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