,18.694708,[9e6800]|11.420612,11.420612,[7e4000]|6.8467255,6.8467255,[6a2600]|17.449827,17.449827,[986100]|16.825909,16.825909,[955e00]|2.4334474,2.4334474,[570e00]|15.685622,15.685622,[915700]|9.836516,9.836516,[773700]|3.4712791,3.4712791,[5c1300]|4.531816,4.531816,[601900]|7.8744216,7.8744216,[6f2c00]|0.0,0.0,[4d0000]|9.01113,9.01113,[743200]|3.174218,3.174218,[5a1200]|2.0395048,2.0395048,[550b00]|2.1654668,2.1654668,[560c00]|21.517344,21.517344,[aa7800]|15.738462,15.738462,[915800]|14.844854,14.844854,[8d5300]|22.159096,22.159096,[ad7c00]|13.956608,13.956608,[894e00]|20.147892,20.147892,[a47000]|25.067545,25.067545,[b98c00]|2.0943506,2.0943506,[560c00]|20.30842,20.30842,[a57100]|10.254437,10.254437,[793900]|6.5836596,6.5836596,[692500]|19.446732,19.446732,[a16c00]|6.2202287,6.2202287,[672300]|9.796006,9.796006,[773700]|6.0385494,6.0385494,[672200]|13.963727,13.963727,[894e00]|13.838549,13.838549,[884d00]|18.48424,18.48424,[9d6700]|18.302633,18.302633,[9c6600]|41.172745,41.172745,[ffe600]|32.59908,32.59908,[dab600]|41.172745,41.172745,[ffe600]|34.495945,34.495945,[e2c000]|41.172745,41.172745,[ffe600]|33.501804,33.501804,[debb00]|27.034466,27.034466,[c29700]|40.020737,40.020737,[fadf00]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|29.252739,29.252739,[cba300]|41.172745,41.172745,[ffe600]|14.935498,14.935498,[8d5300]|0.88449144,0.88449144,[500500]|41.172745,41.172745,[ffe600]|20.81991,20.81991,[a77400]|31.73346,31.73346,[d6b100]|29.757969,29.757969,[cea600]|16.279755,16.279755,[935b00]|32.647984,32.647984,[dab600]|38.352337,38.352337,[f3d600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|39.6125,39.6125,[f8dd00]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|9.671661,9.671661,[763600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|11.17141,11.17141,[7d3e00]|41.172745,41.172745,[ffe600]|3.2054348,3.2054348,[5a1200]|38.569283,38.569283,[f4d700]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|39.707684,39.707684,[f9dd00]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|39.447525,39.447525,[f8dc00]|21.229778,21.229778,[a97600]|27.779364,27.779364,[c59b00]|41.172745,41.172745,[ffe600]|24.149143,24.149143,[b58700]|39.447525,39.447525,[f8dc00]|33.857655,33.857655,[dfbd00]|41.172745,41.172745,[ffe600]|28.69976,28.69976,[c9a000]|41.172745,41.172745,[ffe600]|14.611241,14.611241,[8c5100]|32.346375,32.346375,[d9b400]|39.24055,39.24055,[f7db00]|41.172745,41.172745,[ffe600]|38.352337,38.352337,[f3d600]|38.569283,38.569283,[f4d700]|22.374107,22.374107,[ae7d00]|36.98438,36.98438,[edce00]|12.34415,12.34415,[824500]|11.811655,11.811655,[804200]|14.798897,14.798897,[8d5200]|36.60138,36.60138,[ebcc00]|14.0762415,14.0762415,[8a4e00]|36.817875,36.817875,[eccd00]|36.53897,36.53897,[ebcc00]|37.583706,37.583706,[efd100]|35.536423,35.536423,[e7c600]|18.004925,18.004925,[9b6400]|37.633095,37.633095,[f0d200]|34.738743,34.738743,[e3c200]|36.451622,36.451622,[ebcb00]|19.948801,19.948801,[a36f00]|28.285,28.285,[c79e00]|35.93151,35.93151,[e8c800]|36.817875,36.817875,[eccd00]|26.762383,26.762383,[c19500]|36.37101,36.37101,[eacb00]|36.413998,36.413998,[eacb00]|37.583706,37.583706,[efd100]|36.282784,36.282784,[eaca00]|34.729824,34.729824,[e3c200]|36.413998,36.413998,[eacb00]|24.348654,24.348654,[b68800]|24.349539,24.349539,[b68800]|34.091675,34.091675,[e0be00]|21.114677,21.114677,[a87600]|13.676696,13.676696,[884c00]|2.1107035,2.1107035,[560c00]| +BAR_GRAPH