Shawn Corey wrote:
Andrej Kastrin wrote:
Hello dears,
I have a file in row data format, which stores different terms (e.g.
genes) and look like:
------------
ABH
HD
HDD
etc.
------------
Then I have second file which looks like:
--------------------------------------------------------------
ID- 001 #ID number
TI- analysis of HD patients. #title of article
AB- The present article deals with HD patients. #abstract
ID- 002 #ID number
TI- In reply to analysis of HD patients. #title of article
AB- The present article deals with HDD patients. #abstract
--------------------------------------------------------------
etc., where the separator between records is blank line.
Now I have to extract those ID, TI and AB fields from the second
file, which involves any term in the first file.
Colleague from BioPerl mailing list helps me with the following code:
#!/usr/bin/perl
use strict;
use warnings;
my $file_terms = shift;
my $file_medline = shift;
open (TERM, $file_term) or die "Can't open TERM"; #open list of terms
open (MEDL, $file_medline) or die "Can't open MEDL"; #open records file
my @terms = <TERM>;
while (my ($pmid, $ti, $ab) = split <MEDL>) {
for my $term (@terms) {
if (/$term/ for ($pmid, $ti, $ab)) {
print "$pmid\t$ti\t$ab";
}
}
}
I'm little confused now, while above example doesn't work and I don't
know why (compilation error in 15th and 19th line).
I'm still learning...
So aren't the folks at BioPerl.
Question: Do you want to extract just the fields or the full record if
a field contain terms from file 1? The following will print the entire
record.
#!/usr/bin/perl
use strict;
use warnings;
my $file_terms = shift;
my $file_medline = shift;
open (TERM, $file_terms) or die "Can't open $file_terms: $!"; #open
list of terms
open (MEDL, $file_medline) or die "Can't open $file_medline: $!";
#open records file
chomp( my @terms = <TERM> );
{
local $/ = "\n\n";
while( my $record = <MEDL> ){
print $record if grep { $record =~ /\b$_\b/ } @terms;
}
}
__END__
Answer to your question: just the fields;
and additional question: how does Perl know where are the input files
(while we only wrote: open (TERM, $file_terms) or die "Can't open...)?
Cheers, Adnrej
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