--- /dev/null
+
+ * ReadSeq -- 1 Feb 93
+ *
+ * Reads and writes nucleic/protein sequences in various
+ * formats. Data files may have multiple sequences.
+ *
+ * Copyright 1990 by d.g.gilbert
+ * biology dept., indiana university, bloomington, in 47405
+ * e-mail: gilbertd@bio.indiana.edu
+ *
+ * This program may be freely copied and used by anyone.
+ * Developers are encourged to incorporate parts in their
+ * programs, rather than devise their own private sequence
+ * format.
+ *
+ * This should compile and run with any ANSI C compiler.
+ * Please advise me of any bugs, additions or corrections.
+
+Readseq has been updated. There have been a number of enhancements
+and a few bug corrections since the previous general release in Nov 91
+(see below). If you are using earlier versions, I recommend you update to
+this release.
+
+Readseq is particularly useful as it automatically detects many
+sequence formats, and interconverts among them.
+Formats added to this release include
+ + MSF multi sequence format used by GCG software
+ + PAUP's multiple sequence (NEXUS) format
+ + PIR/CODATA format used by PIR
+ + ASN.1 format used by NCBI
+ + Pretty print with various options for nice looking output.
+
+As well, Phylip format can now be used as input. Options to
+reverse-compliment and to degap sequences have been added. A menu
+addition for users of the GDE sequence editor is included.
+
+This program is available thru Internet gopher, as
+
+ gopher ftp.bio.indiana.edu
+ browse into the IUBio-Software+Data/molbio/readseq/ folder
+ select the readseq.shar document
+
+Or thru anonymous FTP in this manner:
+ my_computer> ftp ftp.bio.indiana.edu (or IP address 129.79.224.25)
+ username: anonymous
+ password: my_username@my_computer
+ ftp> cd molbio/readseq
+ ftp> get readseq.shar
+ ftp> bye
+
+readseq.shar is a Unix shell archive of the readseq files.
+This file can be editted by any text editor to reconstitute the
+original files, for those who do not have a Unix system or an
+Unshar program. Read the top of this .shar file for further
+instructions.
+
+There are also pre-compiled executables for the following computers:
+Silicon Graphics Iris, Sparc (Sun Sparcstation & clones), VMS-Vax,
+Macintosh. Use binary ftp to transfer these, except Macintosh. The
+Mac version is just the command-line program in a window, not very
+handy.
+
+C source files:
+ readseq.c ureadseq.c ureadasn.c ureadseq.h
+Document files:
+ Readme (this doc)
+ Readseq.help (longer than this doc)
+ Formats (description of sequence file formats)
+ add.gdemenu (GDE program users can add this to the .GDEmenu file)
+ Stdfiles -- test sequence files
+ Makefile -- Unix make file
+ Make.com -- VMS make file
+ *.std -- files for testing validity of readseq
+
+
+Example usage:
+ readseq
+ -- for interactive use
+ readseq my.1st.seq my.2nd.seq -all -format=genbank -output=my.gb
+ -- convert all of two input files to one genbank format output file
+ readseq my.seq -all -form=pretty -nameleft=3 -numleft -numright -numtop -match
+ -- output to standard output a file in a pretty format
+ readseq my.seq -item=9,8,3,2 -degap -CASE -rev -f=msf -out=my.rev
+ -- select 4 items from input, degap, reverse, and uppercase them
+ cat *.seq | readseq -pipe -all -format=asn > bunch-of.asn
+ -- pipe a bunch of data thru readseq, converting all to asn
+
+
+The brief usage of readseq is as follows. The "[]" denote
+optional parts of the syntax:
+
+ readseq -help
+readSeq (27Dec92), multi-format molbio sequence reader.
+usage: readseq [-options] in.seq > out.seq
+ options
+ -a[ll] select All sequences
+ -c[aselower] change to lower case
+ -C[ASEUPPER] change to UPPER CASE
+ -degap[=-] remove gap symbols
+ -i[tem=2,3,4] select Item number(s) from several
+ -l[ist] List sequences only
+ -o[utput=]out.seq redirect Output
+ -p[ipe] Pipe (command line, <stdin, >stdout)
+ -r[everse] change to Reverse-complement
+ -v[erbose] Verbose progress
+ -f[ormat=]# Format number for output, or
+ -f[ormat=]Name Format name for output:
+ 1. IG/Stanford 10. Olsen (in-only)
+ 2. GenBank/GB 11. Phylip3.2
+ 3. NBRF 12. Phylip
+ 4. EMBL 13. Plain/Raw
+ 5. GCG 14. PIR/CODATA
+ 6. DNAStrider 15. MSF
+ 7. Fitch 16. ASN.1
+ 8. Pearson/Fasta 17. PAUP
+ 9. Zuker 18. Pretty (out-only)
+
+ Pretty format options:
+ -wid[th]=# sequence line width
+ -tab=# left indent
+ -col[space]=# column space within sequence line on output
+ -gap[count] count gap chars in sequence numbers
+ -nameleft, -nameright[=#] name on left/right side [=max width]
+ -nametop name at top/bottom
+ -numleft, -numright seq index on left/right side
+ -numtop, -numbot index on top/bottom
+ -match[=.] use match base for 2..n species
+ -inter[line=#] blank line(s) between sequence blocks
+
+
+
+Recent changes:
+
+4 May 92
++ added 32 bit CRC checksum as alternative to GCG 6.5bit checksum
+Aug 92
+= fixed Olsen format input to handle files w/ more sequences,
+ not to mess up when more than one seq has same identifier,
+ and to convert number masks to symbols.
+= IG format fix to understand ^L
+30 Dec 92
+* revised command-line & interactive interface. Suggested form is now
+ readseq infile -format=genbank -output=outfile -item=1,3,4 ...
+ but remains compatible with prior commandlines:
+ readseq infile -f2 -ooutfile -i3 ...
++ added GCG MSF multi sequence file format
++ added PIR/CODATA format
++ added NCBI ASN.1 sequence file format
++ added Pretty, multi sequence pretty output (only)
++ added PAUP multi seq format
++ added degap option
++ added Gary Williams (GWW, G.Williams@CRC.AC.UK) reverse-complement option.
++ added support for reading Phylip formats (interleave & sequential)
+* string fixes, dropped need for compiler flags NOSTR, FIXTOUPPER, NEEDSTRCASECMP
+* changed 32bit checksum to default, -DSMALLCHECKSUM for GCG version
+
+1Feb93
+= reverted Genbank output format to fixed left margin
+ (change in 30 Dec release), so GDE and others relying on fixed margin
+ can read this.
git://source.jalview.org / jpred.git / blobdiff