Bio::Tools::Run::PiseApplication::fmtseq # Bio::Tools::Run::PiseApplication::fmtseq Bioperl 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)

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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/fmtseq.html Bio::Tools::Run::PiseApplication Bio::Tools::Run::AnalysisFactory::Pise 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.