Works with huge 1.fa file.
#!/usr/bin/perl
use strict;
use warnings;
while (my $line =<DATA>)
{
$line =~ s/^\s*|\s*$//g;
if ($line =~ /^\d/)
{
print "$line\t";
}
else
{
print "$line\n";
}
}
=Prints
1 AGTCGTAGCAT
2 TGAGCTACG
3 GGCATAGN
4 CGCACNCAGCTACACC
5 NGATAGCTACA
=cut
__DATA__
1
AGTCGTAGCAT
2
TGAGCTACG
3
GGCATAGN
4
CGCACNCAGCTACACC
5
NGATAGCTACA
To prevent blank lines in output caused by blank lines in 1.fa, add
next unless $line =~ /\S/; or similar after removing leading and trailing spaces.
Update: looking back this, if the ">" actually appears in the 1.fa file, then just delete it if seen while processing the line and use the above logic.
