Hi all,

I am trying to separe my data DNA because it has a lot of name.
It has about 43 litte file in one data.
I made the small script to solve one name of data but I did not succes. The result was not enough. My script is below:

#!/usr/bin/perl;
use strict; 
use warnings; 
my $filename3 = 'file_out.txt';
my $filename = 'dna.txt';

open my $fh, '<', $filename or die "Failed to open $filename: $!";
open my $fho, '>', $filename3 or die "Failed to open $filename3: $!";#Open file for output
while (my $rec = <$fh>){
    $rec=~ s/\s//g;
    chomp($rec);
    #my $rec1 = join ('\n',$rec);
   
   my $line = $rec;
if ($line =~'AGQQ01000002.1'){
  
    print $fho "$rec  \n";
}
}
close $fh;

Result :

>gi|354512096|gb|AGQQ01000002.1|CorynebacteriumglutamicumATCC14067Contig02,wholegenomeshotgunsequenceTTAGCCAGGAAACGCTTCGCTGCCGCGACGTTGCGCTTCGGAGAGAGGTAAAAGTCCAGG

I hope I can separe with all the data of "AGQQ01000002.1" expect the name "]>gi|354512096|gb|AGQQ01000002.1|CorynebacteriumglutamicumATCC14067Contig02,wholegenomeshotgunsequence "
I mean:

GTATGCCCACCAGCGGTAATAGCCCGATAGAGGTAGCACCACCTGCCGCCGACCCGGATG  
TAGGTCTCATCCACCCGCCAGGACCGGGCCTGCCAGTCAGGTACCTGCCGGTACCACCGA  
GTGTGCTTGTCCAGCTCAGGGGCGTATTTCTGGACCCAGCGGTGAGAATCGTGGTGTGAT  
CAACTGGCACGCCGCGGCTGAAGTCATCATTTCCTCCAGATCTTAGGTCAGCTCACCCCG  
TAGCGGCAGTGACCTGCGCACTGCCCACAAAATGATGTCACGGGGGAAATGACGACCGGA  
GAAGATACCCATGGCTGTGATTATTTCACGTCGATCTTCCTACTGCCCCAACTTTGCAAC

Could you show me how to solve that problem. Thank you very much!

