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