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1 #!/usr/bin/perl
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2
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3 #------------------------------------------------------------------------------
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4 # Split a fasta file (create one file per sequence)
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5 #
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6 #
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7 #------------------------------------------------------------------------------
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8
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9 use strict;
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10
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11 #------------------------------------------------------------------------------
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12 # Write fasta file
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13 #------------------------------------------------------------------------------
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14 sub writeSeq($$) {
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15 my($name, $seq) = @_;
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16 $name = "chr" . $name . ".fa";
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17 print "Writing to $name\n";
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18 open OUT, "> $name";
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19 print OUT $seq;
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20 close OUT;
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21 }
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22
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23 #------------------------------------------------------------------------------
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24 # Main
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25 #------------------------------------------------------------------------------
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26
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27 my($seq, $name) = ('', '');
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28 my($lineNum, $l, $newName);
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29 #---
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30 # Read fasta file
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31 #---
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32 for($lineNum=0 ; $l = <STDIN> ; $lineNum++ ) {
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33 if( $l =~/^>\s*(.*?)\s+.*/ ) {
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34 $newName = $1;
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35 if( $seq ne "" ) { writeSeq($name, $seq); }
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36 # New sequence
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37 $name = $newName;
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38 $seq = $l;
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39 } else { $seq .= $l; }
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40 }
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41
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42 if( $seq ne "" ) { writeSeq($name, $seq); }
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