Oops, forgot those newlines. Need to add the 'chomp' below...
On Friday, October 4, 2002, at 10:30 AM, James Edward Gray II wrote:
> 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 $long_line = '';
> while (<>) {
chomp;
> if (/^\s*$/) {
> 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
>> AAGAAGGAAGAAGAGGGTAGAGGAGAAGTGCAGCAAGGGTGGAGGGAGGTGCCCGCGCTGGGTCGGAGGA
>> GCAGGAGTAT
>> GGAGGGAAGACTCCTGGGTGGCATGGAGCTCTTGCACCTCTAGGCACTGCCCAGCCCTGTGTCAGCCAGG
>> GCTGAACCCCCACAGGATAAGGAACCTGTGTGTGTGACCAACAATCAAAG
>> CTACATCTGTGACACAACAGGACACTGCTATGGGCAGTCTCAGTTCTGGCTCGCGTGGACCATCACCATC
>> A
>> TCCTGAGCTGCTGCTGTGTCTGCCACCACAGCCAAGCCAGCCCTCAAGTCCAGCAGTAGCAACATGAAAT
>> CAA
>> CCTGCCTGCCTATCCAGAAGCCCGCAATTACTCAGTGCTACCATTTTATTTCACCAAACTATTTATTACC
>> TT
>> CTTATGAGGAAGTGGTGAAC
>> AAGAAGGAAGCAGAGGGAAGAAGAAATGAAGGAGGAGGGTGATAGTGCCATGGTGGAGAAACAGGAGGAG
>> CAGGGGCAGGGGCACTCTACACTGGACACTGTAGTGGACAGTCTCAGTGCTCCAGCTCTGAA
>> TTCTGGTATAAGTCCTTGCCTAGGGAGTTATTGGCATCCCAGGGTCTCAGTTACTGCCTCTGCTCCACAG
>> GCAGAGG
>> AAAGCATGGGGTGTCCAGCCTTTTCTCACTCTTAGGGACAATGTTGACTTCTGACTGATGTGGACCATCA
>> TCATCT
>> TCCGGAGCTGCTGCTGTGTCTGCCACCAATGCTGAGCCCAGGCACTGCCTTCAGACCCAGCAATGACAGC
>> ATGAAATCAA
>> ATTGATGGCCTACCAGGAAGCCCACAATTACTCATCACTGCCATTTTAGTTCAGGTTTTTGCCAAACTAT
>> TTATTACCTC
>> CTTATGAGGAAGTGATGAAC
>>
>> 4 11242 11268 25467376 25467402 - 294
>> TAACCTCCACCTGTTTCCCTCCCTGTC
>> ATCTTCCAATCCCTTCCCCACCCTACC
>>
>>
>>
>>
>>
>>
>> ---------------------------------
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>
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