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#!/usr/bin/perl
#-------------------------------------------------------------------------------
# Extract fasta sequences matching names
#
#
#
# Pablo Cingolani
#-------------------------------------------------------------------------------
$debug = 0;
# Check command line arguments
die "Usage: cat file.fa | ./extractSequences.pl id_1 .... id_N\n" if( $#ARGV < 0 );
# Read sequence names from command line (arguments)
foreach $name ( @ARGV ) {
$names{$name} = 1;
print "names{$name}\n" if $debug;
}
# Read and parse FASTA file from STDIN
$match = 0;
while( $l=<STDIN> ) {
if( $l =~ />(.*)/ ) {
$name = $1;
if( $name =~ /^(.*?)\s+/ ) {
$name = $1;
}
$match = ( $names{$name} ne '' );
print "$l\tSequence name: '$name'\tmatch: $match\n" if $debug;
}
print $l if $match;
}
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