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Full Discussion: Compare two files and write data to second file using awk
Top Forums Shell Programming and Scripting Compare two files and write data to second file using awk Post 302898681 by Ajay Venkatesan on Wednesday 23rd of April 2014 09:54:30 AM
Old 04-23-2014
Tools
Thanks For the reply Frank, it is still not working It is writing the second file as it is in the out put file. It is not appending the data in the record.

Can l you please let me know why are you adding 1 at after the append function?
Code:
awk -F; 'NR==FNR{a[$5]=$4; next} {s=substr($0,13,8)} s in a {$0=$0 a[s]}1' file1 file2

Thanks,
Ajay
Last edited by Scrutinizer; 04-23-2014 at 02:21 PM.. Reason: code tags
 

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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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