All,
I have a requirement where I will need to split a line into multiple lines.
Ex:
Input:
2ABCDEFGH2POIYUY2ASDGGF2QWERTY
Output:
2ABCDEFGH
2POIYUY
2ASDGGF
2QWERTY
The data is of no fixed lenght. Only the lines have to start with 2.
How can this be done. (5 Replies)
I am trying to figure out how to split a file when the data in the new line is different from the current line using a shell script?
For eg..
if my input file contains the following
2341123 ABCAD
2341123 ANCAED
2341123 AVADV
3343434 ASDVAV
3343434 ASDFADF
4231232 ADACVAV
4231232... (3 Replies)
Hi,
I want to split before reading the complete line as the line is very big and its throwing out of memory. can you suggest.
when i say
#cat $inputFile | while read eachLine
and use the eachLine to split its throwing out of memory as the line size is more than 10000000 characters.
Can you... (1 Reply)
Dear All,
I want to split single line into two line or three lines wherever “|” separated values comes using
Input line
test,DEMTEMPUT20100404010012,,,,,,,,|0070086|0070087,
output shoule be
test,DEMTEMPUT20100404010012,,,,,,,,0070086,
test,DEMTEMPUT20100404010012,,,,,,,,0070087, (14 Replies)
Hi all,
I have logs(in a log file) with the following structure
20100916011501559;0.812;null;TRUE;;FALSE;0.812;0;0;;19
20100916011504762;0.015;null;TRUE;;FALSE;0;4|4;0.015;;4
20100916011504762;0;null;TRUE;;FALSE;0;0;0;;4
20100916011501731;3.343;null;TRUE;;FALSE;3.156;131|65;0.172;;11... (14 Replies)
The requirement is, there is a log file which contains a huge data. i need to get a particular field out of it by searching with another field.
ex:
2011-03-28 13:00:07,423 : millis=231 q={ call get_data_account(?,?,?,?,?) }, params=
i need to search for the word "get_data_account" in file... (1 Reply)
HI Guys,
I need to split the file in to number of files . file contains FILEHEADER and EOF . I have to split n number of times . I have to form the file with each splitted message between FILEHEADER and EOF using awk beign and end . how to implement please suggest. (2 Replies)
Hi All,
I have file(File1) with data like below:
102100|LName|Gender|Company|Branch|Bday|Salary|Age
102100|bbbb|male|cccc|dddd|19900814|15000|20|
102101|asdg|male|gggg|ksgu|19911216|||
102102|bdbm|male|kkkk|acke|19931018||23|
102102|kfjg|male|kkkc|gkgg|19921213|14000|24|... (2 Replies)
Hi Gurus,
I have below JSON file, now I want to rewrite this file into a new file.
I will appreciate if anyone can help me to provide the solution...I can't use jq.
{
"_id": "3ad893cb4cf1560add7b4caffd4b6126",
"_rev": "1-1f0ce165e1d210319cf6e9f9c6ff654f",
"name":... (4 Replies)
Discussion started by: manas_ranjan
4 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)