Match all lines in file where specific text pattern is less than
In the below file I am trying to grep or similar, all lines where only AF= is less than 0.4.. Thank you .
grep
Code:
grep "AF=" ,+ .4 file
file
Code:
12 112036782 . T C 34.0248 PASS AF=0.194286;AO=32;DP=170;FAO=34;FDP=175;FR=.;FRO=141;FSAF=20;FSAR=14;FSRF=57;FSRR=84;FWDB=-0.0842492;FXX=0.0056815;HRUN=2;LEN=1;MLLD=83.7705;OALT=C;OID=.;OMAPALT=C;OPOS=112036782;OREF=T;PB=0.5;PBP=1;QD=0.77771;RBI=0.128679;REFB=-0.0310314;REVB=-0.0972646;RO=137;SAF=20;SAR=12;SRF=55;SRR=82;SSEN=0;SSEP=0;SSSB=0.280873;STB=0.645079;STBP=0.067;TYPE=snp;VARB=0.090833;ANN=ATXN2 GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR 0/1:34:170:175:137:141:32:34:0.194286:12:20:55:82:14:20:57:84
12 112036795 . T A 34.0248 PASS AF=0.45121;AO=32;DP=170;FAO=34;FDP=175;FR=.;FRO=141;FSAF=20;FSAR=14;FSRF=57;FSRR=84;FWDB=-0.0842492;FXX=0.0056815;HRUN=2;LEN=1;MLLD=83.7705;OALT=C;OID=.;OMAPALT=C;OPOS=112036782;OREF=T;PB=0.5;PBP=1;QD=0.77771;RBI=0.128679;REFB=-0.0310314;REVB=-0.0972646;RO=137;SAF=20;SAR=12;SRF=55;SRR=82;SSEN=0;SSEP=0;SSSB=0.280873;STB=0.645079;STBP=0.067;TYPE=snp;VARB=0.090833;ANN=ATXN2 GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR 0/1:34:170:175:137:141:32:34:0.194286:12:20:55:82:14:20:57:84
desired output
Code:
12 112036782 . T C 34.0248 PASS AF=0.194286;AO=32;DP=170;FAO=34;FDP=175;FR=.;FRO=141;FSAF=20;FSAR=14;FSRF=57;FSRR=84;FWDB=-0.0842492;FXX=0.0056815;HRUN=2;LEN=1;MLLD=83.7705;OALT=C;OID=.;OMAPALT=C;OPOS=112036782;OREF=T;PB=0.5;PBP=1;QD=0.77771;RBI=0.128679;REFB=-0.0310314;REVB=-0.0972646;RO=137;SAF=20;SAR=12;SRF=55;SRR=82;SSEN=0;SSEP=0;SSSB=0.280873;STB=0.645079;STBP=0.067;TYPE=snp;VARB=0.090833;ANN=ATXN2 GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR 0/1:34:170:175:137:141:32:34:0.194286:12:20:55:82:14:20:57:84
My input:
File_1:
2000_t
g1110.b1
abb.1
2001_t
g1111.b1
abb.2
abb.2
g1112.b1
abb.3
2002_t
.
.
File_2:
2000_t Ali england 135
abb.1 Zoe british 150
2001_t Ali england 305
g1111.b1 Lucy russia 126 (6 Replies)
I am attempting to insert multiple lines of text into a specific place in a text file based on the lines above or below it.
For example, Here is a portion of a zone file.
IN NS ns1.domain.tld.
IN NS ns2.domain.tld.
IN ... (2 Replies)
In Unix, how do I delete lines in a file that match a particular pattern without opening it. File contents are
foo line1
misc
whatever
foo line 2
i want to delete all lines that have the pattern "foo" without opening the file. File should eventually contain
misc
whatever (1 Reply)
Hi
i have a file which have a pattern like this
Nov 10 session closed
Nov 10 Nov 9 08:14:27 EST5EDT 2010 on tty .
Nov 10 Oct 19 02:14:21 EST5EDT 2010 on pts/tk .
Nov 10 afrtetryytr
Nov 10 session closed
Nov 10 Nov 10 03:21:04 EST5EDT 2010
Dec 8 Nov 10 05:03:02 EST5EDT 2010
... (13 Replies)
Hi,
I need help with this-
input.txt :
L B white
X Y white
A B brown
M Y black
Read this input file and if 3rd column is "white", then add specific lines to another file insert.txt.
If 3rd column is brown, add different set of lines to insert.txt, and so on.
For example, the given... (6 Replies)
Hi
I have a file like
# vi require.txt
1,BANK,Read blocks that cycle.
yellow
Read blocks.
2,ACCOUNT,Finished
Red
Finished .
3,LOAN, pipe
white
pipe
4,PROFIT,Resolve.
black
Resolve
Am using like
cat require.txt | grep -w ACCOUNTThe output I get is (8 Replies)
Hi
This is my first post and I'm just a beginner. So please be nice to me.
I have a couple of html files where a pattern beginning with "http://www.site.com" and ending with "/resource.dat" is present on every 241st line. How do I extract this to a new text file?
I have tried sed -n 241,241p... (13 Replies)
I hope this makes sense and is possible.
I am trying to match $1 of panel_genes.txt with $3 of RefSeqGene.txt and when a match is found the value in $6 of RefSeqGene.txt
Example: ACTA2 is $1 of panel_genes.txt
ACTA2 NM_001613.2
ACTA2 NM_001141945.1
awk 'FNR==NR {... (4 Replies)
hi all,
trying this using shell/bash with sed/awk/grep
I have two files, one containing one column, the other containing multiple columns (comma delimited).
file1.txt
abc12345
def12345
ghi54321
...
file2.txt
abc1,text1,texta
abc,text2,textb
def123,text3,textc
gh,text4,textd... (6 Replies)
Discussion started by: shogun1970
6 Replies
LEARN ABOUT XFREE86
zgrep
ZGREP(1) General Commands Manual ZGREP(1)NAME
zgrep - search possibly compressed files for a regular expression
SYNOPSIS
zgrep [ grep_options ] [ -e ] pattern filename...
DESCRIPTION
Zgrep invokes grep on compressed or gzipped files. These grep options will cause zgrep to terminate with an error code:
(-[drRzZ]|--di*|--exc*|--inc*|--rec*|--nu*). All other options specified are passed directly to grep. If no file is specified, then the
standard input is decompressed if necessary and fed to grep. Otherwise the given files are uncompressed if necessary and fed to grep.
If the GREP environment variable is set, zgrep uses it as the grep program to be invoked.
EXIT CODE
2 - An option that is not supported was specified.
AUTHOR
Charles Levert (charles@comm.polymtl.ca)
SEE ALSO grep(1), gzexe(1), gzip(1), zdiff(1), zforce(1), zmore(1), znew(1)ZGREP(1)
12-22-2016
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