Question: (Closed) blast alignemnt query coverage using perl
gravatar for sharmatina189059
2.5 years ago by
United States
sharmatina18905940 wrote:

Dear all I need to calculate query coverage using perl, for which I wrote my own code in perl as well as used -outfmt "6 std qcovs. my perl code is

#!/usr/bin/perl -w
use warnings;
use strict;
my $filename = 'gene_length_u';
my @fields;
open (FH, $filename);
#my $n = 0;
while ( <FH> ) {
 my @fields = split('\t', $_);
#print "$fields[0]\n";
#print "$fields[1]\n";
#print "$fields[2]\n";
#print "$fields[3]\n";
 print "$_";
#$n = $n+1;
#print "\n my line number $n \n";
 my $p = ($fields[2] - $fields[1])+1;
 my $q = $p/$fields[5] * 100;
 print "\t\t$q\n";
#foreach (<$filename>){
#print "$_";
close FH;

Why I am getting different query coverage. I have calculated sequence length using infoseq and I have file (input ) like this.

gene_id                                gene_start  gene_end  gene_id                gene_length
lcl|NZ_CP018664.1_gene_1121 1   303     NZ_CP018664.1_gene_1121 303
lcl|NZ_CP018664.1_gene_1122 1   1053        NZ_CP018664.1_gene_1122 1053
lcl|NZ_CP018664.1_gene_1123 1   768     NZ_CP018664.1_gene_1123 768
lcl|NZ_CP018664.1_gene_1124 1   1698        NZ_CP018664.1_gene_1124 1698
lcl|NZ_CP018664.1_gene_1125 1   657     NZ_CP018664.1_gene_1125 657
blast • 545 views
ADD COMMENTlink modified 2.5 years ago by WouterDeCoster43k • written 2.5 years ago by sharmatina18905940

Hello sharmatina189059!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.


ADD REPLYlink written 2.5 years ago by WouterDeCoster43k

I added (code) markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

101010 Button

ADD REPLYlink written 2.5 years ago by WouterDeCoster43k
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