Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics
annotate phyloconversion/raxify_fasta.pl @ 0:5b9a38ec4a39 draft default tip
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author | osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> |
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date | Tue, 11 Mar 2014 12:19:13 -0700 |
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1 #!/usr/bin/perl -w |
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2 use strict; |
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3 |
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4 my $infile = $ARGV[0]; |
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5 my $outfile = $ARGV[1]; |
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6 |
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7 open(IN, "$infile") or exit; |
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8 open(OUT, ">$outfile") or exit; |
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9 |
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10 while (<IN>) { |
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11 my $line = $_; |
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12 if($line =~ m/\>/ ){ |
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13 $line=raxify($line); |
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14 } |
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15 if($line =~ m/\n/){ |
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16 print OUT $line; |
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17 }else{ |
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18 print OUT $line."\n"; |
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19 } |
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20 } |
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21 close(IN); |
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22 close(OUT); |
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23 |
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24 sub raxify |
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25 { |
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26 my $raxline = shift; |
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27 $raxline = substr($raxline,0,51); |
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28 $raxline =~ s/\./_/g; |
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29 $raxline =~ s/\|/_/g; |
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30 $raxline =~ s/ /_/g; |
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31 return $raxline; |
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32 } |