Attachments
>gi|354511893|gb|AGQQ01000003.1|CorynebacteriumglutamicumATCC14067Contig03,wholegenomeshotgunsequence  
TTCAGGGTCGGGGTCATCGTCGCCGGAGTCGTCATCACCCGGTCCGCCGTCAGGACCGGC  
GTCGGGATTGCCACCATTACCGCCGTTGCCAGATCCAGAGTTTGGCTTCGGTATGGGGTA  
GAGGGAGTGGGCGAGATTGATGCGGTGGTGGGCGCGTGCTTTGGATAGGCCGAAGGTGGT  
GGTGAGGTAGTCGATGAGGTGGGTGGAGCCAATGGTGTGGGCGGCGTTGGTGCGTTCGGC  
GAGGGCTGTGGTTTGGGCGGCGATGGTGGCGTGGTGGTTGATGGTGTGTTCTAGGGCGAT  
GAGGTCGGGCTCAATGGCCTTGTATTGGTCTGGGGTGACACCATGGTCAAGCATGCTGGC  
CAAATGGTTGTCGATGGCGTTGAGTGCTGTGGTGAGTGCTTGGACGTGTGTGGTGATGCT  
CATGGTGTCTTCCCCCTTTCCCAGTTCCCCGTGCTAATACCAACCACCATACCCGCTCAC  
ACTTTCGAACGCAAGGGTGATATTCAAACACTTATTCAAAATCTGATCGCACTAGAGTTA  
CGCCCAATCCTTCCCTAAATCTCTCCAATCTTCCAGGTCAAAGAGAGTTATCCACAGGTA  
ACGCGTACCTCAAAATAGTTATCCACAACGGCAGGCACCTCAAAGCGCCACTCTCCCCCA  
TTCCCTCCTAGCCTATGGGTGTCTCACACTCTAAATTTAAGGAGAAATCATGAAACCTGG  
CCATTTCTACTGCGAACACTGCGGCGTTGCACACTTCGGAGCACCTGCACTTAACCTCAA  
GCTCCCCGACCCCGTTATAGAGGCTCAATCGCGCGGACATCGAGTTTCTACAGGATCATC  
GGTGTGCCAAATTTTGAACCCGAAACCGAAGCGTCATTTCATCAAATCAAACATCGAAAT  
CCCCATCGATGGAGGTAAGAAGAAGCTCGATTATGGAGGTTGGGTTGAGGTGGAACACTC  
TGACCTCATGACATATCTGAATTATCGCAATGTGATGAAAAAGGTTCGCATCCCAGGATT  
CTTGGCAAGCAAATTCCCAGGCCTCGAAGACTCTTATGGGACGCCAGTTCTTTTAACTGT  
GAAGCATGAAGACTATTACCCGCATTTCCAGCCACTCGAAGAATCCTCGAGCATGTACCA  
AGACTTCCACAAAGGAATTTCCTCGAGGGAAGCTGACCTTCGAATCAATAGTTGGCTACT  
AGTGACTCATGAGTACATGCGCTAGTTACAGGATCGAAGTAATGCCCATTATGCACAGAA  
CCAGTGACACGAGATAGCCCGACCATTTGGTGACTCTCTCTTTATTTTGACCAATCAGTT  
CAAACAACCTACCAACAGGACTTTCAGGGTATTTGCGAACCATTCCAACGAGAATTGCCA  
CGATAATCGGCAGACTCAGAGCCAAGGTCGCATAGACCACAAGTCCGCCATACCTAATTT  
CTGGACTGAAATTGCCAACGCTCAAATATCCAAGCCCTGCATAAAAAGGTACAGATGTCG  
CTGACTGAACGATTCCAAGGATCAATCCGGCTCCAACAGTTTTCCAACTAGGAGTTTTTA  
CTGGCGCTAGGAATCCATCAAGCTTTCTAGTGCTGTCGGTTTTAGAAACCAGTGTCGCAA  
CGAAGGAAACGATGCCAGTTACAAGAAGGATGACTCCGAACCAGATTGAATCCAAAAAGC  
CCTGAACTAAATCCTCTAGTCCATCAAAAACGAGCATCACCAAAATACTGAGGAGGAAAA  
CGCCAAGCCAATCGCCGGCAACCAGTAGCGTGGCGATTGGCCCATATTTACCCTTGCGAG  
GCAGCAAAGCAGCAATAGCGACGATTATGCCAATGAGCAGGACATTTACGGAGTCCATTA  
ATGCAAAACTCACGGCATGAAACAATTGGGACACCTTTGATCGACAGCAGTTTTCAACTC  
AAGCAGGGACATAAAAGTCGGGTTGCCTAGATGTTTCGACATTACCCTTGCTTAAAGAAT  
CGACCACAATCCCCGATTGCGTTACTGCGCCGTCAAAACAAACACCGTCAAAACAAGTTA  
