in reply to skipping lines when parsing a file

It might be helpful if you told us what patterns you were looking for using English, because your regexes seem a bit strange.

As for solving your basic problem (print until X line, then stop until Y line, then start again), you might consider a state machine; that is, use a global variable that keeps track of whether you're printing or not, and change it inside the loop if the conditions change--and then just print at the end of the loop when the variable tells you you're supposed to be printing.

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Re^2: skipping lines when parsing a file
by lomSpace (Scribe) on Aug 20, 2009 at 13:41 UTC
    Hi ssandv
    I want to remove the text starting at "COMMENT" and just before the line that starts with FEATURES.
    Read more... (5 kB)

    Then print from "FEATURES" until the end of the line.
    LomSpace
[reply]
[d/l]

      So it appears that sections of the file are defined by words in all caps starting in column 0. This actually lends itself pretty well to keeping track of the state (in this case the file section) you're in.

      There are many other ways to do it, but this is an example of what I was suggesting:

      my $state;

while (my $line=<$in>) {
    if ($line=~/^([A-Z]+)/) {
        $state=$1;
    }
    print $line unless $state eq "COMMENT";
}

      [download]
      which outputs: 
      07:37<sandvik@sat1> ~/perl$ ./pmtest.pl
LOCUS       4                     302276 bp    DNA     linear   HTG 31
+-OCT-2008
DEFINITION  Mus musculus chromosome 4 NCBIM37 partial sequence
            138489260..138791535 reannotated via EnsEMBL
ACCESSION   chromosome:NCBIM37:4:138489260:138791535:-1
KEYWORDS    .
SOURCE      house mouse.
  ORGANISM  Mus musculus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Eutele
+ostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia;
            Sciurognathi; Muroidea; Muridae; Murinae; Mus.
FEATURES             Location/Qualifiers
     source          1..302276
                     /db_xref="taxon:10090"
                     /organism="Mus musculus"
     gene            complement(267261..268504)
                     /note="locus_tag=Rnf186"
                     /gene="ENSMUSG00000070661"
                     /note="ring finger protein 186 [Source:MGI;Acc:MG
+I:1914075]

      [download]
[reply]
[d/l]
[select]
        ssandv,
        Ok, this is pretty simple and straight forward. The regex captures the
        capital letter(word) at the beginning of the line and checks for the next
        line that begins with a capital word. When it comes across that line
        it starts printing again?
        When I run it
        #!/usr/bin/perl -w
use strict;
=cut
The script parses the targeting.gb file and creates a new file
that contains removes the comment info.
=cut

open(my $in, "C:/Documents and Settings/mydir/Desktop/TARGETING.gb");
open(my $out, ">C:/Documents and Settings/mydir/Desktop/TARGET.gb");
my $state;
while(my $line =<$in>){    
    if ($line=~/^([A-Z]+)/) {
        $state=$1;        
    }
    print $out $line unless $state eq "COMMENT";
}
close $in;
close $out

        [download]

        The file is not being parsed. The out file is still the same as the in.
        Any idea?
        LomSpace
[reply]
[d/l]
        I am doing this in windows. Could that be a the problem why it is not parsing?
        LomSpace
[reply]

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