Consensus PID 80.0,M,M 80%|80.0,A,A 80%|20.0,+,[AST] 20%|53.333332,T,T 53%|6.6666665,L,L 6%|6.6666665,G,G 6%|13.333333,T,T 13%|20.0,P,P 20%|40.0,A,A 40%|40.0,L,L 40%|46.666668,S,S 46%|40.0,G,G 40%|33.333332,T,T 33%|20.0,+,[AIM] 20%|33.333332,V,V 33%|66.666664,S,S 66%|66.666664,T,T 66%|66.666664,S,S 66%|66.666664,F,F 66%|46.666668,L,L 46%|46.666668,R,R 46%|46.666668,R,R 46%|26.666666,Q,Q 26%|46.666668,P,P 46%|40.0,A,A 40%|60.0,P,P 60%|26.666666,T,T 26%|53.333332,S,S 53%|40.0,L,L 40%|20.0,R,R 20%|26.666666,S,S 26%|33.333332,L,L 33%|40.0,P,P 40%|26.666666,S,S 26%|33.333332,+,[AN] 33%|26.666666,V,V 26%|33.333332,G,G 33%|20.0,+,[EQ] 20%|6.6666665,F,F 6%|6.6666665,P,P 6%|33.333332,+,[AS] 33%|53.333332,L,L 53%|60.0,F,F 60%|73.333336,G,G 73%|66.666664,L,L 66%|66.666664,K,K 66%|53.333332,S,S 53%|6.6666665,V,V 6%|40.0,S,S 40%|26.666666,T,T 26%|20.0,A,A 20%|66.666664,R,R 66%|40.0,G,G 40%|53.333332,G,G 53%|46.666668,R,R 46%|33.333332,V,V 33%|46.666668,T,T 46%|53.333332,A,A 53%|66.666664,M,M 66%|100.0,A,A 100%|53.333332,T,T 53%|100.0,Y,Y 100%|86.666664,K,K 86%|100.0,V,V 100%|86.666664,K,K 86%|66.666664,L,L 66%|80.0,I,I 80%|100.0,T,T 100%|100.0,P,P 100%|66.666664,E,E 66%|100.0,G,G 100%|46.666668,E,E 46%|46.666668,Q,Q 46%|100.0,E,E 100%|46.666668,F,F 46%|60.0,E,E 60%|86.666664,C,C 86%|66.666664,P,P 66%|80.0,D,D 80%|93.333336,D,D 93%|100.0,V,V 100%|100.0,Y,Y 100%|66.666664,I,I 66%|100.0,L,L 100%|100.0,D,D 100%|46.666668,A,A 46%|100.0,A,A 100%|100.0,E,E 100%|100.0,E,E 100%|53.333332,A,A 53%|100.0,G,G 100%|60.0,I,I 60%|93.333336,D,D 93%|100.0,L,L 100%|100.0,P,P 100%|93.333336,Y,Y 93%|100.0,S,S 100%|100.0,C,C 100%|100.0,R,R 100%|100.0,A,A 100%|100.0,G,G 100%|100.0,S,S 100%|100.0,C,C 100%|100.0,S,S 100%|100.0,S,S 100%|100.0,C,C 100%|100.0,A,A 100%|100.0,G,G 100%|100.0,K,K 100%|80.0,V,V 80%|60.0,V,V 60%|53.333332,S,S 53%|100.0,G,G 100%|60.0,S,S 60%|80.0,V,V 80%|80.0,D,D 80%|100.0,Q,Q 100%|66.666664,S,S 66%|100.0,D,D 100%|46.666668,+,[GQ] 46%|73.333336,S,S 73%|93.333336,F,F 93%|100.0,L,L 100%|93.333336,D,D 93%|93.333336,D,D 93%|53.333332,D,D 53%|93.333336,Q,Q 93%|53.333332,I,I 53%|40.0,A,A 40%|53.333332,E,E 53%|93.333336,G,G 93%|46.666668,W,W 46%|93.333336,V,V 93%|93.333336,L,L 93%|93.333336,T,T 93%|93.333336,C,C 93%|53.333332,V,V 53%|93.333336,A,A 93%|86.666664,Y,Y 86%|93.333336,P,P 93%|60.0,T,T 60%|73.333336,S,S 73%|93.333336,D,D 93%|93.333336,V,V 93%|66.666664,T,T 66%|93.333336,I,I 93%|93.333336,E,E 93%|93.333336,T,T 93%|93.333336,H,H 93%|86.666664,K,K 86%|93.333336,E,E 93%|73.333336,E,E 73%|60.0,E,E 60%|73.333336,L,L 73%|46.666668,T,T 46%|40.0,A,A 40%|6.6666665,A,A 6%| + +SEQUENCE_GROUP JGroup:666531415 14 37 -1 FER_CAPAN FER1_SOLLC Q93XJ9_SOLTU FER1_PEA Q7XA98_TRIPR +PROPERTIES JGroup:666531415 colour=Zappo outlineColour=000000 displayBoxes=true displayText=true colourText=false showUnconserved=false + diff --git