CTGCTTAATTGGCGCCTCGGTGACGATAATTCCGTCAGAGTCCGCGTAGACGTAATGGCC  
AGGAATGAAGTCAATGCCACCAATCGATACCACTACGTCTCGTTCGCCGGAACCAGTTTT  
AGTGGATTTCCGCGGGTTGGTTCCAAGGGCTTTACAACCAAAGGTCATGGTGCCGATGAC  
TGCGGAGTCTCGAATTGCTCCGTTGACAATTACTCCGGACCAACCATGATCTTTTCCAAG  
TCCTGCAATGATGTCGCCAACTAGCGCGGTGTGCACGGATGCGTCGCCGTCGATAACCAG  
CACTCCCCCAGGATTATCCTCGCTCAGGATGGATTTCAGGAGGGCGTTGTCTTGGAAGCA  
TTTCACGGTGGTTATTGTTCCGTGGAATTCTGTGGCACCTCCAAGGTTTTGAAACTGAGT  
GTCGCATGATTGCGCGTTGTCGCCGATGATGTCTACGAGGTCTGCGGTGGCAATGAATTC  
TGGAGCACTTTGAGTCATGCCCACAGCATAGAACTAAAACAGTATGCTTGTCCTGCTAAA  
TGTGAGTTTTTAAGAGATTCATCCCACATAATTATGAAAAAACCAGATTGCCCACAAATT  
AGTCTTCGAACTTTAATCAACACCACACCCAAAGCTAAACTTGCACTCGTTGTGCAAAAT  
TACATTCAGGCTGAAAGATTCCTAAAGGGACTCCGTCCGAATAATTGGAAAGCCCAGAAG  
AACAGTCAACTCCTAGATTAAAGGATAATCGTGGCGAAATTCCTGTATAAGTTAGGCTCC  
ACGGCCTATCAAAAGAAATGGCCGTTTCTTGCGGTCTGGCTCGTGATTCTCATAGGTATC  
ACGGCGCTGGCGGGGCTGTATGCCAAGCCAACGTCGAGTAGCTTCTCTATCCCTGGTCTT  
GATTCTGTCACGACCATGGAGAAGATGCAGGAGCGTTTCCCTGGTTCGGATGATGCAACA  
TCGGCTCCCACTGGTTCTGTCGTCATTCAGGCACCGGAAGGCAAGACCCTCACTGATCCT  
GAGGTTGAGGCTGAAATAAACCAGATGCTTGATGAGGTTCGGGCGACTGGTGTGCTGAAG  
GATGCTGATTCCGTTGTGGATCCTGTGTTGGCTGCGCAGGGTGTGGCTGCTCAGATGACC  
CCAGCCCTGGAGGCTCAGGGTGTACCAGCGGAGAAGATCGCCGCAGATATTGAGTCGATT  
AGTCCACTGAGTGCAGATGAGACTACCGGCATCATCTCGATGACTTTTGATGCAGATTCC  
GCCATGGATGTATCCGCAGAGGATCGTGAGAAGGTCACCAATATTCTTAATGAATACGAT  
GACGGCGATCTGACTGTTGTCTACAACGGCAACGTGTTTGGCGCAGCTGCAACCAGCTTG  
GACATGACCTCTGAGCTCATCGGCCTGCTGGTGGCTGCGGTCGTTCTTATCGTGACCTTC  
GGTTCGTTCATCGCTGCCGGTATGCCGCTGATCTCTGCAATCATTGGTGTCGGAATCGGC  
ATCATGGGCATTCAGTTAGCCACGGCGTTTACTGATTCGGTCAATGACATGACTCCTACC  
CTGGCGTCGATGATTGGTCTGGCTGTCGGTATCGACTACGCGCTGTTCATCGTGTCCCGT  
TTCCGCAATGAGTTGATTTCTCAGACTGGCGCTAATGATCTCGAGCCAAAGGAATTGGCT  
GAGCGTCTGCGCACCATGCCGTTGGCTGCTCGTGCGCATGCGATGGGAATGGCTGTGGGC  
ACTGCGGGTTCTGCGGTTGTATTCGCGGGTACCACGGTGCTGATCGCTCTGGTTGCTCTG  
TCGATCATTAATATTCCATTCCTAACCGTGATGGCCATTGCTGCTGCAATCACCGTTGCC  
ATCGCAGTTCTGGTTGCTCTGTCCTTCCTCCCAGCTCTGCTTGGCCTGCTTGGCACTCGC  
ATCTTCGCAGCACGCGTGCCTGGACCTAAGGTTCCGGATCCTGAGGACGAGAAGCCAACG  
ATGGGTCTGAAGTGGGTCCGCCTTGTGCGCAAGATGCCGGTGGCTTACCTGCTGGTTGGC  
GTCGTTTTGCTTGGTGCAATCGCAATTCCTGCGACCAATATGCGCCTGGCCATGCCGACT  
