* 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, 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.