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bp_sreformat(1p) [debian man page]

BP_SREFORMAT(1p)					User Contributed Perl Documentation					  BP_SREFORMAT(1p)

NAME
bpsreformat - convert sequence formats DESCRIPTION
This script uses the SeqIO system that allows conversion of sequence formats either sequence data or multiple sequence alignment data. The name comes from the fact that Sean Eddy's program sreformat (part of the HMMER pkg) already does this. Sean's program tries to guess the input formats while in our code we currently require your to specify what the input and output formats are and if the data is from a multiple sequence alignment or from straight sequence files. Usage: bpsreformat -if INFORMAT -of OUTFORMAT -i FILENAME -o output.FORMAT -h/--help Print this help -if/--informat Specify the input format -of/--outformat Specify the output format -i/--input Specify the input file name (to pass in data on STDIN use minus sign as filename) -o/--output Specify the output file name (to pass data out on STDOUT use minus sign as filename) --msa Specify this is multiple sequence alignment data --special Will pass on special parameters to the AlignIO/SeqIO object -- most of these are for Bio::AlignIO objects Comma separated list of the following nointerleaved -- for phylip,non-interleaved format idlinebreak -- for phylip, makes it molphy format percentages -- for clustalw, show % id per line perl v5.14.2 2012-03-02 BP_SREFORMAT(1p)

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Bio::AlignIO::proda(3pm)				User Contributed Perl Documentation				  Bio::AlignIO::proda(3pm)

NAME
Bio::AlignIO::proda - proda sequence input/output stream This provides the basic capabilities to parse the output alignments from the ProDA multiple sequence alignment program (http://proda.stanford.edu) SYNOPSIS
Do not use this module directly. Use it via the Bio::AlignIO class. DESCRIPTION
This object can transform Bio::Align::AlignI objects to and from proda files. 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 one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists Support Please direct usage questions or support issues to the mailing list: bioperl-l@bioperl.org rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://redmine.open-bio.org/projects/bioperl/ AUTHORS - Albert Vilella Email: avilella-at-gmail-dot-com APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ new Title : new Usage : $alignio = Bio::AlignIO->new(-format => 'proda', -file => 'filename'); Function: returns a new Bio::AlignIO object to handle proda files Returns : Bio::AlignIO::proda object Args : -verbose => verbosity setting (-1, 0, 1, 2) -file => name of file to read in or to write, with ">" -fh => alternative to -file param - provide a filehandle to read from or write to -format => alignment format to process or produce -percentages => display a percentage of identity in each line of the alignment (proda only) -linelength=> alignment output line length (default 60) next_aln Title : next_aln Usage : $aln = $stream->next_aln() Function: returns the next alignment in the stream Returns : Bio::Align::AlignI object Args : NONE See Bio::Align::AlignI for details write_aln Title : write_aln Usage : $stream->write_aln(@aln) Function: writes the proda-format object (.aln) into the stream Returns : 1 for success and 0 for error Args : Bio::Align::AlignI object percentages Title : percentages Usage : $obj->percentages($newval) Function: Set the percentages flag - whether or not to show percentages in each output line Returns : value of percentages Args : newvalue (optional) line_length Title : line_length Usage : $obj->line_length($newval) Function: Set the alignment output line length Returns : value of line_length Args : newvalue (optional) no_header Title : no_header Usage : $obj->no_header($newval) Function: Set if the alignment input has a CLUSTAL header or not Returns : value of no_header Args : newvalue (optional) perl v5.14.2 2012-03-02 Bio::AlignIO::proda(3pm)
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