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Full Discussion: Adding info to end of line if two columns match from files with different separators
Top Forums Shell Programming and Scripting Adding info to end of line if two columns match from files with different separators Post 302793359 by Sarah_19 on Friday 12th of April 2013 06:30:38 AM
Old 04-12-2013
Adding info to end of line if two columns match from files with different separators
I have two files (csv and vcf) which look exactly like this

S1.csv
Code:
func,gene,start,info
"exonic","AL","2309","het"
"exonic","NEF","6912","hom"

S1.vcf
Code:
##fileinfo
#CHROM POS ID INFO
chr1      4567     rs323211     1/1:84,104,99
chr4      2309     rs346742     1/1:27,213,90
chr6      5834     rs234492     0/1:22,765,22
chr8      6912     rs239299     1/1:56,765,13

I want to add the fourth line in the second file to the end of the line in the first file if the number in column 2 (file2) matches the number in column 3 (file1)

Also the first file is seperate using , and " (except for first line) while the second is tab seperated

The final file should look like:

Code:
func,gene,start,info
"exonic","AL","2309","het","1/1:27,213,90"
"exonic","NEF","6912","hom","1/1:56,765,13"

I have to do this for 200 files, each pair has the same name with either .csv or .vcf
 

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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)
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