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readseq

Langue: en

Version: 260187 (debian - 07/07/09)

Section: 1 (Commandes utilisateur)

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).
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