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
-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).