Following your suggestion, now I get these errors
All the files and codes are running in the same directory. I've also made sure the xlsx has permissions.
It appears that this has been asked and answered in similar fashions previously, but I am still unsure how to approach this.
I have two files containing user information:
fileA
ttim:/home/ttim:Tiny Tim:632
ppinto:/home/ppinto:Pam Pinto:633
fileB
ttim:xkfgjkd*&#^jhdfh... (3 Replies)
Hi , I have the below file with 6 columns.I want to append 'File1' as the 1 column to the file. i have the sample code .It is not working . can u please correct this or make new one .....
awk 'print {'File1',$1,$2,$3,$4,$5,$6}' Source_File> Result_File
Source_File:... (6 Replies)
Hi all,
I have two files with the same number of lines
the first file is a.dat and looks like
0.000 1.000
1.000 2.000
...
the fields are tab separated
the second file is b.dat and looks like
1.2347 0.546
2.3564 0.321
...
the fields are tab separated
I would like to have a file c.dat... (4 Replies)
Hi ,
I have a file with a running sequence number. I need to append a date value mmdd format on to the first column.
for e.g.: The file contains records as
001 abc
002 cde
003 edf
004 fgh
005 hik
The output should be
1111001 abc
1111002 cde
1111003 edf
1111004 ... (1 Reply)
Hi, i want to add another column to existing files containing strings and need to have the final output as a csv file. i have quite a number of files, each with varying number of rows and i need to append the string "test" for all the valid rows for each file. my sample raw files looks like this... (8 Replies)
I have a text file where I want to append a column of numbers in ascending orders.
Input:
57 abc
25 def
32 ghi
54 jkl
Output:57 abc
57 abc 1
25 def 2
32 ghi 3
54 jkl 4
How do I go about doing that? Thanks! (11 Replies)
Hi All,
Input.txt
KGO
Id "003"
..........
..........
Par "CPara"
BIN RECGET
Name "DIR_PATH"
Prompt "DIR_PATH"
END RECGET
KGO
............
..........
...............
KGO
Id "077"
..........
.......... (7 Replies)
Hi,
I have a requirement to append = in particular row in csv file. Data in csv is as follow:
row1,a,a,a
row2,b,b,b
row3,c,c,c
row4,d,d,d
csv should be modified at row3 and no. of columns are not fixed but rows are. output should be as:
row1,a,a,a
row2,b,b,b
row3,=c,=c,=c... (2 Replies)
Hi experts -
I'm relatively new to python, but I have an requirement to automate getting a file from a WebLib server using an API.
The file I'm requesting from this sever is an excel spreadsheet (.xlsx).
I get a valid response back via an xml doc from the server.
In this xml file I get... (8 Replies)
Source Code of the original script is down below please run the script and try to solve this problem
this is my data and I want it column wise
2019-03-20 13:00:00:000
2019-03-20 15:00:00:000
1
Operating System
LAB
0
1
1
1
1
1
1
1
1
1
0
1 (5 Replies)
Discussion started by: Shubham1182
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)