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

I don't want this?
So how do you want it?
Like this?

while(<DATA>){
  chomp;
  print $_ unless /^\s*$/;
}


__DATA__
GAGGGTGCAATCTACAAGAGTGCGGGTTCGCGTTCAGTCCAAGCTGAACATAAACGCAAC
GCAAGGCCCCTCGACGCAGATACCGCGCTCAGGAGCATTCGAGAAGCCGAAGAAAATTCG
AAGACGAGGACCAGCTACACTGCGGACGGACTTCGGGCATGGAGGGCCAGTTCCAG

GTTGGCAAGGAGGAGGTCATCCAAGCATGGTACATGGACGACAGTGAAGAGGACCAGAGG
CTTCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTCGACAAACTTTCCG

AACTAGGAATATTAAGCTGGCGCCTAAATGCTGATGATTGGGAGAATGATGAGAACCTCA
AGAAAATTCGTGAAGCCAGGGGTTACTCTTACATG

GACATTTGTGATGTGTGCCCAGAGAAGTTGCCAAATTACGAGGCTAAGATAAAGAATTTC
TTTGAAGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCG

GCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAAAGAAAGGGG
GCATGATCGTTTTGCCTGCAGGAATGTATCATCGCTTTACGTTGGATAGTGACAACTACA
TCAAG

GCAATGCGTCTATTTGTGGGTGAGCCTGTCTGGACACCATACAATCGTCCGCATGACCAT
CTCCCGGCTAG
[download]

Update: I think davido have what you wanted in Re^3: How do I remove spaces between sequences in a file

If you tell me, I'll forget.
If you show me, I'll remember.
if you involve me, I'll understand.
--- Author unknown to me

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

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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
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 [download]	[reply] [d/l]
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