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Bio::Tools::Run::PiseApplication::fmtseq.3pm
Langue: en
Version: 2008-11-10 (debian - 07/07/09)
Section: 3 (Bibliothèques de fonctions)
Sommaire
NAME
Bio::Tools::Run::PiseApplication::fmtseqSYNOPSIS
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DESCRIPTION
Bio::Tools::Run::PiseApplication::fmtseqBioperl class for: fmtseq sequence conversion (J. R. Knight) Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/fmtseq.html for available values): fmtseq (String) seq (InFile) Sequence File pipe: readseq_ok_alig outfile (OutFile) pipe: seqsfile outformat (Excl) Output Sequence Format gapin (Excl) Set the gap symbol for the input (-gapin) informat (Excl) Input sequence format (-inf[ormat]) caselower (Switch) convert to lowercase (-c) CASEUPPER (Switch) convert to upper case (-C) degap (Switch) Remove gaps from sequences (-degap) gapout (Excl) Set the gap symbol for the output (-gapout) list (Switch) Only list sequence information (-li) long (Switch) Long form conversion (input header included as comment) (-long) raw (Excl) Gaps in sequences (-raw) reverse (Switch) Reverse-complement each sequence (-re) interleave (Excl) Output interleaved sequences (-interleave) width (Integer) Sequence line width (-width) tab (Integer) Indent sequence (-tab) colspace (Integer) Add space columms in sequence lines (-colspace) gapcount (Excl) Count gap chars in sequence numbers (-gapcount) nameleft (Integer) Name on left side (-nameleft) nameright (Integer) Name on left side (-nameright) nametop (Switch) Name at top (-nametop) numleft (Excl) Sequence index on left/right side numtop (Excl) Index on top/bottom match (Switch) Replace matches to first sequence with . (-match) interline (Integer) How many blank line(s) between sequence blocks (-interline) skipempty (Switch) Do not output lines with only gap characters (-skipempty) bigalign (Switch) Convert FASTA program output to big alignment (-bigalign)
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:http://bugzilla.open-bio.org/
AUTHOR
Catherine Letondal (letondal@pasteur.fr)COPYRIGHT
Copyright (C) 2003 Institut Pasteur & Catherine Letondal. All Rights Reserved.This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
DISCLAIMER
This software is provided ``as is'' without warranty of any kind.SEE ALSO
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- http://bioweb.pasteur.fr/seqanal/interfaces/fmtseq.html
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- Bio::Tools::Run::PiseApplication
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- Bio::Tools::Run::AnalysisFactory::Pise
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- Bio::Tools::Run::PiseJob
new
Title : new() Usage : my $fmtseq = Bio::Tools::Run::PiseApplication::fmtseq->new($location, $email, @params); Function: Creates a Bio::Tools::Run::PiseApplication::fmtseq object. This method should not be used directly, but rather by a Bio::Tools::Run::AnalysisFactory::Pise instance. my $factory = Bio::Tools::Run::AnalysisFactory::Pise->new(); my $fmtseq = $factory->program('fmtseq'); Example : - Returns : An instance of Bio::Tools::Run::PiseApplication::fmtseq.
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre