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

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
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Comment on Re^2: How do I remove spaces between sequences in a file Download Code

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Re^3: How do I remove spaces between sequences in a file by davido (Cardinal) 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 [download] ...produces... GAGGGTGCAATCTACAAGAGTGCGGGTTCGCGTTCAGTCCAAGCTGAACATAAACGCAA CGCAAGGCCCCTCGACGCAGATACCGCGCTCAGGAGCATTCGAGAAGCCGAAGAAAATT CGAAGACGAGGACCAGCTACACTGCGGACGGACTTCGGGCATGGAGGGCCAGTTCCAGG TTGGCAAGGAGGAGGTCATCCAAGCATGGTACATGGACGACAGTGAAGAGGACCAGAGG CTTCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTCGACAAACTTTCCGAACTAGG AATATTAAGCTGGCGCCTAAATGCTGATGATTGGGAGAATGATGAGAACCTCAAGAAAA TTCGTGAAGCCAGGGGTTACTCTTACATGGACATTTGTGATGTGTGCCCAGAGAAGTTG CCAAATTACGAGGCTAAGATAAAGAATTTCTTTGAAGAACACTTGCATACTGATGAAGA GATACGATATTGCCTTGAGGGTAGCGGCTACTTTGATGTGAGGGACCAAGATGATCAGT GGATCCGTGTAGCGGTAAAGAAAGGGGGCATGATCGTTTTGCCTGCAGGAATGTATCAT CGCTTTACGTTGGATAGTGACAACTACATCAAGGCAATGCGTCTATTTGTGGGTGAGCC TGTCTGGACACCATACAATCGTCCGCATGACCATCTCCCGGCTAG [download] Dave	[reply] [d/l] [select]
Re^4: How do I remove spaces between sequences in a file by bingalee (Acolyte) on Jun 20, 2013 at 15:19 UTC
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"; } }` [download] but yours looks worked too. thanks :)	[reply] [d/l]
Re^5: How do I remove spaces between sequences in a file by davido (Cardinal) on Jun 20, 2013 at 15:24 UTC
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++ )` [download] ...or better... `for( my $i = 0; $i < $#detail; $i++ )` [download] ...or even... `foreach my $i ( 0 .. $#detail ) {` [download] Dave	[reply] [d/l] [select]

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