--- name: "Bio::AlignIO::phylip" section: "3pm" platform: "linux" package: "libbio-perl-perl" version: "1.7.8-1" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/Bio::AlignIO::phylip" --- # Bio::AlignIO::phylip(3pm) PHYLIP format sequence input/output stream ## NAME Bio::AlignIO::phylip - PHYLIP format sequence input/output stream ## SYNOPSIS Do not use this module directly. Use it via the Bio::AlignIO class. This example shows how to write to phylip format: ``` use Bio::AlignIO; use Bio::SimpleAlign; # Use -idlength to set the name length to something other than # the default 10 if you need longer ids. my $phylipstream = Bio::AlignIO->new(-format => 'phylip', -fh => \*STDOUT, -idlength => 30); # Convert data from one format to another my $gcgstream = Bio::AlignIO->new(-format => 'msf', -file => 't/data/cysprot1a.msf'); while( my $aln = $gcgstream->next_aln ) { $phylipstream->write_aln($aln); } # With phylip sequential format format $phylipstream->interleaved(0); # Or initialize the object like this $phylipstream = Bio::AlignIO->new(-interleaved => 0, -format => 'phylip', -fh => \*STDOUT, -idlength => 20 ); $gcgstream = Bio::AlignIO->new(-format => 'msf', -file => 't/data/cysprot1a.msf'); while( my $aln = $gcgstream->next_aln ) { $phylipstream->write_aln($aln); } ``` This example shows how to read phylip format: ``` my $in = Bio::AlignIO->new( -file => $inFile, -format => 'phylip', -interleaved => 0, -longid => 1 ); my $out = Bio::AlignIO->new( -file => ">$outFile", -format => 'fasta' ); while ( my $aln = $in->next_aln() ) { $out->write_aln($aln); } ``` The -longid argument is required if the input phylip format file has ids with lengths greater then 10 characters. ## DESCRIPTION This object can transform Bio::SimpleAlign objects to and from PHYLIP format. By default it works with the interleaved format. By specifying the flag -interleaved =\> 0 in the initialization the module can read or write data in sequential format. Reading phylip format with long IDs up to 50 characters is supported by the flag -longid =\>1. ID strings can be surrounded by single quotes. They are mandatory only if the IDs contain spaces. ## FEEDBACK ### 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://github.com/bioperl/bioperl-live/issues ``` ## AUTHORS - Heikki Lehvaslaiho and Jason Stajich Email: heikki at ebi.ac.uk Email: jason at bioperl.org ## APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a \_ ### new ``` Title : new Usage : my $alignio = Bio::AlignIO->new(-format => 'phylip' -file => '>file', -idlength => 10, -idlinebreak => 1); Function: Initialize a new L reader or writer Returns : L object Args : [specific for writing of phylip format files] -idlength => integer - length of the id (will pad w/ spaces if needed) when writing phylip -interleaved => boolean - whether interleaved or sequential format required -line_length => integer of how long a sequence lines should be -idlinebreak => insert a line break after the sequence id so that sequence starts on the next line -flag_SI => whether or not write a "S" or "I" just after the num.seq. and line len., in the first line -tag_length => integer of how long the tags have to be in each line between the space separator. set it to 0 to have 1 tag only. -wrap_sequential => boolean for whether or not sequential format should be broken up or a single line default is false (single line) -longid => boolean to read arbitrary long IDs (default is false) ``` ### next\_aln ``` Title : next_aln Usage : $aln = $stream->next_aln() Function: returns the next alignment in the stream. Throws an exception if trying to read in PHYLIP sequential format. Returns : L object Args : ``` ### write\_aln ``` Title : write_aln Usage : $stream->write_aln(@aln) Function: writes the $aln object into the stream in phylip format Returns : 1 for success and 0 for error Args : L object ``` ### interleaved ``` Title : interleaved Usage : my $interleaved = $obj->interleaved Function: Get/Set Interleaved status Returns : boolean Args : boolean ``` ### flag\_SI ``` Title : flag_SI Usage : my $flag = $obj->flag_SI Function: Get/Set if the Sequential/Interleaved flag has to be shown after the number of sequences and sequence length Example : Returns : boolean Args : boolean ``` ### idlength ``` Title : idlength Usage : my $idlength = $obj->idlength Function: Get/Set value of id length Returns : string Args : string ``` ### line\_length ``` Title : line_length Usage : $obj->line_length($newval) Function: Returns : value of line_length Args : newvalue (optional) ``` ### tag\_length ``` Title : tag_length Usage : $obj->tag_length($newval) Function: Example : my $tag_length = $obj->tag_length Returns : value of the length for each space-separated tag in a line Args : newvalue (optional) - set to zero to have one tag per line ``` ### id\_linebreak ``` Title : id_linebreak Usage : $obj->id_linebreak($newval) Function: Returns : value of id_linebreak Args : newvalue (optional) ``` ### wrap\_sequential ``` Title : wrap_sequential Usage : $obj->wrap_sequential($newval) Function: Returns : value of wrap_sequential Args : newvalue (optional) ``` ### longid ``` Title : longid Usage : $obj->longid($newval) Function: Returns : value of longid Args : newvalue (optional) ```