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Re^2: How do I remove spaces between sequences in a file

by bingalee (Acolyte)
on Jun 19, 2013 at 22:12 UTC ( #1039854=note: print w/ replies, xml ) Need Help??


in reply to Re: How do I remove spaces between sequences in a file
in thread How do I remove spaces between sequences in a file

No- like this

CCTGCCCGGGCGGAGGGAGGCGCGGCGCAACGGACTTCATGCTGCCACCCGCCGACCCG CACCTCACCGGCTCACCTACACCCTCCTCTTCGTTCGTCTCTTATCCATGCAATGCATC GTCTGACCTTGCCTTTTGTCTTTTACAAACACTGCCATCAGCAAATCATGCTATTTTTA TGCCGTCACGTTTCATGCAGCTATGTGTAAATAAATAAAACGTATATAACGCATTTTAA TCATAGATCCCCGACGCAACAACAATTGCAGCCACACCCCCGCGGAGCCATCACCTTTC ACTCTAATTAGAAACATCGACCTGCTCAACCCACCGAGGAATATAGACTGTTTTTTTTT CTATGTGGAAATACCAAGTAGTAGTGCCAAACGCTAAAAGGGTATGCATCTTAATTGAT GAGCTGTGAGGGTGCAATCTACAAGAGTGCGGGTTCGCGTTCAGTCCAAGCTGAACATA AACGCAACGCAAGGCCCCTCGACGCAGATACCGCGCTCAGGAGCATTCGAGAAGCCGAA GAAAATTCGAAGACGAGGACCAGCTACACTGCGGACGGACTTCGGGCATGGAGGGCCAG TTCCAGGTTGGCAAGGAGGAGGTCATCCAAGCATGGTACATGGACGACAGTGAAGAGGA CCAGAGGCTTCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTCGACAAACTTTCCG AACTAGGAATATTAAGCTGGCGCCTAAATGCTGATGATTGGGAGAATGATGAGAACCTC AAGAAAATTCGTGAAGCCAGGGGTTACTCTTACATGGACATTTGTGATGTGTGCCCAGA GAAGTTGCCAAATTACGAGGCTAAGATAAAGAATTTCTTTGAAGAACACTTGCATACTG ATGAAGAGATACGATATTGCCTTGAGGGTAGCGGCTACTTTGATGTGAGGGACCAAGAT GATCAGTGGATCCGTGTAGCGGTAAAGAAAGGGGGCATGATCGTTTTGCCTGCAGGAAT GTATCATCGCTTTACGTTGGATAGTGACAACTACATCAAGGCAATGCGTCTATTTGTGG GTGAGCCTGTCTGGACACCATACAATCGTCCGCATGACCATCTCCCGGCTAGGAAGGAG TACGTCGAGAAAATCATCAACCGAGGTGGAAACCAAGCCGTCGAAGCTCGTTGAGCGTG TCCACTCTACATGTCCTCCTGCCGTCTCAGCCTCTTGTGTTTTACACCCTACAACTCCT AGTACCGCCGAATAAGATTTGCTATCTGCAATGTGCTCATGCCACCGCTGTGTGTGCCA GTTAACAGTTTGCACGAAACCCTAGATATTTTGTTATACGAATGAATGACATGTGGTGT TTGATAAATGATGAAACGATGATGGTTCAAATCAACCCACCTGTCTTTCACAAGTTCGA TGAAACGTTGCGCGCAATGGTTGTTTACTGAAAAGGATGCCTCTAACCAGCCGTCAGTC TGACTGGATGTCGTGGATCAACTGCCGACCAACATCTTGTCTGCGCTCGTGCCGCGTGA GTAACTGCTGTCGTTCTCACTGAGGGCGAGCAGGGCCTTGGTAATGATGTACTGTTTCA CAGTAACAGTTCTGTTGATCACCGAAAGGTTTGTGCAGGTTGATGTGATGTGACGATGC TGGGTGGCTCCTGCCTAGAAAACGTGTGGTGGTTGAAATGAACGCGTTCCATGTCTGTC GTCTAGTCACTCGTCGAGCTTTGGTCGGCGGAGCCGATCACCGGCCAAGAACATTTGTG ATCTCGATGATATACTTGTGTGCGGCTGCATTGCCGCACAAAAGGTTCATATTGCCATC ATCGTTCCTGCTCACAGATGGTAGTGGTGACGCACTGGCAAATAGACCTGATTTCATTG CGCAGCCAGATTCATCTATGGCTGAC


