see perlvar
$LIST_SEPARATOR
$"
When an array or an array slice is interpolated into a double-quoted string or a similar context such as /.../ , its elements are separated by this value. Default is a space. For example, this:
print "The array is: @array\n";
is equivalent to this:
print "The array is: " . join($", @array) . "\n";
Either use
{
local $" = '';
print FH "@fasta";
}
or
print FH join '',@fasta;
or just print out each line as it is read
#!/usr/local/bin/perl
use strict;
use Text::CSV;
use Data::Dumper qw(Dumper);
print "Enter input file name : ";
my $file = <STDIN>;
chomp $file;
open my $in, '<', $file
or die "Could not open '$file' $!\n";
print "Enter output file name: ";
my $ofile = <STDIN>;
chomp $ofile;
open my $out, '>', $ofile
or die "Could not open '$ofile' $!\n";
my $csv = Text::CSV->new({ sep_char => ',' });
my $count = 0;
while (my $line = <$in>) {
if ($csv->parse($line)) {
my @fields = $csv->fields();
$fields[4]=~s/\s//g; #removes spaces within the sequence
print $out '>'.(join '_',@fields[0..3])."\n$fields[4]\n";
} else {
warn "Line could not be parsed: $line\n";
}
++$count;
}
close $in;
close $out;
print "$count lines read from $file to $ofile\n";
poj
