annotate rapsodyn/PileupVariant.pl @ 2:761fecc07fa9 draft

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author mcharles
date Thu, 11 Sep 2014 03:10:47 -0400
parents 442a7c88b886
children 3f7b0788a1c4
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 #!/usr/bin/perl
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2 use strict;
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3
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4 my $inputfile = $ARGV[0];
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5 open(IF, $inputfile) or die("Can't open $inputfile\n");
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6
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7 #Extraction des variants
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8 my $nb_line=0;
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9 while (my $line=<IF>){
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10 my $test = $line;
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11 $test =~ s/\$//g; #the read start at this position
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12 $test =~ s/\^.//g; #the read end at this position followed by quality char
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13 my @field = split(/\s+/,$test);
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14
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15 if ($field[4]=~/[ATGCN]/i){
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16 print $line;
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17 }
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18 }
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19 close(IF);