How do I remove spaces between sequences in a file

bingalee has asked for the wisdom of the Perl Monks concerning the following question:

I thought this would be an easy task.Basically I have a file with sequences separated by white spaces and new lines.

Like this

GAGGGTGCAATCTACAAGAGTGCGGGTTCGCGTTCAGTCCAAGCTGAACATAAACGCAAC
GCAAGGCCCCTCGACGCAGATACCGCGCTCAGGAGCATTCGAGAAGCCGAAGAAAATTCG
AAGACGAGGACCAGCTACACTGCGGACGGACTTCGGGCATGGAGGGCCAGTTCCAG

GTTGGCAAGGAGGAGGTCATCCAAGCATGGTACATGGACGACAGTGAAGAGGACCAGAGG
CTTCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTCGACAAACTTTCCG

AACTAGGAATATTAAGCTGGCGCCTAAATGCTGATGATTGGGAGAATGATGAGAACCTCA
AGAAAATTCGTGAAGCCAGGGGTTACTCTTACATG

GACATTTGTGATGTGTGCCCAGAGAAGTTGCCAAATTACGAGGCTAAGATAAAGAATTTC
TTTGAAGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCG

GCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAAAGAAAGGGG
GCATGATCGTTTTGCCTGCAGGAATGTATCATCGCTTTACGTTGGATAGTGACAACTACA
TCAAG

GCAATGCGTCTATTTGTGGGTGAGCCTGTCTGGACACCATACAATCGTCCGCATGACCAT
CTCCCGGCTAG
[download]

when I used split and then joined it I got the entire sequence in one line..I dont want that.

The same thing happened when I did this

foreach $value (values(%seq))
    {
    
    
    $value=~s/\n|\t|\r//g;
    
    }
[download]

Any idea how I can format my sequence file?

Comment on How do I remove spaces between sequences in a file Select or Download Code

Replies are listed 'Best First'.
Re: How do I remove spaces between sequences in a file by pvaldes (Chaplain) on Jun 19, 2013 at 21:56 UTC
See $/ in perldoc perlvar. (And read this ) `$/: The input record separator, newline by default. This influences Perl's idea of what a "line" is.`	[reply] [d/l]
Re: How do I remove spaces between sequences in a file by 2teez (Vicar) on Jun 19, 2013 at 22:10 UTC
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	[reply] [d/l]
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
Re^5: How do I remove spaces between sequences in a file by davido (Cardinal) on Jun 20, 2013 at 15:24 UTC
Re: How do I remove spaces between sequences in a file by rnaeye (Friar) on Jun 20, 2013 at 00:44 UTC
How about something like this: $length determines the width of the column undef $/; my $sequence = <DATA>; $sequence =~ s/\s+//g; my $length = 60; for ( my $pos = 0 ; $pos < length($sequence) ; $pos += $length ) { print substr($sequence, $pos, $length), "\n"; } __DATA__ GAGGGTGCAATCTACAAGAGTGCGGGTTCGCGTTCAGTCCAAGCTGAACATAAACGCAAC GCAAGGCCCCTCGACGCAGATACCGCGCTCAGGAGCATTCGAGAAGCCGAAGAAAATTCG AAGACGAGGACCAGCTACACTGCGGACGGACTTCGGGCATGGAGGGCCAGTTCCAG GTTGGCAAGGAGGAGGTCATCCAAGCATGGTACATGGACGACAGTGAAGAGGACCAGAGG CTTCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTCGACAAACTTTCCG AACTAGGAATATTAAGCTGGCGCCTAAATGCTGATGATTGGGAGAATGATGAGAACCTCA AGAAAATTCGTGAAGCCAGGGGTTACTCTTACATG GACATTTGTGATGTGTGCCCAGAGAAGTTGCCAAATTACGAGGCTAAGATAAAGAATTTC TTTGAAGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCG GCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAAAGAAAGGGG GCATGATCGTTTTGCCTGCAGGAATGTATCATCGCTTTACGTTGGATAGTGACAACTACA TCAAG GCAATGCGTCTATTTGTGGGTGAGCCTGTCTGGACACCATACAATCGTCCGCATGACCAT CTCCCGGCTAG [download]	[reply] [d/l]