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Home: Perl Programming Help: Intermediate:
HELP! he cant find my word?!

 



andreiareis
Novice

Oct 26, 2012, 11:42 AM

Post #1 of 3 (1419 views)
HELP! he cant find my word?! Can't Post

Hi guys :)

so i have another question for you ... im doing another script ...


Code
 
sub WriteFasta {

my $hash_string = $_[0]; my $outfile = $_[1]; my $dna = ""; my $sp = ""; my $id = "";

open (OUTFILE , ">>$outfile") or die ("Cannot open outfile fasta: $outfile. $!\n");
foreach my $string (keys $hash_string) {
if ($string =~ m/LOCUS (\s+)((\D+)\_(\d+)).+/o){
$id = $2;
}
if ($string =~ m/\tORGANISM(.+)/o) {
print $2;
# $sp = $3;
}

if ($string =~ m/^ORIGIN/) {
print "x";
while ($string =~ (/.+/)) {
my $dna .= $string;

}
print $dna;
$dna =~ s/[\s0-9]//g;
}

print OUTFILE ">" , $id , ' ' , "[", $sp , "]", "\n" , $dna;

}

close OUTFILE;
return;
}


this only one of my subroutine the other its only for read the file and its working ... i check it! and the problem its the first if ... he cant find that match or word ORGANISM ... i checked if is write correctly .. it is ... i dont know ... the for loop in back is working! And file input is from genbank file (teste.gbk)

Thanks :)


(This post was edited by andreiareis on Oct 26, 2012, 6:20 PM)
Attachments: teste.gbk (32.7 KB)


wickedxter
User

Oct 27, 2012, 3:47 AM

Post #2 of 3 (1410 views)
Re: [andreiareis] HELP! he cant find my word?! [In reply to] Can't Post

do u know there is a bio perl module that can shorten ur code and do the dirty wrk for ya as well as phraseing the file in to a perl data structure.... search cpan.org for bio perl or someone will post a link.


rovf
Veteran

Oct 30, 2012, 2:11 AM

Post #3 of 3 (1385 views)
Re: [andreiareis] HELP! he cant find my word?! [In reply to] Can't Post

Did you verify that ORGANISM in your input indeed is preceeded by a tab, and followed by at least one non-newline character?

BTW, you don't need the 'o' flag with this regexp, since no variables are interpolated.

 
 


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