With something like the script below. (I haven't tested it.) I
assumed the blank lines in the sample data really exist. If they
don't, you'll need to change it a bit.
#!/usr/bin/perl
use strict;
use warnings;
my $long_line = '';
while (<>) {
if (/^\s*$/) {
print "$long_line\n\n";
$long_line = '';
}
else { $long_line .= $_; }
}
__END__
On Friday, October 4, 2002, at 10:00 AM, s wang wrote:
>
> i have just started writing some scripts in PERL and i am trying to
> catch a deadline, i really wish i could get some help for this
> problem. any suggestion is greatly appreciated.
>
> i have a set of files with sequences aligned in the following format.
> i wonder how i can eliminate the new line characters within each
> sequence without touching those between sequences?
>
> .....
>
> 2 chr1 10761 10775 chr19 46520370 46520384 + 941
> acaGGAAAAGAACAA
> acaggaaaagaaggg
>
> 3 chr1 10776 11241 chrUn 45411478 45411944 - 12857
> AAGAAGGAAGAAGAGGGTAGAGGAGAAGTGCAGCAAGGGTGGAGGGAGGTGCCCGCGCTGGGTCGGAGGAG
> CAGGAGTAT
> GGAGGGAAGACTCCTGGGTGGCATGGAGCTCTTGCACCTCTAGGCACTGCCCAGCCCTGTGTCAGCCAGGG
> CTGAACCCCCACAGGATAAGGAACCTGTGTGTGTGACCAACAATCAAAG
> CTACATCTGTGACACAACAGGACACTGCTATGGGCAGTCTCAGTTCTGGCTCGCGTGGACCATCACCATCA
> TCCTGAGCTGCTGCTGTGTCTGCCACCACAGCCAAGCCAGCCCTCAAGTCCAGCAGTAGCAACATGAAATC
> AA
> CCTGCCTGCCTATCCAGAAGCCCGCAATTACTCAGTGCTACCATTTTATTTCACCAAACTATTTATTACCT
> T
> CTTATGAGGAAGTGGTGAAC
> AAGAAGGAAGCAGAGGGAAGAAGAAATGAAGGAGGAGGGTGATAGTGCCATGGTGGAGAAACAGGAGGAG
> CAGGGGCAGGGGCACTCTACACTGGACACTGTAGTGGACAGTCTCAGTGCTCCAGCTCTGAA
> TTCTGGTATAAGTCCTTGCCTAGGGAGTTATTGGCATCCCAGGGTCTCAGTTACTGCCTCTGCTCCACAGG
> CAGAGG
> AAAGCATGGGGTGTCCAGCCTTTTCTCACTCTTAGGGACAATGTTGACTTCTGACTGATGTGGACCATCAT
> CATCT
> TCCGGAGCTGCTGCTGTGTCTGCCACCAATGCTGAGCCCAGGCACTGCCTTCAGACCCAGCAATGACAGCA
> TGAAATCAA
> ATTGATGGCCTACCAGGAAGCCCACAATTACTCATCACTGCCATTTTAGTTCAGGTTTTTGCCAAACTATT
> TATTACCTC
> CTTATGAGGAAGTGATGAAC
>
> 4 11242 11268 25467376 25467402 - 294
> TAACCTCCACCTGTTTCCCTCCCTGTC
> ATCTTCCAATCCCTTCCCCACCCTACC
>
>
>
>
>
>
> ---------------------------------
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