Comment on Re^2: How do I remove spaces between sequences in a file
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Re^3: How do I remove spaces between sequences in a file
by davido (Archbishop) on Jun 19, 2013 at 22:24 UTC

    Are you trying to say that you want to remove all spaces (including newlines) and then ensure that there's a newline after every 59th character?

    my $input = do { local $/ = undef; <DATA> }; $input =~ s/\s//mg; # Remove all whitespace. $input =~ s/(.{59})/$1\n/g; # Place a \n after every 59th character. print "$input\n"; __DATA__ GAGGGTGCAATCTACAAGAGTGCGGGTTCGCGTTCAGTCCAAGCTGAACATAAACGCAAC GCAAGGCCCCTCGACGCAGATACCGCGCTCAGGAGCATTCGAGAAGCCGAAGAAAATTCG AAGACGAGGACCAGCTACACTGCGGACGGACTTCGGGCATGGAGGGCCAGTTCCAG GTTGGCAAGGAGGAGGTCATCCAAGCATGGTACATGGACGACAGTGAAGAGGACCAGAGG CTTCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTCGACAAACTTTCCG AACTAGGAATATTAAGCTGGCGCCTAAATGCTGATGATTGGGAGAATGATGAGAACCTCA AGAAAATTCGTGAAGCCAGGGGTTACTCTTACATG GACATTTGTGATGTGTGCCCAGAGAAGTTGCCAAATTACGAGGCTAAGATAAAGAATTTC TTTGAAGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCG GCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAAAGAAAGGGG GCATGATCGTTTTGCCTGCAGGAATGTATCATCGCTTTACGTTGGATAGTGACAACTACA TCAAG GCAATGCGTCTATTTGTGGGTGAGCCTGTCTGGACACCATACAATCGTCCGCATGACCAT CTCCCGGCTAG

    ...produces...

    GAGGGTGCAATCTACAAGAGTGCGGGTTCGCGTTCAGTCCAAGCTGAACATAAACGCAA CGCAAGGCCCCTCGACGCAGATACCGCGCTCAGGAGCATTCGAGAAGCCGAAGAAAATT CGAAGACGAGGACCAGCTACACTGCGGACGGACTTCGGGCATGGAGGGCCAGTTCCAGG TTGGCAAGGAGGAGGTCATCCAAGCATGGTACATGGACGACAGTGAAGAGGACCAGAGG CTTCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTCGACAAACTTTCCGAACTAGG AATATTAAGCTGGCGCCTAAATGCTGATGATTGGGAGAATGATGAGAACCTCAAGAAAA TTCGTGAAGCCAGGGGTTACTCTTACATGGACATTTGTGATGTGTGCCCAGAGAAGTTG CCAAATTACGAGGCTAAGATAAAGAATTTCTTTGAAGAACACTTGCATACTGATGAAGA GATACGATATTGCCTTGAGGGTAGCGGCTACTTTGATGTGAGGGACCAAGATGATCAGT GGATCCGTGTAGCGGTAAAGAAAGGGGGCATGATCGTTTTGCCTGCAGGAATGTATCAT CGCTTTACGTTGGATAGTGACAACTACATCAAGGCAATGCGTCTATTTGTGGGTGAGCC TGTCTGGACACCATACAATCGTCCGCATGACCATCTCCCGGCTAG

    Dave

      Hey Dave, that's EXACTLY what I wanted. Thank you so much :D. This is the code I used,

      for($i=1;$i<=scalar(@detail);$i++) { print OUT "$detail[$i-1]"; if($i%59==0) { print OUT "\n"; } }

      but yours looks worked too. thanks :)

        It's an interesting choice that you decided to produce an off-by-one error in the generation of indexes in your loop control, and then remove it by subtracting one from the array indexing. Using a C-style loop you could have done this:

        for( my $i = 0; $i < @detail - 1; $i++ )

        ...or better...

        for( my $i = 0; $i < $#detail; $i++ )

        ...or even...

        foreach my $i ( 0 .. $#detail ) {

        Dave

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