GATGGCACCTCCACGCTGGGCACCGCGCCGCGCACGGCGTATGACATGACGGCAGATGCG  
TTCGGCCCGGGCCGCAACGCGCCCATGATTGCGCTTATCGACGCAACCGACGTCCCTGAG  
GAAGAACGCCCATTGGTGTTTGGACAGGCGGTGGAGCAATTCTTGAACACTGATGGTGTG  
AAGAATGCTCAGATCACTCAGACCACGGAGAATTTCGATACCGCGCAGATCCTGATTACC  
CCAGAATTTGATGCGATCGATGAGCGCACCTCTGAAACTCTCGCAACTCTTCGTGCAGAT  
GCTGAGACCTTCGCTGATGACACCGGCGCGACGTATGGCATTACTGGCGTCACCCCAATT  
TACGATGACATCTCTGCTCGCCTCGGCGACGTCCTGGTTCCTTACGTTCTGATCGTTTTG  
GTTCTAGCGTTCCTCGTGCTGTTGCTCGTGTTCCGGTCCATTTGGGTTCCATTGATCGCG  
GCTCTGGGCTTTGGCTTGTCAGTTCTGGCTACCTTTGGTGCTACCGTGGCGATCTTCCAA  
GAAGGTGCTTTCGGCATCATCGACGATCCTCAGCCACTGCTGTCCTTCTTGCCGATCATG  
CTCATCGGCCTGGTATTTGGTCTGGCCATGGATTACCAGATCTTCCTCGTTACTCGTATG  
CGTGAGGGCTTCACCAAGGGCAAGACTGCGGGCAACGCAACGTCGAATGGTTTCAAGCAC  
GGTGCCCGCGTGGTCACTGCTGCGGCGCTGATCATGGTGTCTGTGTTCGCGGCATTCATA  
GCGCAGGACATGGCGTTTATTAAGACCATGGGCTTTGCTCTGGCCGTTGCTGTGTTCTTC  
GATGCCTTCGTTGTTCGCATGATGATTATCCCTGCAACAATGTTCCTGCTTGATGACAAG  
GCTTGGTGGCTACCTAAGTGGTTGGATAAGATTCTTCCCAACGTTGATGTTGAAGGTGAG  
GGTCTTAGTGAACTACATGAGGCTCGCACCGAGGAACTGAAGGAAAATGTAGGTGTCGGG  
GCTTAGAGAAACAAAAAAGGCTGCTACGCGGACAGCATTGTCACGTGCTGCTGCGGAGAT  
CGCCTTGATGGAAGGCCCTGAGGCGTTCACGGTTGCGGCCATTGCAGCTGCAGCCGGGGT  
CTCCCCCCGGACTTTTCATAACTACTTCCCTTCTCGGGAAGACGCATTGGTGCAATTTGT  
GGTCATTCGCGTTCAGGAACTCACGGATCAGCTATACGAGTTTCCTACAAGCGTGCCCCC  
ACGAGATGCCATTGAACAATTGGTGATCAACCAATTGCGGGATGGCGATGACGCTATGGA  
TTCTTTCAGCGCAATGTTTCGAATCGGTGAGATCCTTGAAAATCTTGACCCCATCAAGTG  
TGTTATCGATAAGGAGCGACTCATTGCTCCGTTGCTTGAGTTCATGGTTGAACGTGACAA  
AGACCTTGACAAGTTCGATGCGGCAACTCTGATCCATTTGCATGCAGCGGCAATTGCAAC  
CTCGCTGCATACGTTTTACCAAGCTCCCGAGCCCCGGGACATAGAAGATGGAGTCGCATT  
GATCCGTCGGGCATGCGCCTGGATTAAGAAATAAAAATTGTGGTGTGTGAACCTCCCCCA  
AACCTCCCCCAAGATTCACACACCACAATTTTTTATTCGTAGAAGCTTCCTGTTGATTGG  
CTTGATCCGGAGCTTCCTGCAAGGAACTCTCGGACGCTGCTGCCTTCACTGGATCCAGAG  
CTTCCCGCTACGCTGCCGATAACGGTGCCAAGACTCACATCAGACGACAGCTCAGAAGAA  
GACTCACTAGAGGACACACCGTTAGGGTTATAGATCGGGATCGGACCACCATCAAGCCCG  
AAGCCCTGCATCATCAACGGGAAGAAGCGGTGGAGCGCTTCGTTCCAGTAATCCCAGGCG  
TGGGTTCCGGTTGGTCGGAAATCATAGTTAATGTTGTCAATGCCCATTTGATCAGTCGCA  
GCCTTAAGATTATGGGTGCAGGTGTTGGACATAGC  
>gi|354512096|gb|AGQQ01000002.1|CorynebacteriumglutamicumATCC14067Contig02,wholegenomeshotgunsequence
TTAGCCAGGAAACGCTTCGCTGCCGCGACGTTGCGCTTCGGAGAGAGGTAAAAGTCCAGG  