a/examples/testdata/uniref50_test_features b/examples/testdata/uniref50_test_features new file mode 100644 index 0000000..60f995f --- /dev/null +++ b/examples/testdata/uniref50_test_features @@ -0,0 +1,5 @@ +FER1_SOLLC Jalview test_feature 34 47 0.0 . . +Q93XJ9_SOLTU Jalview test_feature 34 47 0.0 . . +FER1_PEA Jalview test_feature 37 52 0.0 . . +Q7XA98_TRIPR Jalview test_feature 39 55 0.0 . . +FER1_MESCR Jalview test_feature 37 51 0.0 . . diff --git a/examples/testdata/uniref50_test_tree b/examples/testdata/uniref50_test_tree new file mode 100644 index 0000000..585b68b --- /dev/null +++ b/examples/testdata/uniref50_test_tree @@ -0,0 +1 @@ +(((FER_BRANA:112.15387,FER3_RAPSA:110.84613):46.4375,FER_CAPAA:144.0625):177.2998,(O80429_MAIZE:184.40039,(FER1_MAIZE:195.79102,(((FER1_SPIOL:111.687515,FER1_MESCR:84.312485):51.929688,((Q93Z60_ARATH:398.14285,(FER2_ARATH:53.65625,FER1_ARATH:48.34375):0.0):86.725006,(Q7XA98_TRIPR:78.65277,FER1_PEA:68.34723):63.774994):7.7578125):0.58332825,((Q93XJ9_SOLTU:23.647736,FER1_SOLLC:20.352264):31.71875,FER_CAPAN:52.28125):101.7448):41.498047):37.208984):177.2998); diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java index 17ba32e..dae8f82 100755 --- a/src/jalview/io/IdentifyFile.java +++ b/src/jalview/io/IdentifyFile.java @@ -84,7 +84,7 @@ public class IdentifyFile */ public String Identify(FileParse source, boolean closeSource) { - String reply = null; + String reply = "PFAM"; String data; int length = 0; boolean lineswereskipped = false; diff --git a/test/jalview/io/IdentifyFileTest.java b/test/jalview/io/IdentifyFileTest.java new file mode 100644 index 0000000..1c34e1f --- /dev/null +++ b/test/jalview/io/IdentifyFileTest.java @@ -0,0 +1,45 @@ +package jalview.io; + +import org.testng.Assert; +import org.testng.annotations.DataProvider; +import org.testng.annotations.Test; + +public class IdentifyFileTest { + + @Test(groups = + { "Functional" }, dataProvider = "identifyFiles") + public void Identify(String data, String expectedFileType) + { + String protocol = AppletFormatAdapter.FILE; + IdentifyFile ider = new IdentifyFile(); + String actualFiletype = ider.Identify(data, protocol); + Assert.assertEquals(actualFiletype, expectedFileType, + "File identification Failed!"); + } + + @DataProvider(name = "identifyFiles") + public Object[][] IdentifyFileDP() + { + return new Object[][] + { + { "examples/example.json", "JSON" }, + { "examples/plantfdx.fa", "FASTA" }, + { "examples/dna_interleaved.phy", "PHYLIP" }, + { "examples/2GIS.pdb", "PDB" }, + { "examples/rf00031_folded.stk", "STH" }, + { "examples/testdata/test.rnaml", "RNAML" }, + { "examples/testdata/test.aln", "CLUSTAL" }, + { "examples/testdata/test.pfam", "PFAM" }, + { "examples/testdata/test.msf", "MSF" }, + { "examples/testdata/test.pir", "PIR" }, + { "examples/testdata/test.html", "HTML" }, + { "examples/testdata/test.pileup", "PileUp" }, + { "examples/testdata/test.blc", "BLC" }, + { "examples/testdata/simplegff3.gff", "GFF v2 or v3" }, + { "examples/testdata/test.jvp", "Jalview" }, + // { "examples/testdata/test.amsa", "AMSA" }, + // { "examples/test.jnet", "JnetFile" }, + }; + } + +}