[Buffalo-pm] Where is the extra newline coming from?

G Shankar vieweremail at gmail.com
Mon Oct 30 13:47:55 PST 2006


Hello all,

I've gotten back to hacking with perl again.  I'm confused by the output of
a little program I'm writing.  It builds a query in the form of a url to
PubMed and parses the returning xml for the 'count' field.  Fine so far.
After that, I'm trying to print out results in a particular format; namely,
query term(gene), tab, count, newline.

But the output is coming out query term(gene), newline,tab, count, newline.
O Great Mongers! Where is the extra newline coming from? I've tried to chop
and chomp both variables ($gene and $NumAbstracts) but to no avail.

Any help would be appreciated.
Thanks,
Ganesh

</code>

#!/usr/bin/perl
use strict;
use warnings;
use LWP;


if ($#ARGV != 0) {
    print "usage: getCitNum geneFileName \n";
    exit;
}

my $geneFile = $ARGV[0];
my @gene=();
my $size;
# Creates the URL to search Pubmed
my $baseurl="http://www.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?";
my $request;
my $response;
my $query;

open( FILE, "< $geneFile" ) or die "Can't open $geneFile : $!";

    while( <FILE> ) {
    next if /^(\s)*$/;  # skip blank lines
    ##chomp;              # remove trailing newline characters
    ##print "pushed ".$_." into array";
       push @gene, $_;    # push the data line onto the array
    }

    close FILE;


$size = scalar @gene;
print "Number of genes: $size.\n";


## iterate through the gene array

foreach my $gene (@gene){

##print "going through the array!","\t", $gene;

##$query=join(" ", $gene);
my $url=$baseurl . "db=Pubmed&retmax=1&usehistory=y&term=" . $gene;
$request=LWP::UserAgent->new();
$response=$request->get($url);
my $results= $response->content;
die unless $response->is_success;
$results=~/<Count>(\d+)<\/Count>/;
## $1 is the symbol for the matched content
   my $NumAbstracts=$1;

print $gene,"\t",$NumAbstracts."\n";

}#end foreach gene array

</code>

</output>

$ perl o3.pl test_f
Number of genes: 8.
Actn1
        5
Actn4
        68
Adfp
        74
Aldh2
        656
"Siahbp1, simi"
        0
1810057F21Rik
        0
2310035N23Rik
        0
2310040G17Rik   0

</output>
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