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

[G Shankar]

D'Oh!

Never mind!

Thanks,
Ganesh
On 10/30/06, G Shankar <vieweremail at gmail.com> wrote:
>
> 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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