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Help with program for proteins

by jemswira (Novice)
on Jan 05, 2012 at 01:39 UTC ( #946311=perlquestion: print w/ replies, xml ) Need Help??
jemswira has asked for the wisdom of the Perl Monks concerning the following question:

So I recently posted up this code on perlmonks asking for help, and got it to work properly(THANKS)

$/="\/\/"; our @acnumbers=qw(P0A252 Q9AT80 Q0HKB6); our $acnumbers; foreach $acnumbers(@acnumbers){ my $unit; foreach $unit(<PFAMDB>){ my @units= split /#/,$unit; my @pfx=grep(/=GF AC/,@units); our $units; foreach $units(@units){ if ($units=~/.*AC $acnumbers/){ push (@list, @pfx); }else{next} } } print "$acnumbers is in:"; print @list; undef @list; }

So what it did was to take this data

# STOCKHOLM 1.0

#=GF ID 1-cysPrx_C

#=GF AC PF10417.4

#=GF DE C-terminal domain of 1-Cys peroxiredoxin

...

#=GS D8BPP0_ECOLX/154-186 AC D8BPP0.1

#=GS D6I5T0_ECOLX/154-186 AC D6I5T0.1

...

//

...

find the PFxxxx number and whether the AC xxxxxx number was in it.

There's another file, which has many lines of:

>tr|A0A171|A0A171_PYRHR Glutamate synthase small subunit-like protein 1 OS=Pyrococcus horikoshii GN=gltY PE=4 SV=1

and i need to get the A0A171, and A0A171_PYRHR Glutamate synthase small subunit-like protein 1 out also, then run the first code. So i got this:

foreach (<DATABASE>){push (@uniprot,$_);} my $i; my $name; foreach $uniprot(@uniprot){ our $acc; my @splitted=split /\||=/,$uniprot; foreach $i(@splitted){ if ($i=~/\b\w{6}\b/ and $i !~/\_/){ $acc=$i; } elsif ($i=~ /.+(?= OS)/){ $name=$i; } else {next;} my $unit; $/="\/\/"; open PFAMDB, 'C:\Users\Jems\Desktop\Perl\PFAM.txt' or die $!; foreach $unit(<PFAMDB>){ my @units= split /#/,$unit; my @pfx=grep(/=GF AC/,@units); our $units; foreach $units(@units){ if ($units=~/.*AC $acc/){ push (@list, @pfx); }else{next} } } print "$acc, also called $name, is in:" print @list; undef @list; }}

however it no longer seems to get @list out. @pfx is still correct when i print tested, but it no longer pushes to @list. (I THINK)

so is it that i am doing anything wrong? also, how would i remove the OS at the back of $name, and the #=GF AC and everything after the fullstop in @pfx? Thanks in advance!

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Re: Help with program for proteins
by RichardK (Priest) on Jan 05, 2012 at 11:46 UTC

    Are you using strict and warnings?

    Where does $acc come from in

    if ($units =~ /.*AC $acc/)
      foreach $i(@splitted){ if ($i=~/\b\w{6}\b/ and $i !~/\_/){ $acc=$i;

      If the accession number in the first file matched one in a line of the second one, then I'd push @pfx into @list. at least that was the plan

Re: Help with program for proteins
by umasuresh (Hermit) on Jan 05, 2012 at 13:46 UTC

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