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* 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.
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