GTATGCCCACCAGCGGTAATAGCCCGATAGAGGTAGCACCACCTGCCGCCGACCCGGATG  
TAGGTCTCATCCACCCGCCAGGACCGGGCCTGCCAGTCAGGTACCTGCCGGTACCACCGA  
GTGTGCTTGTCCAGCTCAGGGGCGTATTTCTGGACCCAGCGGTGAGAATCGTGGTGTGAT  
CAACTGGCACGCCGCGGCTGAAGTCATCATTTCCTCCAGATCTTAGGTCAGCTCACCCCG  
TAGCGGCAGTGACCTGCGCACTGCCCACAAAATGATGTCACGGGGGAAATGACGACCGGA  
GAAGATACCCATGGCTGTGATTATTTCACGTCGATCTTCCTACTGCCCCAACTTTGCAAC  
AGCACCGTTTTGAGTTTATTGGCAAGAGTTAAGACTGGGGTGTTTTCACCTGAGCATTGG  
GGCGGGGCAGGGCACGCCCCGCCGGGACTACCTCGATACCGCCGGGGATGACCGGAGCTC  
GTGTCGTGGCTTCTGGCCGCGGTGCGTGTGAGTGGTGGTCGATCAGGCTGCGGTCATATC  
AATCACGATTTTGCCGGTGGCGTGGCCGTCTTCAACCACGGCTAGTGCCTCCCCGGCCCG  
ATCGAGGGGATACCGGCTGGTGACCTGCGGGTCAACCAGGCCGTATTTGATCACATCGGT  
GATCTTCGCCATCGCCTCCGGGGTTCGCTCCAGGCCCACTCCACCGAGTTCTGCGGCGGT  
AGCCGGATCAACGGCAGAGATGAGATGGGAGGGGTCGGTGACCAGTCCGGCGACCTCGCG  
CAGTGCCTGCCCGCCGACCAGGTCGACGATGAGGTCGACTCCGTCCGGGGCTAGGTGGCG  
GACCCGGCCGGCCACAGCATCCCCCGACGGGATGAAGGTGGCACCGGTGGCTTCGACGAC  
CTGGCGTTTAGCTTCACTGGCCACTCCGAGCACGGTGAACTTATGGACCCGACCGATCTG  
GGCGGCCATCAAGCCGACACCCCCACCGGCCCCGACGATCAGCAGAACCTGGCCGGGATC  
GAGCTCGATCTGGTGGGTGACATCATAAGCGGTCGCTGCGGCCACCGGGATGGTGGCGGC  
ATCAGTGAAGGAAATCTCCTCCGGCTTGACCACCGCGTCGACCGCGGCGACCAGGGTGTC  
TTCAGCGAAGCCGCCGTAACCCGGGACGACTGGGCCCAGGATCTCCTGGCCAACGGTGAA  
CTCCTCGACTCCGGCTCCCACGGCGGTGATCACGCCGGCGACTTCCTGGCCCATCGGGGC  
TGGCAGCGCCAGATCGGTGCCCAGGGCGCCGGAGCGGATCTTCCAGTCGACGGGGTTGAC  
CCCGGCGGCACGAACGTTCACCGCGAGTTCTCCCGGTCCTGGTTGCGGGGCTGGACGGTC  
AATCAACTTCTGAGTGTCAGGCCTATCGAAGATGTGGAACGCATATACCTTGGACATGGT  
TGTTCTCTTCTTTCTGTGAGTGGTTCTCGTAGGTGTCAGAGCCGTGATGGTGATCAGCTC  
TCCGGCGGGGTGTCTCGCCCCTCGGCTTCAGCTGCCTCCGCCTCAGTGCGGGTGGCGTGG  
GCGCTATCGACGGCGTGCTCGGGCGGGGCGTAGATCGTATAAAGCACCAGCGGTTCATCC  
CCGGTGTTGCGGAAGTTATGTCGGGCTCCAGCCGACACGGCGCACTGGTCACCGGGTCCG  
ATGAGATGGGTTTCGCCGTCGAGATCGGCCTTACCGGTGCCGGCGACAAACGTCAGGATT  
TGGTCGGTGGTGTCGTGGACTTCCTCGCCGATCTCTTCTCCGGGTGGAATGGTCATCACG  
ACGGTCTGGGCATGGTGACCGGTCCACAGCACCCGGCGGAAGTCCGGGTTGTCTGTGGCG  
ATATCGGCGATGGTGAAGTGCTTAATGTTGTCACCGATGTGGAAGTTTTTCGATGAAACC  
ATGGTGTCCTCTTTCTTTCCTGCGGCACTGCCGCTGGTGGGGTGGCGGGTGATGGTTGGT  
TATGTGGTGGCGGTCTGGTGGGTATCGGCGGCGGCCTTCTTGGCCGCGGCCTGCGGTTCC
#!/usr/bin/perl;
use strict; 
use warnings; 
my $filename3 = 'file_out.txt';
my $filename = 'dna.txt';

