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 -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).