got rid of all disembl parameters as they were pointless to change dues to the fact...

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3693 e3abac25-378b-4346-85de-24260fe3988d

diff --git a/binaries/src/disembl/DisEMBL.py b/binaries/src/disembl/DisEMBL.py
index f6187bf..d9618e2 100644 (file)
--- a/binaries/src/disembl/DisEMBL.py
+++ b/binaries/src/disembl/DisEMBL.py
@@ -12,14 +12,13 @@ import os
 from os import system,popen3
 
 relpath = re.sub("/DisEMBL.py$","",argv[0])
-cwd = re.sub("/$","", os.getcwd())
-newpath =cwd+"/"+relpath+"/biopython-1.50"
+# cwd = re.sub("/$","", os.getcwd())
+newpath = relpath + "/biopython-1.50"
 sys.path.append(newpath)
 
 from Bio import File
 from Bio import Fasta
 
-
 import fpformat
 import tempfile
 
@@ -131,25 +130,25 @@ def reportSlicesTXT(slices, sequence):
 
 def runDisEMBLpipeline():
     try:
-        smooth_frame = int(sys.argv[1])
-        peak_frame = int(sys.argv[2])
-        join_frame = int(sys.argv[3])
-        fold_coils = float(sys.argv[4])
-        fold_hotloops = float(sys.argv[5])
-        fold_rem465 = float(sys.argv[6])
-        #file = str(sys.argv[7])
+        smooth_frame = 8
+        peak_frame = 8
+        join_frame = 4
+        fold_coils = 1.2
+        fold_hotloops = 1.4
+        fold_rem465 = 1.2
+        mode = 'scores'
         try:
-            mode = sys.argv[7]
+            file = open(sys.argv[1],'r')
         except:
             mode = 'default'
     except:
-        print '\nDisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops fold_rem465 sequence_file [mode]\n'
-        print 'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2  fasta_file'
+        print '\nDisEMBL.py sequence_file \n'
+        print 'A default run would be: ./DisEMBL.py fasta_file'
         print 'Mode: "default"(nothing) or "scores" which will give scores per residue in TAB seperated format'
         raise SystemExit
-    db = sys.stdin
+    #db = sys.stdin
     parser = Fasta.RecordParser()
-    iterator = Fasta.Iterator(db,parser)
+    iterator = Fasta.Iterator(file,parser)
     while 1:
         try:
             cur_record = iterator.next()
@@ -178,6 +177,7 @@ def runDisEMBLpipeline():
                 raise SystemExit
         except AttributeError:
             break
+    file.close()
     return
 
 runDisEMBLpipeline()

