Bio::Tools::Run::PiseApplication::readseq # Bio::Tools::Run::PiseApplication::readseq Bioperl class for: READSEQ (D. Gilbert) Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/readseq.html for available values): readseq (String) seq (InFile) Sequence File pipe: readseq_ok_alig outfile (OutFile) pipe: seqfile outformat (Excl) Output Sequence Format items (String) select Item number(s) from several allseq (Switch) lowcase (Switch) Change to lower case (-c) uppcase (Switch) Change to UPPER case (-C) degap (Switch) Remove gap symbols (-degap) reverse (Switch) Change to Reverse-complement (-r) listonly (Switch) List sequences only (-l) width (Integer) Sequence line width (-width) tab (Integer) Left indent (-tab) col (Integer) Column space within sequence line on output (-col) gap (Integer) Count gap chars in sequence numbers (-gap) nameleft (Excl) Name on left/right side nametop (Switch) Name at top (-nametop) numleft (Excl) Sequence index on left/right side numtop (Excl) Index on top/bottom match (Switch) Use match base (.) for 2..n species (-match) interline (Integer) How many blank line(s) between sequence blocks

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/MailList.shtml - 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.bioperl.org/ Catherine Letondal (letondal@pasteur.fr) 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. This software is provided "as is" without warranty of any kind. http://bioweb.pasteur.fr/seqanal/interfaces/readseq.html Bio::Tools::Run::PiseApplication Bio::Tools::Run::AnalysisFactory::Pise Bio::Tools::Run::PiseJob

new
Title : new() Usage : my $readseq = Bio::Tools::Run::PiseApplication::readseq->new($location, $email, @params); Function: Creates a Bio::Tools::Run::PiseApplication::readseq 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 $readseq = $factory->program('readseq'); Example : - Returns : An instance of Bio::Tools::Run::PiseApplication::readseq.