READSEQ(1)
NAME
readseq - Reads and writes nucleic/protein sequences in various formats
SYNOPSIS
readseq [-options] in.seq > out.seq
DESCRIPTION
This manual page documents briefly the readseq command. This manual
page was written for the Debian GNU/Linux distribution because the
original program does not have a manual page. Instead, it has documentation in text form, see below.
readseq reads and writes biosequences (nucleic/protein) in various formats. Data files may have multiple sequences. readseq is particularly
useful as it automatically detects many sequence formats, and interconverts among them.
FORMATS
- Formats which readseq currently understands:
- * IG/Stanford, used by Intelligenetics and others
* GenBank/GB, genbank flatfile format
* NBRF 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.
- + LinAll format, limited use (LinAll and ConStruct programs)
+ Vienna format used by ViennaRNA programs - See the included "Formats" file for detail on file formats.
OPTIONS
-help Show summary of 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 11. Phylip3.2
2. GenBank/GB 12. Phylip
3. NBRF 13. Plain/Raw
4. EMBL 14. PIR/CODATA
5. GCG 15. MSF
6. DNAStrider 16. ASN.1
7. Fitch 17. PAUP/NEXUS
8. Pearson/Fasta 18. Pretty (out-only)
9. Zuker (in-only) 19. LinAll - 10. Olsen (in-only) 20. Vienna
- 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
EXAMPLES
- 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 -num
- top -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 upper
- case them
- cat *.seq | readseq -pipe -all -format=asn > bunch-of.asn
-- pipe a bunch of data thru readseq, converting all to - asn
SEE ALSO
The programs are documented fully in text form. See the files in
/usr/share/doc/readseq
AUTHOR
- This manual page was written by Stephane Bortzmeyer
<bortzmeyer@debian.org>, for the Debian GNU/Linux system (but may be
used by others).