Re: Parsing help

Since it's not clear from your sample data where the tabs ought be (and it doesn't matter for demonstration purposes anyway) I've changed the sample code to use spaces instead and changed it to get input from the __DATA__ section:

use strict;
use warnings;

my @partsList;

push @partsList, [split] while <DATA>;

my $geneName = '';

$geneName = $_->[5] ||= $geneName for reverse @partsList;
print join ("\t", @{$_}[0 .. 5]), "\n" for @partsList;

__DATA__
NT_113797    CDS    122829    123323    -  gene=LOC644591  ProteinID=X
+P_932799.1  
NT_113798    CDS    4457    4636    -
NT_077932    CDS    9894    9928    -
NT_077932    CDS    65297    65828    +
NT_077932    CDS    89196    89690    -  gene=LOC653505  ProteinID=BJD
+ND993
[download]

Prints:

NT_113797    CDS    122829    123323    -    gene=LOC644591
NT_113798    CDS    4457    4636    -    gene=LOC653505
NT_077932    CDS    9894    9928    -    gene=LOC653505
NT_077932    CDS    65297    65828    +    gene=LOC653505
NT_077932    CDS    89196    89690    -    gene=LOC653505
[download]

True laziness is hard work

Comment on Re: Parsing help Select or Download Code

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Re^2: Parsing help by citromatik (Curate) on Apr 01, 2009 at 09:08 UTC
Very elegant solution, but may has the drawback of having to load the whole file in memory and traverse the whole list 3 times (1 - reading, 2 - filling the field #5 and 3 - printing). Since the size of this kind of genomic files may be an issue, here is another version a bit more resource-friendly: `use strict; use warnings; my @acc = (); while (<DATA>) { my @recs = split; push @acc, [@recs]; if (my $geneName = $recs[5]) { print join ("\t", @{$_}[0 .. 4], $geneName, "\n") for @acc; @acc = (); } } __DATA__ NT_113797 CDS 122829 123323 - gene=LOC644591 ProteinID=X +P_932799.1 NT_113798 CDS 4457 4636 - NT_077932 CDS 9894 9928 - NT_077932 CDS 65297 65828 + NT_077932 CDS 89196 89690 - gene=LOC653505 ProteinID=BJD +ND993` [download] Outputs the desired result: `NT_113797 CDS 122829 123323 - gene=LOC644591 NT_113798 CDS 4457 4636 - gene=LOC653505 NT_077932 CDS 9894 9928 - gene=LOC653505 NT_077932 CDS 65297 65828 + gene=LOC653505 NT_077932 CDS 89196 89690 - gene=LOC653505 p` [download] Hope this helps citromatik	[reply] [d/l] [select]

Replies are listed 'Best First'.

Re^2: Parsing help
by citromatik (Curate) on Apr 01, 2009 at 09:08 UTC

Very elegant solution, but may has the drawback of having to load the whole file in memory and traverse the whole list 3 times (1 - reading, 2 - filling the field #5 and 3 - printing).

Since the size of this kind of genomic files may be an issue, here is another version a bit more resource-friendly:

use strict;
use warnings;

my @acc = ();
while (<DATA>) {
  my @recs = split;
  push @acc, [@recs];
  if (my $geneName = $recs[5]) {
    print join ("\t", @{$_}[0 .. 4], $geneName, "\n") for @acc;
    @acc = ();
  }
}


__DATA__
NT_113797    CDS    122829    123323    -  gene=LOC644591  ProteinID=X
+P_932799.1  
NT_113798    CDS    4457    4636    -
NT_077932    CDS    9894    9928    -
NT_077932    CDS    65297    65828    +
NT_077932    CDS    89196    89690    -  gene=LOC653505  ProteinID=BJD
+ND993
[download]

Outputs the desired result:

NT_113797       CDS     122829  123323  -       gene=LOC644591
NT_113798       CDS     4457    4636    -       gene=LOC653505
NT_077932       CDS     9894    9928    -       gene=LOC653505
NT_077932       CDS     65297   65828   +       gene=LOC653505
NT_077932       CDS     89196   89690   -       gene=LOC653505
p
[download]

Hope this helps

citromatik

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