Re: how can I print my hash values once?

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Re^2: how can I print my hash values once? by lomSpace (Scribe) on Mar 10, 2011 at 14:29 UTC
ikegami, Thanks that was simple enough. I failed to mention that there are counts for the x and y chr. example: #!/usr/bin/perl -w use strict; #open file open(my $in,"/Users/mgavibrathwaite/Desktop/CCDS.current.txt") or die +" Can't open file: $!"; #open out file open(OUT, ">/Users/mgavibrathwaite/Desktop/genesperchrcnt.txt"); # initialize the hash my %geneids=(); #open the file and push the info from the designated columns into it # remove header my $firstline = <$in>; chomp $firstline; while(<$in>){ chomp; # remove the newline character my @fields = split (/\t/); #extract the columns that we are interested in. # Populate the key value pairs of the hash with $gene and $id $geneids{$fields[2]} = $fields[0]; # initialize an array to store hash values my @chr; push @chr, $fields[0]; #count chromosome number which is the value in the hash $geneids{$fields[0]}++; next if $geneids{$fields[0]} > 1; } foreach my $geneid ( sort { $geneids{$a} <=> $geneids{$b} } keys %geneids ) { print OUT "Chromosome $geneid has $geneids{$geneid} genes\n"; } close($in); close(OUT); =cut Output Chromosome has X genes Chromosome KLHL13 has X genes Chromosome UTY has Y genes Chromosome SPIN2B has X genes Chromosome PIR has X genes Chromosome ADRBK2 has 22 genes Chromosome SLC2A11 has 22 genes Chromosome SELO has 22 genes Chromosome PIK3IP1 has 22 genes Chromosome 21 has 323 genes Chromosome 18 has 358 genes Chromosome 13 has 402 genes Chromosome 22 has 553 genes Chromosome 20 has 724 genes Chromosome 15 has 733 genes Chromosome 14 has 772 genes Chromosome 8 has 827 genes Chromosome 4 has 922 genes Chromosome 9 has 982 genes Chromosome 10 has 1007 genes Chromosome 16 has 1009 genes Chromosome X has 1045 genes Chromosome 5 has 1054 genes Chromosome 7 has 1137 genes Chromosome 12 has 1283 genes Chromosome 6 has 1298 genes Chromosome 3 has 1354 genes Chromosome 17 has 1412 genes Chromosome 11 has 1543 genes Chromosome 2 has 1624 genes Chromosome 19 has 1660 genes Chromosome 1 has 2611 genes [download] I am only interested in output that contains the "Chromosome "num/x/y" has "num" genes. How can I accomplish that? Thanks Ikegami! DeepSpace	[reply] [d/l]
Re^3: how can I print my hash values once? by ikegami (Patriarch) on Mar 10, 2011 at 19:55 UTC
Just a quick note, you seem to be placing some garbage in your hash: `Chromosome has X genes Chromosome KLHL13 has X genes Chromosome UTY has Y genes Chromosome SPIN2B has X genes Chromosome PIR has X genes` [download] The values in the hash should only be counts. Once you fix that bug, you can use `foreach my $geneid ( sort { $geneids{$a} <=> $geneids{$b} } keys %geneids ) { if ($geneid =~ /^(?:[0-9]+\|X\|Y)\z/) { print OUT "Chromosome $geneid has $geneids{$geneid} genes\n"; } }` [download]	[reply] [d/l] [select]
Re^4: how can I print my hash values once? by lomSpace (Scribe) on Mar 11, 2011 at 15:17 UTC
Ikegami, I removed the garbage lines by counting them then I used a perl one liner at the command line to remove the the unwanted garbage lines I would have preferred to fix that bug within the code. DeepSpace	[reply]
Re^5: how can I print my hash values once? by ikegami (Patriarch) on Mar 11, 2011 at 21:50 UTC
Re^3: how can I print my hash values once? by umasuresh (Hermit) on Mar 10, 2011 at 14:59 UTC
Untested: You could add something like `if ($geneid =~ /[0-9]+\|X\|Y/ && $geneids{$geneid} =~/[0-9]+/) { print "..."; }` [download]	[reply] [d/l]