diff --git a/binaries/src/disembl/default.out b/binaries/src/disembl/default.out
deleted file mode 100644 (file)
index 78821a0..0000000
--- a/binaries/src/disembl/default.out
+++ /dev/null
@@ -1,21 +0,0 @@
-> Foobar_dundeefriends_COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343, 350-391, 429-485, 497-506, 539-547
-mtadgprellqlraavrhrpqdfvawlmladaeLGMGDTTAgemavqrgLALHPGHPEavarlgrvrwtqqrhaeaavllqqASDAAPEHPgialwlghaledagqaeaaaaaytraHQLLPEEPYItaqllnwrrrlcdwraldvlsaqvraavaqgvGAVEPFAFLSedasaaeqlacartraqaiaaSVRPLAPTRVRSKGPLRVGFVSNGFGAHPTglltvalfealqrrqpdlqmhlFATSGDDGSTlrtrlaqastlhdvtalghlatakhirhhgidllFDLRGWGGGGRPEVFALRPAPVQVNWLAYPGTSGAPWMDYVLGDAFALPPALEPFYSehvlrlQGAFQPSDTSRVVAEPPSRTQCGLPEQGVVLCCFNNSYKLNPqsmarmlavlrevpdsvlwllsgpgeadarlrafahaQGVDAQRLVFMPKLPHPQYLARYRHADLFLDTHPYNAHTTASDALWTGCPVLTTPGEtfaarvagslnHHLGLDEMNVaddaafvakavalasdpaaltalharvdvlrrESGVFEMDGfaddfgallqalarrhgwlgi
-> Foobar_dundeefriends_REM465 355-368
-mtadgprellqlraavrhrpqdfvawlmladaelgmgdttagemavqrglalhpghpeavarlgrvrwtqqrhaeaavllqqasdaapehpgialwlghaledagqaeaaaaaytrahqllpeepyitaqllnwrrrlcdwraldvlsaqvraavaqgvgavepfaflsedasaaeqlacartraqaiaasvrplaptrvrskgplrvgfvsngfgahptglltvalfealqrrqpdlqmhlfatsgddgstlrtrlaqastlhdvtalghlatakhirhhgidllfdlrgwggggrpevfalrpapvqvnwlaypgtsgapwmdyvlgdafalppalepfysehvlrlqgafqPSDTSRVVAEPPSRtqcglpeqgvvlccfnnsyklnpqsmarmlavlrevpdsvlwllsgpgeadarlrafahaqgvdaqrlvfmpklphpqylaryrhadlfldthpynahttasdalwtgcpvlttpgetfaarvagslnhhlgldemnvaddaafvakavalasdpaaltalharvdvlrresgvfemdgfaddfgallqalarrhgwlgi
-> Foobar_dundeefriends_HOTLOOPS 190-204
-mtadgprellqlraavrhrpqdfvawlmladaelgmgdttagemavqrglalhpghpeavarlgrvrwtqqrhaeaavllqqasdaapehpgialwlghaledagqaeaaaaaytrahqllpeepyitaqllnwrrrlcdwraldvlsaqvraavaqgvgavepfaflsedasaaeqlacartraqaiaASVRPLAPTRVRSKGplrvgfvsngfgahptglltvalfealqrrqpdlqmhlfatsgddgstlrtrlaqastlhdvtalghlatakhirhhgidllfdlrgwggggrpevfalrpapvqvnwlaypgtsgapwmdyvlgdafalppalepfysehvlrlqgafqpsdtsrvvaeppsrtqcglpeqgvvlccfnnsyklnpqsmarmlavlrevpdsvlwllsgpgeadarlrafahaqgvdaqrlvfmpklphpqylaryrhadlfldthpynahttasdalwtgcpvlttpgetfaarvagslnhhlgldemnvaddaafvakavalasdpaaltalharvdvlrresgvfemdgfaddfgallqalarrhgwlgi
-
-> Foobar_COILS 32-40, 65-73, 85-133, 156-165, 200-256, 263-304, 342-398, 410-419, 452-460
-mgdttagemavqrglalhqqrhaeaavllqqASDAAPEHPgialwlhaledagqaeaaaaytraHQLLPEEPYitaqllnavaqGVGAVEPFAFLSEDASAAESVRPLAPTRVRSKGPLRVGFVSNGFGAHPTglltvalfealqrrqpdlqmhlFATSGDDGSTlrtrlaqastlhdvtalghlatakhirhhgidllFDLRGWGGGGRPEVFALRPAPVQVNWLAYPGTSGAPWMDYVLGDAFALPPALEPFYSehvlrlQGAFQPSDTSRVVAEPPSRTQCGLPEQGVVLCCFNNSYKLNPqsmarmlavlrevpdsvlwllsgpgeadarlrafahaQGVDAQRLVFMPKLPHPQYLARYRHADLFLDTHPYNAHTTASDALWTGCPVLTTPGEtfaarvagslnHHLGLDEMNVaddaafvakavalasdpaaltalharvdvlrrESGVFEMDGfaddfgallqalarrhgwlgi
-> Foobar_REM465 1-11, 268-281
