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Re: how to process very large tab limited pileup file

by lima1 (Curate)
on Oct 01, 2010 at 21:13 UTC ( #863014=note: print w/ replies, xml ) Need Help??


in reply to how to process very large tab limited pileup file

What have you tried so far, apart from this awk command? It's quite difficult to understand what you are trying to do...

Show some code and explain where it fails and you will get help. If you don't know that already, you can and should use Text::CSV to parse the file.


Comment on Re: how to process very large tab limited pileup file
Re^2: how to process very large tab limited pileup file
by gudluck (Novice) on Oct 01, 2010 at 21:31 UTC
    My failed attempt:
    my $countref = ($t[8] =~ tr/.,//); my $ratioo = $countref/$t[7] ; if ($countref/$t[7] >0.95) { # print "$t[1]\t$t[2]\t$t[3]: $ratioo \n"; $seq .=$t[2]; } elsif ($countref/$t[7] <=0.95){ $t[8] =~ s/[.,]/$t[2]/g; my $counta = ($t[8] =~ tr/aA//); my $countt = ($t[8] =~ tr/tT//); my $countg = ($t[8] =~ tr/gG//); my $countc = ($t[8] =~ tr/cC//); my ($ratioa, $ratiot, $ratiog, $ratioc, $rat); my @rat = (); $ratioa = $counta/$t[7]; $ratiot = $countt/$t[7]; $ratiog = $countg/$t[7]; $ratioc = $countc/$t[7]; print " $t[1] : A $ratioa T $ratiot G $ratiog C $ratioc "; my $rrat = \@rat; push (@rat, "$ratioa", "$ratiot", "$ratiog", "$ratioc"); my $countnut = 0; my $i; my @ncode; my $ccode; for $i(0..$#rat){ if ( $rrat->[$i] >= 0.05){ $i++; push (@ncode, $i); $countnut ++; $i--; } $ccode = join ("", @ncode); if ($countnut >= 3) { # print "N\n"; $seq .= "N"; } #print " code:$ccode count $countnut\n"; else { my %hash; %hash = {1, 'A', 2, 'T', 3, 'G', 4, 'C', 12, 'W', 21, 'W', 13, 'R', 31, 'R', 14, 'M', 41, 'M', 23, 'K', 32, 'K', 24, 'Y', 42, 'Y', }; print "cc", $hash{$ccode},"\n" ; } } }
      Like the other monks, I don't have a clue what your goals really are. (Try using shorter sentences when explaining things.) I took your code and data as posted, and put them together into a single file like this:
      #!/usr/bin/perl while (<DATA>) { next if (/^#/ or /^\s*$/); chomp; @t = split /\t/; # your code goes here } __DATA__ # your data goes here
      (update: I initially forgot to mention "split")

      I had to edit the data to make it tab-delimited -- maybe the tabs were converted to spaces because of the way you posted it (or the way I downloaded it), but you may need to check and make sure whether your file really has the right number of tabs per line.

      Anyway, your code ran and produced output with no errors. So what's the problem? If you were expecting some different sort of output, you'll need to explain how the actual output differs from the desired output.

      I took the liberty of fixing the indentation in the code -- this really helps for making the code readable, and a good editor should make it easy to use proper indentation (e.g. emacs, vi, ...)

      I also did some refactoring, to remove unnecessary variables, make the output more informative, and use loops where possible.

      I couldn't tell what you were trying to do with your "$seq" variable... that (and the output format) is the only place where my version does something different from yours -- but I'm just guessing about what you really want.

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