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comparison snpEff_2_1a/snpEff_2_1a/scripts/fastaSample.pl @ 3:c052639fa666 default tip

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author pcingola
date Fri, 20 Apr 2012 11:22:59 -0400
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2:8d0de9212f4f 3:c052639fa666
1 #!/usr/bin/perl
2
3 #---
4 # Initialize parameters
5 #---
6 $sampleStart = $ARGV[0];
7 $sampleEnd = $ARGV[1];
8 if(( $ARGV[0] eq '' ) || ($ARGV[1] eq '')) { die "Usage: fastaSample sampleStart sampleEnd\n"; }
9
10 $sampleStart--;
11 $sampleEnd--;
12 $sampleLen = $sampleEnd - $sampleStart + 1;
13
14 #---
15 # Read fasta file
16 #---
17 for($lineNum=0 ; $l = <STDIN> ; $lineNum++ ) {
18 if( $l =~/^>/ ) {
19 # Sample if not empty
20 if( $seq ne "" ) {
21 $s = substr( $seq, $sampleStart, $sampleLen);
22 print "$s\n";
23 }
24 # New sequence
25 $seq = "";
26 } else {
27 chomp($l);
28 $seq .= $l;
29 }
30 }
31
32 # Sample if not empty
33 if( $seq ne "" ) {
34 $s = substr( $seq, $sampleStart, $sampleLen);
35 print "$s\n";
36 }
37
38 $len = length($seq);
39 print STDERR "Lines: $lineNum\n";
40 print STDERR "Sequence size: $len\n";
41 print STDERR "Sample size: $sampleLen\n";