In the attached file I am using awk to skip the header row, search for specific text, and print particular values that are next to it all from the same field.
Desired output:
I also tried the below and it runs but the output is empty
Hi,
I need to find a string, if it finds then I need to print it , otherwise it has to goto next line....
input is====>
uid = shashi, india uid ,uid= asia
uid= none, uid=india. none
==========
output shold be
uid = shashi, india
uid ,
uid= asia
uid= none,
uid=india. none
... (1 Reply)
Can any one help us in finding the the last word of each line from a text file and print it.
eg:
1st --> aaa bbbb cccc dddd eeee ffff ee
2nd --> aab ered er fdf ere ww ww f
the o/p should be a below.
ee
f (1 Reply)
hi all
I would like to help me find the problem with this script to find and print to the screen a specific date of a log file that I have on my server, the date it is received as the first argument in the script $ 1
Here I show you a few lines that made the idea of my log file:
****... (4 Replies)
Can I do this in one awk session. Solution I have is poor.
I want to return the number after PID.
echo "Start: 12345 is used by PID:11111 username" | awk -F: '{print $3}' | awk '{print $1}' (6 Replies)
Hi,
I'm using awk to print columns from a tab delimited text file:
awk '{print " "$2" "$3" $6"}' file
The problem I have is column 6 contains text with spaces etc which means awk only prints the first word.
How can I tell awk to print the whole column content as column 6?
Thanks, (10 Replies)
I am trying to use awk to print the unique entries in $2
So in the example below there are 3 lines but 2 of the lines match in $2 so only one is used in the output.
File.txt
chr17:29667512-29667673 NF1:exon.1;NF1:exon.2;NF1:exon.38;NF1:exon.4;NF1:exon.46;NF1:exon.47 703.807... (5 Replies)
Trying to print the unique values in $2 before the -, currently the count is displayed. Hopefully, the below is close. Thank you :).
file
chr2:46603668-46603902 EPAS1-902|gc=54.3 253.1
chr2:211471445-211471675 CPS1-1205|gc=48.3 264.7
chr19:15291762-15291983 NOTCH3-1003|gc=68.8 195.8... (3 Replies)
I am trying to use awk skip each line with a ## or # and check each line after for STB= and if that value in greater than or = to 0.8, then at the end of line the text "STRAND BIAS" is written in else "GOOD".
So in the file of 4 entries attached.
awk tried:
awk NR > "##"' "#" -F"STB="... (6 Replies)
Hello,
I have some text data that is in the form of multi-line records. Each record ends with the string $$$$ and the next record starts on the next line.
RDKit 2D
15 14 0 0 0 0 0 0 0 0999 V2000
5.4596 2.1267 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 ... (5 Replies)
Ubuntu, Bash 4.3.48
Hi,
I have this input file with many columns separated with ":"
ARC=121:ERF=12244:IDE=2334:ADA=34 ....
ERF=124:ARC=123:IDE=2344:ADA=54 ....
ERF=16254:IDE=2434:ADA=78:ARC=134 ....
and I want this:
ARC=121:IDE=2334
ARC=123:IDE=2344
ARC=134:IDE=2434
I need to... (5 Replies)
Discussion started by: echo manolis
5 Replies
LEARN ABOUT DEBIAN
vcf-annotate
VCF-ANNOTATE(1) User Commands VCF-ANNOTATE(1)NAME
vcf-annotate - annotate VCF file, add filters or custom annotations
SYNOPSIS
cat in.vcf | vcf-annotate [OPTIONS] > out.vcf
DESCRIPTION
About: Annotates VCF file, adding filters or custom annotations. Requires tabix indexed file with annotations.
Currently annotates only the INFO column, but it will be extended on demand.
OPTIONS -a, --annotations <file.gz>
The tabix indexed file with the annotations: CHR FROM[ TO][ VALUE]+.
-c, --columns <list>
The list of columns in the annotation file, e.g. CHROM,FROM,TO,-,INFO/STR,INFO/GN. The dash in this example indicates that the third
column should be ignored. If TO is not present, it is assumed that TO equals to FROM.
-d, --description <file|string>
Header annotation, e.g. key=INFO,ID=HM2,Number=0,Type=Flag,Description='HapMap2 membership'. The descriptions can be read from a
file, one annotation per line.
-f, --filter <list>
Apply filters, list is in the format flt1=value/flt2/flt3=value/etc.
-h, -?, --help
This help message.
Filters:
+ Apply all filters with default values (can be overridden, see the example below).
-X Exclude the filter X
1, StrandBias
FLOAT Min P-value for strand bias (given PV4) [0.0001]
2, BaseQualBias
FLOAT Min P-value for baseQ bias [1e-100]
3, MapQualBias
FLOAT Min P-value for mapQ bias [0]
4, EndDistBias
FLOAT Min P-value for end distance bias [0.0001]
a, MinAB
INT Minimum number of alternate bases [2]
c, SnpCluster
INT1,INT2 Filters clusters of 'INT1' or more SNPs within a run of 'INT2' bases []
D, MaxDP
INT Maximum read depth [10000000]
d, MinDP
INT Minimum read depth [2]
q, MinMQ
INT Minimum RMS mapping quality for SNPs [10]
Q, Qual
INT Minimum value of the QUAL field [10]
r, RefN
Reference base is N []
W, GapWin
INT Window size for filtering adjacent gaps [10]
w, SnpGap
INT SNP within INT bp around a gap to be filtered [10]
Example:
zcat in.vcf.gz | vcf-annotate -a annotations.gz -d descriptions.txt | bgzip -c >out.vcf.gz zcat in.vcf.gz | vcf-annotate -f
+/-a/c=3,10/q=3/d=5/-D -a annotations.gz -d descriptions.txt | bgzip -c >out.vcf.gz
Where descriptions.txt contains:
key=INFO,ID=GN,Number=1,Type=String,Description='Gene Name' key=INFO,ID=STR,Number=1,Type=Integer,Description='Strand'
vcf-annotate 0.1.5 July 2011 VCF-ANNOTATE(1)