| * ReadSeq.Help -- 30 Dec 92
| * 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: email@example.com
| * 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 is particularly useful as it automatically detects many sequence formats, and interconverts among them.
Formats which readseq currently understands:
IG/Stanford, used by Intelligenetics and others
GenBank/GB, genbank flatfile format
EMBL, EMBL flatfile format
GCG, single sequence format of GCG software
DNAStrider, for common Mac program
Fitch format, limited use
Pearson/Fasta, a common format used by Fasta programs and others
Zuker format, limited use. Input only.
Olsen, format printed by Olsen VMS sequence editor. Input only.
Phylip3.2, sequential format for Phylip programs
Phylip, interleaved format for Phylip programs (v3.3, v3.4)
Plain/Raw, sequence data only (no name, document, numbering)
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. Output only.
See the included "Formats" file for detail on file formats.
-- 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 (27Dec92), multi-format molbio sequence reader.
usage: readseq [-options] in.seq > out.seq
-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
In use, readseq will respond to command line arguments, or to interactive use. Command line arguments cannot be combined but must each follow a switch character (-). In this release, the command line options are now words, with an equals (=) to separate parameter(s) fromt he command. You cannot put a space between a command and its parameter, as is usual for Unix programs (this is to preserve compatibility with VMS). The command line syntax of the earlier versions is still supported.
See the file Formats for details of the sequence formats which are supported by readseq. The auto-detection feature of readseq which distinguishes these formats looks for some of the unique keywords and symbols that are found in each format. It is not infallible at this, though it attempts to exclude unknown formats. In general, if you feed to readseq a sequence file that you know is one of these common formats, you are okay. If you feed it data that might be oddball formats, or non-sequence data, you might well get garbage results. Also, different developers are always thinking up minor twists on these common formats (like PAUP requiring a blank line between blocks of Phylip format, or IG adding form feeds between sequences), which may cause hassles.
In general, output supports only minimal subsets of each format needed for sequence data exchanges. Features, descriptions and other format-unique information is discarded.
The pretty format requires additional options to generate a nice output. Try the various pretty options to see what you like. Pretty format is OUPUT only, readseq cannot read a Pretty format file.
Readseq is NOT optimized for LARGE files. It generally makes several reads thru each input file (one per sequence output at present, future version may optimize this). It should handle input and output files and sequences of any size, but will slow down quite a bit for very large (multi megabyte) sized files. It is NOT recommended for converting databanks or large subsets there-of. It is primarily directed at the small files that researchers use to maintain their personal data, which they frequently need to interconvert for the various analysis programs which so frequently require a special format.
Users of Olsen multi sequence editor (VMS). The Olsen format
here is produced with the print command:
Use Genbank output from readseq to produce a format that this
editor can read, and use the command
Dan Davison has a VMS program that will convert to/from the
Olsen native binary data format. E-mail firstname.lastname@example.org
Warning: Phylip format input is now supported (30Dec92), however the auto-detection of Phylip format is very probabilistic and messy, especially distinguishing sequential from interleaved versions. It is not recommended that one use readseq to convert files from Phylip format to others unless essential.
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 18.104.22.168)
ftp> cd molbio/readseq
ftp> get readseq.shar
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
Readme (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
Recent changes (see also readseq.c for all history of changes):
4 May 92