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Full Discussion: Compare and Merge files
Top Forums Shell Programming and Scripting Compare and Merge files Post 302752783 by LMHmedchem on Monday 7th of January 2013 01:34:40 PM
Old 01-07-2013
Quote:
Originally Posted by nua7
Thanks LMHmedchem But I need to do this in awk or sed.

Also found another way of doing it , incase it is helpful for others.


Code:
awk -v input_file=file1 'BEGIN { FS="|"; while((getline<input_file)>0){sub1=substr($0,1,11); subArr[sub1]=""}}{ if ($1 in subArr) print $0;}' file2  > file3


.
I used a hard language because I needed some specific exception handling and a variety of checks and such. I also have a version of this where one file is always bigger than the other and the code searches the bigger file for the matching row. I am sure there are ways to do this kind of thing with stream interpreters, but that's well past what I know how to do.

Thanks for the post, it is always nice to see a different way. It's terribly funny that these three lines do, in essence, what it takes me 300 lines to do in cpp, plus your version will work on most any os without needing to be recompiled.

LMHmedchem
 

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LEARN ABOUT DEBIAN

vcf-compare

VCF-COMPARE(1)							   User Commands						    VCF-COMPARE(1)

NAME

       vcf-compare - compare bgzipped and tabix indexed VCF files

SYNOPSIS

       compare-vcf [OPTIONS] file1.vcf file2.vcf ...

DESCRIPTION

       About: Compare bgzipped and tabix indexed VCF files. (E.g. bgzip file.vcf; tabix -p vcf file.vcf.gz)

OPTIONS

       -c, --chromosomes <list|file>
	      Same as -r, left for backward compatibility. Please do not use as it will be dropped in the future.

       -d, --debug
	      Debugging information. Giving the option multiple times increases verbosity

       -H, --cmp-haplotypes
	      Compare haplotypes, not only positions

       -m, --name-mapping <list|file>
	      Use  with -H when comparing files with differing column names. The argument to this options is a comma-separated list or one mapping
	      per line in a file. The names are colon separated and must appear in the same order as the files on the command line.

       -R, --refseq <file>
	      Compare the actual sequence, not just positions. Use with -w to compare indels.

       -r, --regions <list|file>
	      Process the given regions (comma-separated list or one region per line in a file).

       -s, --samples <list>
	      Process only the listed samples. Excluding unwanted samples may increase performance considerably.

       -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.

vcf-compare 0.1.5						     July 2011							    VCF-COMPARE(1)
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