Why does the lines in bold repeat? I have tried different combinations with no luck in figuring it out. The lines in italics are correct, but the lines in bold are at the beginning and do not need to be there. Thank you very much .
Code:
perl -plae '
BEGIN{ %h = qw(0/0 hom 0/1 het 1/1 hom 1/2 het 2/2 hom) }
/^[^#].*FDP=(\d+);.*STB=(\d+\.\d+);.*([0-2]\/[0-2])/ and
$_ .= join "\t", ("", ($2 >= 0.8 ? "STRAND BIAS" : "GOOD"), $1, $h{$3}, int($F[5]/33+0.5))
' input > result
result
Code:
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE
chr1 9324670 . A G 672.016 PASS AF=0.528369;AO=148;DP=281;FAO=149;FDP=282;FR=.;FRO=133;FSAF=59;FSAR=90;FSRF=60;FSRR=73;FWDB=0.00343606;FXX=0;HRUN=1;LEN=1;MLLD=155.207;OALT=G;OID=.;OMAPALT=G;OPOS=9324670;OREF=A;PB=0.5;PBP=1;QD=9.53214;RBI=0.00594431;REFB=-0.0181827;REVB=0.00485061;RO=130;SAF=59;SAR=89;SRF=57;SRR=73;SSEN=0;SSEP=0;SSSB=-0.0352973;STB=0.526882;STBP=0.323;TYPE=snp;VARB=0.0184938;ANN=H6PD GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR 0/1:527:281:282:130:133:148:149:0.528369:89:59:57:73:90:59:60:73 GOOD 282 readsGOOD 282 het 20
chr1 10318652 . C G 360.217 PASS AF=0.566929;AO=72;DP=129;FAO=72;FDP=127;FR=.;FRO=55;FSAF=36;FSAR=36;FSRF=31;FSRR=24;FWDB=0.00760676;FXX=0.0155027;HRUN=2;LEN=1;MLLD=115.62;OALT=G;OID=.;OMAPALT=G;OPOS=10318652;OREF=C;PB=0.5;PBP=1;QD=11.3454;RBI=0.0125905;REFB=-0.0312889;REVB=-0.0100329;RO=55;SAF=36;SAR=36;SRF=31;SRR=24;SSEN=0;SSEP=0;SSSB=-0.0505108;STB=0.527551;STBP=0.492;TYPE=snp;VARB=0.0181889;ANN=KIF1B GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR 1/1:203:129:127:55:55:72:72:0.566929:36:36:31:24:36:36:31:24 GOOD 127 readsGOOD 127 hom 11
chr1 10355834 . C T 504.995 PASS
using sed to replace a specific string on a specific line number using variables
this is where i am at
grep -v WARNING output | grep -v spawn | grep -v Passphrase | grep -v Authentication | grep -v '/sbin/tfadmin netguard -C'| grep -v 'NETWORK>' >> output.clean
grep -n Destination... (2 Replies)
Hello!
I need to delete one line in a file which matches one very precise instance of a string only. When searching the forum I unfortunately only found a solution which would delete each line on which a particular string occurs.
Let's assume I have a file composed of thousands of lines... (4 Replies)
Say the input was as follows:
Brat 20 x 1000 32rf
Pour 15 p 1621 05pr
Dart 10 z 1111 22xx
My program prompts for an input, what I want is to use the input to locate a specific field. Like if I type in, "Pou" then it would return "Pour" and just "Pour"
I currently have this line but it is... (6 Replies)
I'm trying to update a text file via sed/awk, after a lot of searching I still can't find a code snippet that I can get to work.
Brief overview:
I have user input a line to a variable, I then find a specific value in this line 10th field in this case. After asking for new input and doing some... (14 Replies)
Hi,
I have an issue to combine multiple lines of a file. I have records as below.
Fields are delimited by TAB. Each lines are ending with a new line char (\n)
Input
--------
ABC 123456 abcde 987
890456 7890 xyz
ght gtuv
ABC 5tyin 1234 789
ghty kuio
ABC ghty jind 1234
678 ght
... (8 Replies)
Hi,
I want to achieve something similar to what described in another post:
The difference is I want to add the line if the pattern is not found.
File 1:
A123, valueA, valueB
B234, valueA, valueB
C345, valueA, valueB
D456, valueA, valueB
E567, valueA, valueB
F678, valueA, valueB
... (11 Replies)
Hi All,
I'm having a hard time finding a starting point for my issue. I have a 30k line file (fspsec.txt) that I would like to parse into smaller files based on any character existing in field 1.
ACCOUNTANT LEVEL 1 (ACCT.ACCOUNTANT)
OPERATORS: DOEJO (418)
TOOLS: Branch Maintenance
... (2 Replies)
In the perl below, which does execute, I am having trouble with the else in Rule 3. The digit in f{8} is extracted and used to update f accordinly along with the value in f.
There can be either - * or + before the number that is extracted but the same logic applies, that is if the value is greater... (5 Replies)
I have been reading old posts and trying to come up with a solution for the below: Use a tab-delimited input file to assign
point to variables that are used to update a specific field, Rank. I really couldn't find too much in the way of assigning points
to variable, but made an attempt at an awk... (4 Replies)
I have an input file with
A=xyz
B=pqr
I would want the value in Second Field (xyz or pqr) updated with a value present in Shell Variable based on the value passed in the first field. (A or B )
while read line
do
NEW_VALUE = `some functionality done on $line`
If $line=First Field-... (1 Reply)
Discussion started by: infernalhell
1 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)
06-30-2016
.