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 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 -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
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).
