If f[54] has a . in it, the value associated with it is zero. In order to prevent column shifting due to null values I use a . in these fields.
So, I think I follow but just to make sure the abs($Score) is only used if f[54] is not a .? Is that right? Also, could you please comment the code so I may try to learn from more from it, if possible. Thank you very much .
Code:
#!/usr/bin/perl # call perl
use strict; # use exactdefined criteria
use warnings; # display warning messages
print scalar <>; # skip header line
while (<>) # start conditional checks
{
my @f = split /\t/; # split on tabs
my ( $FuncIDPrefGene, # field 1
$AAChangeIDPrefGene, # field 2
$PopFreqMax, # field 3
$GeneDetailIDPrefGene, # field 4
$ClinSig, # field 5
$Score ) = @f[6,11,13,8,46,54]; # field 6 and define field locations using 0 coordinate
if (abs($Score) < 5) { # check field 6 for value and ensure its less than 5
if($FuncIDPrefGene eq 'exonic') { # check field 1 and if exonic and conditon above met
pj(\@f,'Likely Benign'); # set field 55 to Likely Benign
} # end condition 1 block
else {
my $scored = $GeneDetailIDPrefGene=~/\.\d+[\+\-](\d+)/; # use field 4 and split on the . and +/1 and read value into variable
pj(\@f, 'Likely Benign') if $scored > 10; # if variable greater then 10 then field 55 is Likely Benign
} # end condition 2 block
}
else {
pj(\@f, 'VUS'); # if niether condition is meet set field 55 to VUS
}
} # end while block
sub pj # define subroutine
{ # start sub block
my $fr = shift; # define variable
$fr->[55] = shift; # use field 55 as variable
print join "\t", @{$fr}; # print value in field
} # end sub block
Last edited by cmccabe; 04-09-2017 at 11:18 AM..
Reason: added comment question
Hi
I have a file from which i need to remove the first 4 and the last 2 lines.. i know how to do it with sed but i need to do it in a perl script.. can you please help me how to do that.
Thanks (10 Replies)
Can anyone tell me what could be the solution to following :
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here is the contents of .txt... (5 Replies)
I've hunted and hunted but nothing seems to apply to what I need. Any help will be much appreciated!
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marker,allele1,allele2
RS1002244,1,1
RS1002244,1,3
RS1002244,3,3
RS1003719,2,2
RS1003719,2,4
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i try to do this for a long time
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...
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Hi,
I want to match the time in the file and retrieve those contents of the file.
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file1.dat
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I have 500 MB of file.
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VANITHA (3 Replies)
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Discussion started by: engkemo2002
6 Replies
LEARN ABOUT PLAN9
dh_perl
DH_PERL(1) Debhelper DH_PERL(1)NAME
dh_perl - calculates Perl dependencies and cleans up after MakeMaker
SYNOPSIS
dh_perl [debhelperoptions] [-d] [librarydirs...]
DESCRIPTION
dh_perl is a debhelper program that is responsible for generating the ${perl:Depends} substitutions and adding them to substvars files.
The program will look at Perl scripts and modules in your package, and will use this information to generate a dependency on perl or
perlapi. The dependency will be substituted into your package's control file wherever you place the token ${perl:Depends}.
dh_perl also cleans up empty directories that MakeMaker can generate when installing Perl modules.
OPTIONS -d In some specific cases you may want to depend on perl-base rather than the full perl package. If so, you can pass the -d option to make
dh_perl generate a dependency on the correct base package. This is only necessary for some packages that are included in the base
system.
Note that this flag may cause no dependency on perl-base to be generated at all. perl-base is Essential, so its dependency can be left
out, unless a versioned dependency is needed.
-V By default, scripts and architecture independent modules don't depend on any specific version of perl. The -V option causes the current
version of the perl (or perl-base with -d) package to be specified.
library dirs
If your package installs Perl modules in non-standard directories, you can make dh_perl check those directories by passing their names
on the command line. It will only check the vendorlib and vendorarch directories by default.
CONFORMS TO
Debian policy, version 3.8.3
Perl policy, version 1.20
SEE ALSO debhelper(7)
This program is a part of debhelper.
AUTHOR
Brendan O'Dea <bod@debian.org>
11.1.6ubuntu2 2018-05-10 DH_PERL(1)
04-09-2017
.