03-25-2018
Yes. How about posting a decent, representative sample of your data including gaps? So proposals given could be tested against samples reflecting reality?
This User Gave Thanks to RudiC For This Post:
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I have a large text-file with tab-delimited genetic data that looks like:
KSC112 KSC234 0 0 1 1 A G C T
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Hi all,
I'm new to Unix and work primarily in bioinformatics. I am in need of a script which will allow me to replace "1" with "chr1" in only the first column of a file which looks like such:
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I have a file which looks like this:
73450 articles and news developmental psychology 2006-03-30 16:22:40 1 http://www.usnews.com
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I have a file having the following entries:
test1 test2 test3
11 22 33
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99 99 44
---
I want to add a column so that the above file becomes:
test1 test2 test3 notest
11 22 33 *
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---
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Hi all,
I have a 3 columns input file like this:
CPLX9PC-4943 CPLX9PC-4943 1
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Hi,
Can anyone please tell me about how we can delete an entire column from a tab delimited file?
Mu input_file.txt looks like this:
And I want the output as:
I used the below code
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I have tried the following to no avail.
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Hello Everyone..
I want to replace the retail col from FileI with cstp1 col from FileP if the strpno matches in both files
FileP.txt
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LEARN ABOUT DEBIAN
vcf-isec
VCF-ISEC(1) User Commands VCF-ISEC(1)
NAME
vcf-isec - create intersections, unions, complements on bgzipped and tabix indexed VCF or tab-delimited files
SYNOPSIS
vcf-isec [OPTIONS] file1.vcf file2.vcf ...
DESCRIPTION
About: Create intersections, unions, complements on bgzipped and tabix indexed VCF or tab-delimited files.
Note that lines from all files can be intermixed together on the output, which can yield unexpected results.
OPTIONS
-C, --chromosomes <list|file>
Process the given chromosomes (comma-separated list or one chromosome per line in a file).
-c, --complement
Output positions present in the first file but missing from the other files.
-d, --debug
Debugging information
-f, --force
Continue even if the script complains about differing columns.
-o, --one-file-only
Print only entries from the left-most file. Without -o, all unique positions will be printed.
-n, --nfiles [+-=]<int>
Output positions present in this many (=), this many or more (+), or this many or fewer (-) files.
-p, --prefix <path>
If present, multiple files will be created with all possible isec combinations. (Suitable for Venn Diagram analysis.)
-t, --tab <chr:pos:file>
Tab-delimited file with indexes of chromosome and position columns. (1-based indexes)
-w, --win <int>
In repetitive sequences, the same indel can be called at different positions. Consider records this far apart as matching (be it a
SNP or an indel).
-h, -?, --help
This help message.
EXAMPLES
bgzip file.vcf; tabix -p vcf file.vcf.gz bgzip file.tab; tabix -s 1 -b 2 -e 2 file.tab.gz
vcf-isec 0.1.5 July 2011 VCF-ISEC(1)