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annotate phyloconversion/phylip2fasta.pl @ 0:5b9a38ec4a39 draft default tip

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First commit of old repositories
author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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1 #!/usr/bin/perl -w
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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4 my $infile = $ARGV[0];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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5 my $interlv = $ARGV[1];
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6 my $idlen = $ARGV[2];
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7 my $outfile = $ARGV[3];
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8
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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9 #open (OUT, ">$outfile");
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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11 use strict;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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12 use Bio::AlignIO;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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13 use Bio::SimpleAlign;
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14 #you can set the name length to something other than the default 10
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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15 #if you use a version of phylip (hacked) that accepts ids > 10
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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16 my $outstream = Bio::AlignIO->new(-format => 'fasta',
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17 -fh => \*STDOUT );
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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19 # convert data from one format to another
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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20 my $phylipstream = Bio::AlignIO->new(-interleaved => $interlv,
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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21 -format => 'phylip',
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22 -file => '<'.$infile,
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23 -idlength=>$idlen );
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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24 while( my $aln = $phylipstream->next_aln ) {
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25 $outstream->write_aln($aln);
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26 }
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