Beefy Boxes and Bandwidth Generously Provided by pair Networks
There's more than one way to do things
 
PerlMonks  

Re: Hello im new to programming i need help

by jethro (Monsignor)
on Feb 10, 2013 at 00:54 UTC ( #1018005=note: print w/ replies, xml ) Need Help??


in reply to Hello im new to programming i need help

You don't say exactly what's wrong with it. I didn't see any obvious bug in the code you commented out and I don't want to spend the time testing your code when you simply could tell us what exactly was wrong with it.

But I can tell you that you won't have a great performance anyway if you reread the one file once for every one of the many files as you seem to be doing.

If that one file fits into your memory, better read it first (and only once) and keep it in an array or hash.

If it doesn't fit you could create a hash on disk (for example with the help of a module like DBM::Deep) with a key made out of the comma-separated concatenation of x,y and z).


Comment on Re: Hello im new to programming i need help
Re^2: Hello im new to programming i need help
by fahadm89 (Initiate) on Feb 10, 2013 at 01:17 UTC

    Here is what i just tried

    #!/usr/bin/perl -w $dir = "/net/klab2/u2/home/fmohammad/GFP2/run1"; opendir (DIR, $dir) or die $!; @one = readdir (DIR); foreach $file (@one) { $initialfile2 = "$file"; open FILETWO, "$initialfile2" or die "cannot open $initialfile +2 for read\n"; while ($line2 = <FILETWO>) { chomp $line2; @one=split(/\s+/, $line2); if ($one[0]=~m/^HETATM/) { if ($one[2]eq "C4") { $xC4=$one[6]; $yC4=$one[7]; $zC4=$one[8]; } if ($one[2]eq "C1") { $xC1=$one[6]; $yC1=$one[7]; $zC1=$one[8]; } if ($one[2]eq "C13") { $xC13=$one[6]; $yC13=$one[7]; $zC13=$one[8]; } } } close FILETWO; $initialfile = "1GFL.pdb"; open FILEONE, "$initialfile" or die "cannot open $initialfile +for read\n"; while ($line = <FILEONE>) { chomp $line; @two=split(/\s+/, $line); if ($two[0]=~m/^ATOM/) { if ($two[1]eq "479") { $xS=$two[6]; $yS=$two[7]; $zS=$two[8]; } if ($two[1]eq "484") { $xY=$two[6]; $yY=$two[7]; $zY=$two[8]; } if ($two[1]eq "496") { $xG=$two[6]; $yG=$two[7]; $zG=$two[8]; } } } close FILEONE; $part1 = ((($xC1 - $xS)**2) + (($yC1 - $yS)**2) + (($zC1 - $zS +)**2)); $part2 = ((($xC4 - $xY)**2) + (($yC4 - $yY)**2) + (($zC4 - $zY +)**2)); $part3 = ((($xC13 - $xG)**2) + (($yC13 - $yG)**2) + (($zC13 - +$zG)**2)); $sum = $part1 + $part2 + $part3; $sum1 = $sum / 3; $rmsd = sqrt ($sum1); print"$rmsd\n"; }

    and here is the error:

    Use of uninitialized value $xC1 in subtraction (-) at getrmsd2.pl line + 80. Use of uninitialized value $yC1 in subtraction (-) at getrmsd2.pl line + 80. Use of uninitialized value $zC1 in subtraction (-) at getrmsd2.pl line + 80. Use of uninitialized value $xC4 in subtraction (-) at getrmsd2.pl line + 81. Use of uninitialized value $yC4 in subtraction (-) at getrmsd2.pl line + 81. Use of uninitialized value $zC4 in subtraction (-) at getrmsd2.pl line + 81. Use of uninitialized value $xC13 in subtraction (-) at getrmsd2.pl lin +e 82. Use of uninitialized value $yC13 in subtraction (-) at getrmsd2.pl lin +e 82. Use of uninitialized value $zC13 in subtraction (-) at getrmsd2.pl lin +e 82. 70.8509364158301 Use of uninitialized value $xC1 in subtraction (-) at getrmsd2.pl line + 80. Use of uninitialized value $yC1 in subtraction (-) at getrmsd2.pl line + 80. Use of uninitialized value $zC1 in subtraction (-) at getrmsd2.pl line + 80. Use of uninitialized value $xC4 in subtraction (-) at getrmsd2.pl line + 81. Use of uninitialized value $yC4 in subtraction (-) at getrmsd2.pl line + 81. Use of uninitialized value $zC4 in subtraction (-) at getrmsd2.pl line + 81. Use of uninitialized value $xC13 in subtraction (-) at getrmsd2.pl lin +e 82. Use of uninitialized value $yC13 in subtraction (-) at getrmsd2.pl lin +e 82. Use of uninitialized value $zC13 in subtraction (-) at getrmsd2.pl lin +e 82. 70.8509364158301 1.68309110468408

      Well, this means that for example the variable $xC1 didn't get set to any value when you use it in line 80. Now lets look at the lines where you want to set the variable. It is in a part that is executed only when two if-clauses are true.

      The warnings indicate that all variables that depend on the outer if-clause "if ($one[0]=~m/^HETATM/)" have the same problem. So this if-clause probably is never true for at least the first two executions of the outermost loop i.e. for the first two files (and it seems from your test output that there is a third file where the if-clause is successfully run through). Because of that the variables are empty and you get the warnings.

      So you have to change your script so that when the information you seek is not in the file the rest of the loop isn't executed anymore.

      For example:

      foreach $file (@one) { my $allfound=0; ... if ($one[2]eq "C4") { $allfound&=1; $xC4=$one[6]; $yC4=$one[7]; $zC4=$one[8]; } if ($one[2]eq "C1") { $allfound&=2; $xC1=$one[6]; $yC1=$one[7]; $zC1=$one[8]; } if ($one[2]eq "C13") { $allfound&=4; $xC13=$one[6]; $yC13=$one[7]; $zC13=$one[8]; } } } close FILETWO; next if ($allfound!=7);

      I'm using the first three bits in the variable $allfound to tell me if all if-clauses where run through at least once for this file.

Log In?
Username:
Password:

What's my password?
Create A New User
Node Status?
node history
Node Type: note [id://1018005]
help
Chatterbox?
and the web crawler heard nothing...

How do I use this? | Other CB clients
Other Users?
Others browsing the Monastery: (15)
As of 2014-08-01 17:12 GMT
Sections?
Information?
Find Nodes?
Leftovers?
    Voting Booth?

    Who would be the most fun to work for?















    Results (33 votes), past polls