I am trying to begin to troubleshoot this perl error that I keep getting, yet I get output is produced. The error is Use of uninitialized value in join or string line 175, <MANNO> line 7138 and below is line 175:
I am not too sure what the error is but since not every line has an error on it, I suspect maybe null values may be causing the issue. Thank you .
Code:
if (@prefield and join ("\t", @field[@name+3 .. $#field]) eq join ("\t", @prefield[@name+3 .. $#field])) { #same locus, multiple alternative allele
input
Code:
chr1 949608 . G A 3843.99 PASS AF=1;AO=1297;DP=1303;FAO=399;FDP=399;FR=.;FRO=0;FSAF=204;FSAR=195;FSRF=0;FSRR=0;FWDB=0.0462861;FXX=0.00249994;HRUN=1;LEN=1;MLLD=151.783;OALT=A;OID=.;OMAPALT=A;OPOS=949608;OREF=G;PB=0.5;PBP=1;QD=38.5362;RBI=0.0475491;REFB=0;REVB=-0.0108863;RO=3;SAF=657;SAR=640;SRF=1;SRR=2;SSEN=0;SSEP=0;SSSB=0.000764295;STB=0.5;STBP=1;TYPE=snp;VARB=8.63542e-06;ANN=ISG15 GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR 1/1:181:1303:399:3:0:1297:399:1:640:657:1:2:195:204:0:0 GOOD 399 hom 116
chr1 949654 . A G 3787.59 PASS AF=1;AO=1352;DP=1360;FAO=397;FDP=397;FR=.;FRO=0;FSAF=185;FSAR=212;FSRF=0;FSRR=0;FWDB=0.003541;FXX=0.00749981;HRUN=1;LEN=1;MLLD=133.768;OALT=G;OID=.;OMAPALT=G;OPOS=949654;OREF=A;PB=0.5;PBP=1;QD=38.1622;RBI=0.0270794;REFB=0.0316329;REVB=-0.0268469;RO=6;SAF=679;SAR=673;SRF=2;SRR=4;SSEN=0;SSEP=0;SSSB=0.00142636;STB=0.5;STBP=1;TYPE=snp;VARB=-0.000104249;ANN=ISG15 GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR 1/1:161:1360:397:6:0:1352:397:1:673:679:2:4:212:185:0:0 GOOD 397 hom 115
chr1 955597 . G T 555.77 PASS
perl regexp error , I cant understand what is wrong
Hello all
I have simple perl regexp that is searching for pattern in string and replace it with the same string + addition string
here is what I have :
my $rec = q| new Array("Attributes Management" ... (4 Replies)
Hello, I need advice on how to check if started processes are finished in perl, here's explanation :
OS is RHEL 4, perl -v = "This is perl, v5.8.0 built for i386-linux-thread-multi"
The logic of the script :
#!/usr/bin/perl
use warnings;
$param1 = $ARGV;
$param2 = $ARGV;
$param3 =... (2 Replies)
I'm Using this script to find the time of a file. I'm very much new to PERL
and found this script posted by some one on this forum.
It runs perfectly fine, just that it gives me following errors with the
accurate output as well. I jus want the output to be stored in another file
so that i can... (0 Replies)
Hey forum,
I have a problem with a script what used to work, but suddenly is not working anymore. I have been trying different things for an hour now and I give up :D .
#!/bin/sh
asukoht=`pwd`
template=$1
for values in... (4 Replies)
I'm just trying to confirm that I understand someone's code correctly.
If someone has code that says:
$foo ||= mysub();
I'm assuming that it means if $foo is nothing or undef, then assign it some value via mysub(). If I'm wrong on this, please let me know.
Also, what's the difference... (4 Replies)
this is my program i am trying to compile
/* filedata -- display information about a file */
#include <stdlib.h>
#include <stdio.h>
#include <sys/stat.h>
#include <sys/types.h>
/*
* use octarray for determing
* if permission bits set
*/
static short octarray = {0400, 0200, 0100,... (2 Replies)
#!/usr/bin/perl
use strict;
use warnings;
print "Demo of array slicing \n";
my @abc="a b c d e f g h i j k l m n o p q r s t u v w x y z";
my @a=@abc;
my @random=@abc;
my @comp=@abc;
my @comp1=(@abc,"Hello",@abc);
print "abc is @abc \n";
print "a is @a \n";
print "random is @random \n";... (1 Reply)
co
#! /usr/bin/perl
use strict;
use warnings;
use diagnostics;
my $amount=""; my $bain; ; my $code="";
my $date;my $day;my $line; my $mo; my $LNUM = 0;
my $xyz=""; my $yr;
$yr = 2015;
my $F; my @F;
while (<>) {
chop;
++$LNUM;
@F = split(';');
if ( $F eq "Date" )... (1 Reply)
Hi Folks -
I'm getting the following error message when executing my script:
$ chmod +x Winexe_Admin.sh
$ ./Winexe_Admin.sh
Script Name: Winexe_Admin.sh
Script Name without EXT: Winexe_Admin
./Winexe_Admin.sh: line 43: ${_MAINPATH}${_LOGPATH}${LOGPATH$}${_YEAR}_${_MONTH}${_DAY}: bad... (2 Replies)
I have a file with two line, one is header, the other actual value:
TYPCD|ETID2|ETID|LEG ID|PTYP|PTYP SUB|TRD STATUS|CXL REASON|CACT|CACTNM|ENCD|ENC
D NM|TRDR|ASDT|TRDT|MTDT|STDT|LS|SECID|SECID TYP|SECNM|PAR|STCC|MARKET PRICE|DIS
MARKET PRICE|MARKET PRICE CURRENCY|SRC OF SETTLEMENT... (2 Replies)
Discussion started by: digioleg54
2 Replies
LEARN ABOUT DEBIAN
pfunc
PFUNC(1p) User Contributed Perl Documentation PFUNC(1p)NAME
pfunc - grep for perl functions
SYNOPSIS
pfunc subroutine FILES...
DESCRIPTION
pfunc searches the named FILES for all calls to the given subroutine. It will report back the file and line number each call is found on
along with what sort of call it is
function foo()
class method Class->foo()
object method $obj->foo()
EXAMPLE
$ pfunc isa /usr/share/perl/5.6.1/*.pm
Called as function in /usr/share/perl/5.6.1/CGI.pm at line 316
Called as function in /usr/share/perl/5.6.1/CGI.pm at line 327
Called as function in /usr/share/perl/5.6.1/CGI.pm at line 397
Called as function in /usr/share/perl/5.6.1/CGI.pm at line 494
Called as function in /usr/share/perl/5.6.1/CGI.pm at line 495
Called as object method in /usr/share/perl/5.6.1/CPAN.pm at line 4957
Called as function in /usr/share/perl/5.6.1/Dumpvalue.pm at line 191
Called as function in /usr/share/perl/5.6.1/Dumpvalue.pm at line 218
Called as function in /usr/share/perl/5.6.1/Dumpvalue.pm at line 248
Called as function in /usr/share/perl/5.6.1/Dumpvalue.pm at line 251
Called as function in /usr/share/perl/5.6.1/Dumpvalue.pm at line 254
Called as object method in /usr/share/perl/5.6.1/Shell.pm at line 28
Called as object method in /usr/share/perl/5.6.1/base.pm at line 12
NOTES
Its not fast, but its accurate.
AUTHOR
Michael G Schwern <schwern@pobox.com>
SEE ALSO
Module::Info
perl v5.10.1 2010-10-03 PFUNC(1p)
08-29-2016
.