NAME

Bio::Tools::Run::PiseApplication::mspcrunch

SYNOPSIS

#

DESCRIPTION

Bio::Tools::Run::PiseApplication::mspcrunch

      Bioperl class for:

	MSPcrunch	a BLAST post-processing filter (Sonnhammer, Durbin)


      Parameters: 

        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/mspcrunch.html 
         for available values):


		mspcrunch (String)

		blast_output (InFile)
			BLAST output File
			pipe: blast_output

		outfile (OutFile)
			Result file

		gapped (Switch)
			Make gapped alignment of ungapped-MSP contigs (-G)

		big_pict (Switch)
			Big Picture (-P)

		sfs (Switch)
			Produce SFS    output (-H)

		seqbl (Switch)
			Produce seqbl  output (for Blixem) (-q)

		ace (Switch)
			Produce .ace   output (for ACEDB 4) (-4)

		exblx (Switch)
			Produce exblx  output (for easy parsing) (-x)

		exbldb (Switch)
			Produce exbldb output (as exblx with query names) (-d)

		fasta (Switch)
			Produce fasta  output (unaligned, for mult.alignm.) (-2)

		three_frame (Switch)
			Print 3 frame translation (blastn only) (-3)

		footer (Switch)
			Print footer with parameters and stats (-f)

		matches_one_line (Switch)
			For -P output, force all matches to the same subject on one line (-F)

		percentage_id (Switch)
			Print percentage identity (seqbl output only) (-i)

		stats_file (OutFile)
			Output coverage stats to file (-o)

		domainer (Switch)
			Produce output for Domainer (trim overlaps) (-D)

		silent_mutations (Switch)
			Do Statistics of Silent mutations (only cDNA!) (-S)

		all_expected (Switch)
			Print all Expected scores (default only when positive) (-X)

		matrix_stats (Switch)
			Print statistics on used matrices (-E)

		stats_without_X (Switch)
			Recalculate percentage identity, ignoring X residues. (-j)

		ignore_hits (Switch)
			Ignore hits to earlier seqnames (for All-vs-All). (-A)

		line_length (Integer)
			Line length of Wrapped alignment (0 -> no wrapping) (-W)

		wublast_numbered (Switch)
			indicate query insertions with numbers (For seqbl output from Wublast) (-N)

		dont_reject (Switch)
			Don't reject any MSPs (-w)

		report_rejected (Switch)
			Report only rejected MSPs (-r)

		threshold (Float)
			Reject all matches with less than this % identity (-I)

		expect (Float)
			Reject all matches with E-value higher than this value (-e)

		whole_contig (Switch)
			Coverage limitation requires whole contig to be covered (always for Blastp) (-a)

		hits_to_self (Switch)
			Accept hits to self (-s)

		no_hits_to_earlier (Switch)
			Ignore hits to earlier seqnames (for All-vs-All) (-A)

		dont_mirror (Switch)
			Don't mirror (i.e. print the subject object) in ACE4 format (-M)

		old_cutoff (Switch)
			 Use old step cutoffs for adjacency instead of the new continuous system. (-O)

		force_blastp (Switch)
			Force Blastp mode (default Blastx) (-p)

		force_blastn (Switch)
			Force Blastn mode (default Blastx) (-n)

		matrix (String)
			Scoring matrix (PAM or BLOSUM, see help) (-m)

		query (Sequence)
			Read in query seq (for rereading .seqbl files) (-Q)

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

• http://bioweb.pasteur.fr/seqanal/interfaces/mspcrunch.html

• Bio::Tools::Run::PiseApplication

• Bio::Tools::Run::AnalysisFactory::Pise

• Bio::Tools::Run::PiseJob

new

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