The output seems to be only 3 of the 4 lines (in this example there are 4 lines, but that is variable depending on the input.
Is the next only processing one of the lines because they both do not have SVTYPE=Fusion so it only sees one line?. Thank you .
Code:
Locus Type Function Gene Reads
chr12:12006495-chr15:88483984 Fusion Gain-of-Function ETV6NTRK3-E4N15 1868chr12:12022903-chr15:88483984 Fusion Gain-of-Function ETV6NTRK3-E5N15 414833chr17 7577108 COSM10749;COSM43737 C A,T 149.594 PASS AF=0.0830415,0.0;AO=372,2;DP=4420;FAO=166,0;FDP=1999;FR=.,.,REALIGNEDx0.0865;FRO=1833;FSAF=82,0;FSAR=84,0;FSRF=952;FSRR=881;FWDB=0.0072184,-0.0207142;FXX=4.99998E-4;HRUN=1,1;LEN=1,1;MLLD=293.795,80.5366;OALT=A,T;OID=COSM10749,COSM43737;OMAPALT=A,T;OPOS=7577108,7577108;OREF=C,C;PB=.,.;PBP=.,.;QD=0.299338;RBI=0.00721997,0.02565;REFB=1.40155E-4,-7.81395E-4;REVB=1.50579E-4,0.0151276;RO=4043;SAF=187,1;SAR=185,1;SRF=2118;SRR=1925;SSEN=0,0;SSEP=0,0;SSSB=-0.0251826,-5.12306E-4;STB=0.52327,0.5;STBP=0.541,1.0;TYPE=snp,snp;VARB=-0.00153404,0.0;HS;FUNC=[{'origPos':'7577108','origRef':'C','normalizedRef':'C','gene':'TP53','normalizedPos':'7577108','normalizedAlt':'A','polyphen':'1.0','gt':'pos','codon':'TTT','coding':'c.830G>T','sift':'0.0','grantham':'205.0','transcript':'NM_000546.5','function':'missense','protein':'p.Cys277Phe','location':'exonic','origAlt':'A','exon':'8','oncomineGeneClass':'Loss-of-Function','oncomineVariantClass':'Hotspot'}] GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR:QT 0/1:149:4420:1999:4043:1833:372,2:166,0:0.0830415,0.0:185,1:187,1:2118:1925:84,0:82,0:952:881:1
hi..im new to UNIX...
ok i have this information in the normal shell...
there are 2 lines display like this:
h@hotmail.com
k@hotmail.com
i want it to display like this with a space betweem them
h@hotmail.com k@hotmail.com
the information is stored in a text file....
anyone... (10 Replies)
Hi All,
I have 1 "keyword" file like this:
00-1F-FB-00-04-18
00-19-CB-8E-66-DF
00-1F-FB-00-48-9C
00-1F-FB-00-AA-4F
....
and the 2nd "details" file like this:
Wed Feb 11 00:00:02 2009
NAS-IP-Address = xxxxxxxxxxxxxxxxxx
Class = "P1-SHT-AAA01;1233704662;4886720"
... (6 Replies)
Hello, can someone help me how to find a word and 2 lines after it and then send the output to another file.
For example, here is myfile1.txt. I want to search for "Error" and 2 lines below it and send it to myfile2.txt
I tried with grep -A but it's not supported on my system.
I tried with awk,... (4 Replies)
Hello everyone,
Maybe somebody could help me with an awk script.
I have this input (field separator is comma ","):
547894982,M|N|J,U|Q|P,98,101,0,1,1
234900027,M|N|J,U|Q|P,98,101,0,1,1
234900023,M|N|J,U|Q|P,98,54,3,1,1
234900028,M|H|J,S|Q|P,98,101,0,1,1
234900030,M|N|J,U|F|P,98,101,0,1,1... (2 Replies)
URGENT HELP IS NEEDED!!
I am looking to move matching lines (01 - 07) from File1 and 77 tab the matching string from File2, to File3.txt. I am almost done but
- Currently, script is not printing lines to File3.txt in order.
- Also the matching lines are not moving out of File1.txt
... (1 Reply)
If a file has following kind of data, comma delimited
1,2,3,4
1
1
1,2,3,4
1,2
2
2,3,4
My required output must have only 4 columns with comma delimited
1,2,3,4
111,2,3,4
1,222,3,4
I have tried many awk command using ORS="" but couldnt progress (10 Replies)
I am trying to combine lines with these conditions:
1. First line starts with text of "libname VALUE db2 datasrc" where VALUE can be any text.
2. If condition1 is met then continue to combine lines through a line that ends with a semicolon.
3. Ignore case when matching patterns and remove any... (5 Replies)
I'm trying to use awk to count the occurrences of two matching fields of a CSV file.
For instance, for data that looks like this...
Joe,Blue,Yes,No,High
Mike,Blue,Yes,Yes,Low
Joe,Red,No,No,Low
Joe,Red,Yes,Yes,Low
I've been trying to use code like this...
countvar=`awk ' $2~/$color/... (4 Replies)
I am trying to combine all matching lines in the tab-delimited using awk. The below runs but no output results. Thank you :).
input
chrX 110925349 110925532 ALG13
chrX 110925349 110925532 ALG13
chrX 110925349 110925532 ALG13
chrX 47433390 47433999 SYN1... (3 Replies)
I have been searching and trying to come up with an awk that will perform the following on a
converted text file (original is a pdf).
1. Since the first two lines are (begin with) text they are removed
2. if $1 is a number then all text is merged (combined) into one line until the next... (3 Replies)
Discussion started by: cmccabe
3 Replies
LEARN ABOUT LINUX
igawk
IGAWK(1) Utility Commands IGAWK(1)NAME
igawk - gawk with include files
SYNOPSIS
igawk [ all gawk options ] -f program-file [ -- ] file ...
igawk [ all gawk options ] [ -- ] program-text file ...
DESCRIPTION
Igawk is a simple shell script that adds the ability to have ``include files'' to gawk(1).
AWK programs for igawk are the same as for gawk, except that, in addition, you may have lines like
@include getopt.awk
in your program to include the file getopt.awk from either the current directory or one of the other directories in the search path.
OPTIONS
See gawk(1) for a full description of the AWK language and the options that gawk supports.
EXAMPLES
cat << EOF > test.awk
@include getopt.awk
BEGIN {
while (getopt(ARGC, ARGV, "am:q") != -1)
...
}
EOF
igawk -f test.awk
SEE ALSO gawk(1)
Effective AWK Programming, Edition 1.0, published by the Free Software Foundation, 1995.
AUTHOR
Arnold Robbins (arnold@skeeve.com).
Free Software Foundation Nov 3 1999 IGAWK(1)
05-14-2017
.