open my $fh, '<', $filename or die "Failed to open $filename: $!";
open my $fho, '>', $filename3 or die "Failed to open $filename3: $!";#Open file for output

my $name;
while (my $rec = <$fh>){
    $rec=~ s/\s//g;
    chomp($rec);
    #If reading first line of data (starts with '>') for a name, save the name
    if ($rec =~ m/^>/){
        my @flds = split(/\|/, $rec);#split first line of group to get name
        $name = $flds[3];
        next; #Read next line (you don't want to print first line of group)
    }
    
    if ($name eq 'AGQQ01000002.1'){
        print $fho "$rec  \n";
    }
}
close $fh;

See if this does what you want.

#!/usr/bin/perl
use strict;
use warnings;
if ( !defined($ARGV[0])){
  print "\nUsage: $0 <name>\n";
  print "  Example:  $0 AGQQ01000003.1\n\n";
  exit;
}
my ($filename3,$filename,$printIt) = ('file_out.txt','dna.txt',0);
my @columns;
my $pat = quotemeta($ARGV[0]);
open my $fh, '<', $filename or die "Failed to open $filename: $!";
open my $fho, '>', $filename3 or die "Failed to open $filename3: $!";#Open file for output
while (my $rec = <$fh>){
 chomp($rec);
 @columns = split(/\|/,$rec);
 if ( $#columns >= 3 ) {
    if ( $columns[3] =~ /$pat/ ){
       #print $fho "$columns[3]: ";
       $printIt = 1;
    }
    else {
       $printIt = 0;
    }
 }
 print $fho "$rec\n" if ( $printIt && $#columns == 0 ); 
} 
close $fh;
Comments
Looks good

See if this does what you want.

#!/usr/bin/perl
use strict;
use warnings;
if ( !defined($ARGV[0])){
  print "\nUsage: $0 <name>\n";
  print "  Example:  $0 AGQQ01000003.1\n\n";
  exit;
}
my ($filename3,$filename,$printIt) = ('file_out.txt','dna.txt',0);
my @columns;
my $pat = quotemeta($ARGV[0]);
open my $fh, '<', $filename or die "Failed to open $filename: $!";
open my $fho, '>', $filename3 or die "Failed to open $filename3: $!";#Open file for output
while (my $rec = <$fh>){
 chomp($rec);
 @columns = split(/\|/,$rec);
 if ( $#columns >= 3 ) {
    if ( $columns[3] =~ /$pat/ ){
       #print $fho "$columns[3]: ";
       $printIt = 1;
    }
    else {
       $printIt = 0;
    }
 }
 print $fho "$rec\n" if ( $printIt && $#columns == 0 ); 
} 
close $fh;

That way looks good too, histrungalot. One thing: I notice you left out the $rec=~ s/\s//g; statement the original script had. That may or may not be wanted depending on whether you want to keep the Windows-style CRLF newlines or if you want to replace them with those of the current platform (in my case, linux).

I was 2 minutes to slow. True, I would not have remove the space at the end.

Edited 4 Years Ago by histrungalot: n/a

I was 2 minutes to slow. True, I would not have remove the space at the end.

It's not an ordinary space character at the end of each line. It's a carriage return character that causes my text editor to warn me "This line does not end with the expected EOL: 'LF'..." (see attached screenshot.) The input file has Windows format newlines (CRLF) but linux expects linux-type newlines so perl's chomp command removes only the LF. When the script prints it re-adds LF to every line. If all the lines have carriage return characters except for the last then the output file has CRLF newline characters on all lines but the last, which will have only LF.

That's not a biggie normally, unless the output file will be processed as input by another script that gets confused by mixed line endings.

Edited 4 Years Ago by d5e5: n/a

Attachments Screenshot.png 129.43 KB

Thanks a lot d5e5 and histrungalot ! It works beautifully!

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