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Re^3: Iso electric point calculation using perl

by Anonymous Monk
on Jul 22, 2013 at 05:41 UTC ( #1045588=note: print w/ replies, xml ) Need Help??


in reply to Re^2: Iso electric point calculation using perl
in thread Iso electric point calculation using perl

repost what you have after corrections.What you posted the first time makes no sense.


Comment on Re^3: Iso electric point calculation using perl
Re^4: Iso electric point calculation using perl
by yuvraj_ghaly (Sexton) on Jul 22, 2013 at 05:49 UTC
    may be this code help you to know what I'm trying to do</p> <code> #! /usr/bin/perl -w use strict; $ph=0; $qn1=''; $qn2=''; $qn3='';$qn4='';$qn5=''; $qp1='';$qp2='';$qp3='';$qp4=''; $nq=''; open (S, "$ARGV[0]") || die "cannot open FASTA file to read: $!"; my %s;# a hash of arrays, to hold each line of sequence my %seq; #a hash to hold the AA sequences. my $key; while (<S>){ #Read the FASTA file. chomp; if (/>/){ s/>//; $key= $_; }else{ push (@{$s{$key}}, $_); } } foreach my $a (keys %s){ my $s= join("", @{$s{$a}}); $seq{$a}=$s; #print("$a\t$s\n"); } my @aa= qw(Length); #my @aa= qw(A R N D C Q E G H I L K M F P S T W Y V); my $aa= join("\t", @aa); print ("Sequence\t$aa\n"); foreach my $k (keys %seq){ my %count; # a hash to hold the count for each amino acid in the p +rotein. my @seq= split(//, $seq{$k}); foreach my $r(@seq){ $count{$r}++; } my @row; push(@row, $k); foreach my $a (@aa){ $count{$a}||=0; $count{$a}=length($seq{$k}); # $count{$a}= sprintf("%0.6f",($count{$a}/length($seq{$k}))); push(@row,$count{$a}); } my $row= join("\t",@row); print("\n$row\n"); } my $pkaC= 9.0; my $pkaD= 4.05; my $pkaE= 4.45; my $pkaY= 10.0; my $pkaH= 5.98; my $pkaK= 10.0; my $pkaR= 12.0; foreach my $pka (@row){ $qn1= -1/(1+10^(3.65-$ph)); $qn2= -$cys/(1+10^(9.0-$ph)); $qn3= -$asp/(1+10^(4.05-$ph)); $qn4= -$glu/(1+10^(4.45-$ph)); $qn5= -$tyr/(1+10^(10.0-$ph)); $qp1= 1/(1+10^($ph-8.2)); $qp2= $his/(1+10^($ph-5.98)); $qp3= $lys/(1+10^($ph-10.0)); $qp4= $arg/(1+10^($ph-12.0)); $nq= $qn1+$qn2+$qn3+$qn4+$qn5+$qp1+$qp2+$qp3+$qp4; } if ($ph>=7){ next; } if ($nq<=0){ next; $ph++= 0.01; } open (OUT, ">"."$nq"."_"."$number".".xls") or die "Cannot open file!"; print OUT "$nq";

      What does this mean?

      @aa= qw(Length);

      Because it's not ok.

      correct this:

      my @aa= qw(A R N D C Q E G H I L K M F P S T W Y V); my $aa= join("\t", @aa);
      assign a new variable for $aa.

      and this:

      $ph++= 0.01;

      into:

      $ph+= 0.01;

      and plz. explain what it is you're trying to do here:

      $qn2= -$cys/(1+10^(9.0-$ph));
Re^4: Iso electric point calculation using perl
by Anonymous Monk on Jul 22, 2013 at 17:03 UTC

    And this needs explanation:

    while (<S>){ #Read the FASTA file. chomp; if (/>/){ s/>//; $key= $_; }else{ push (@{$s{$key}}, $_); } }
Re^4: Iso electric point calculation using perl
by Anonymous Monk on Jul 22, 2013 at 17:03 UTC

    And this needs explanation:

    while (<S>){ #Read the FASTA file. chomp; if (/>/){ s/>//; $key= $_; }else{ push (@{$s{$key}}, $_); } }
Re^4: Iso electric point calculation using perl
by Anonymous Monk on Jul 22, 2013 at 17:24 UTC

    After having a good look at your entire program i must conclude i cannot help you unless i learn biology myself. good luck.

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