-MGDTTAGEMAVqrglalhqqrhaeaavllqqasdaapehpgialwlhaledagqaeaaaaytrahqllpeepyitaqllnavaqgvgavepfaflsedasaaesvrplaptrvrskgplrvgfvsngfgahptglltvalfealqrrqpdlqmhlfatsgddgstlrtrlaqastlhdvtalghlatakhirhhgidllfdlrgwggggrpevfalrpapvqvnwlaypgtsgapwmdyvlgdafalppalepfysehvlrlqgafqPSDTSRVVAEPPSRtqcglpeqgvvlccfnnsyklnpqsmarmlavlrevpdsvlwllsgpgeadarlrafahaqgvdaqrlvfmpklphpqylaryrhadlfldthpynahttasdalwtgcpvlttpgetfaarvagslnhhlgldemnvaddaafvakavalasdpaaltalharvdvlrresgvfemdgfaddfgallqalarrhgwlgi
-> Foobar_HOTLOOPS 100-118
-mgdttagemavqrglalhqqrhaeaavllqqasdaapehpgialwlhaledagqaeaaaaytrahqllpeepyitaqllnavaqgvgavepfaflsedaSAAESVRPLAPTRVRSKGPlrvgfvsngfgahptglltvalfealqrrqpdlqmhlfatsgddgstlrtrlaqastlhdvtalghlatakhirhhgidllfdlrgwggggrpevfalrpapvqvnwlaypgtsgapwmdyvlgdafalppalepfysehvlrlqgafqpsdtsrvvaeppsrtqcglpeqgvvlccfnnsyklnpqsmarmlavlrevpdsvlwllsgpgeadarlrafahaqgvdaqrlvfmpklphpqylaryrhadlfldthpynahttasdalwtgcpvlttpgetfaarvagslnhhlgldemnvaddaafvakavalasdpaaltalharvdvlrresgvfemdgfaddfgallqalarrhgwlgi
-
-> dundeefriends_COILS 33-40, 49-57, 82-90, 99-112, 132-141, 163-192, 215-224, 259-315, 322-363, 401-457, 469-478
-mtadgprellqlraavrhrpqdvawlmladaeLGMGDTTAgemavqrgLALHPGHPEavarlgrvrwtqqrhaeaavllqqASDAAPEHPgialwlghALEDHQLLPEEPYItaqldvlsaqvraavaqgvGAVEPFAFLSedasaaeqlacartraqaiaaSVRPLAPTRVRSKGPLRVGFVSNGFGAHPTglltvalfealqrrqpdlqmhlFATSGDDGSTlrtrlaqastlhdvtalghlatakhirhhgidllFDLRGWGGGGRPEVFALRPAPVQVNWLAYPGTSGAPWMDYVLGDAFALPPALEPFYSehvlrlQGAFQPSDTSRVVAEPPSRTQCGLPEQGVVLCCFNNSYKLNPqsmarmlavlrevpdsvlwllsgpgeadarlrafahaQGVDAQRLVFMPKLPHPQYLARYRHADLFLDTHPYNAHTTASDALWTGCPVLTTPGEtfaarvagslnHHLGLDEMNVaddaafvakavalasdpaaltalharvdvlrresi
-> dundeefriends_REM465 327-340
-mtadgprellqlraavrhrpqdvawlmladaelgmgdttagemavqrglalhpghpeavarlgrvrwtqqrhaeaavllqqasdaapehpgialwlghaledhqllpeepyitaqldvlsaqvraavaqgvgavepfaflsedasaaeqlacartraqaiaasvrplaptrvrskgplrvgfvsngfgahptglltvalfealqrrqpdlqmhlfatsgddgstlrtrlaqastlhdvtalghlatakhirhhgidllfdlrgwggggrpevfalrpapvqvnwlaypgtsgapwmdyvlgdafalppalepfysehvlrlqgafqPSDTSRVVAEPPSRtqcglpeqgvvlccfnnsyklnpqsmarmlavlrevpdsvlwllsgpgeadarlrafahaqgvdaqrlvfmpklphpqylaryrhadlfldthpynahttasdalwtgcpvlttpgetfaarvagslnhhlgldemnvaddaafvakavalasdpaaltalharvdvlrresi
-> dundeefriends_HOTLOOPS 162-176
-mtadgprellqlraavrhrpqdvawlmladaelgmgdttagemavqrglalhpghpeavarlgrvrwtqqrhaeaavllqqasdaapehpgialwlghaledhqllpeepyitaqldvlsaqvraavaqgvgavepfaflsedasaaeqlacartraqaiaASVRPLAPTRVRSKGplrvgfvsngfgahptglltvalfealqrrqpdlqmhlfatsgddgstlrtrlaqastlhdvtalghlatakhirhhgidllfdlrgwggggrpevfalrpapvqvnwlaypgtsgapwmdyvlgdafalppalepfysehvlrlqgafqpsdtsrvvaeppsrtqcglpeqgvvlccfnnsyklnpqsmarmlavlrevpdsvlwllsgpgeadarlrafahaqgvdaqrlvfmpklphpqylaryrhadlfldthpynahttasdalwtgcpvlttpgetfaarvagslnhhlgldemnvaddaafvakavalasdpaaltalharvdvlrresi
-

diff --git a/binaries/src/disembl/sav_gol_2.1_i386 b/binaries/src/disembl/sav_gol_2.1_i386
new file mode 100644 (file)
index 0000000..0a517e3
Binary files /dev/null and b/binaries/src/disembl/sav_gol_2.1_i386 differ