Hi,
I tried parsing a multi-record genbank file (from this site: http://biopython.org/DIST/docs/tutorial/examples/ls_orchid.gbk) using the code below.
The code returned an error:
readline() on unopened filehandle at parser.pl line 62.
The code:
#!/usr/local/bin/perl -w
use strict;
my $record;
print "Please type in the name of a file\n";
my $file = <STDIN>;
chomp $file;
while( $record = get_next_record($file) ) {
my ($annotation, $seq) = get_dna ($record);
open my $fh, '>', 'oufile.txt', or die "cant't open outfile:$!";
print "Sequence:\n\n", $seq, "\n";
close $fh or die "cant't open outfile:$!";
}
sub get_dna {
my ($file) = @_;
my @annotation = ();
my $seq = '';
my $in_sequence = 0;
open FILE, $file or die "Can't open $file, Perl says $!\n";
while ( my $line = <FILE> ) {
last if $line =~ m|^//\n|; # stop if line has just // on it
$in_sequence = 1 if $line =~ m/^ORIGIN/;
if ($in_sequence) {
$seq .= $line;
} else {
push @annotation, $line;
}
}
close FILE;
# remove all spaces and digits from $seq. add \n to remove newlines
$seq =~ s/[\s0-9]//g;
# return @annotation array as a scalar reference and scalar $seq
return \@annotation, $seq;
}
sub get_next_record {
my($file) = @_;
my($offset);
my($record) = '';
my($save_input_separator) = $/;
$/ = "//\n";
$record = <$file>;
$/ = $save_input_separator;
return $record;
}
Can someone help me fix this error please.
Thank you