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Full Discussion: Comparing two files and creating a new file
Top Forums Shell Programming and Scripting Comparing two files and creating a new file Post 302761213 by begin_shell on Friday 25th of January 2013 10:29:50 AM
Old 01-25-2013
Comparing two files and creating a new file
Hi,

I want to compare two files based on the data in their first column. Both the files are not equal in their number of columns and number of entries or rows.

The entries (only the first column) of the file1 should be compared with the entries (only the first column) of the file2. If the data in the first column matches in both the files, then that data's corresponding row in the file2 should be printed fully into a new file (file3). This should be done as long as the entries in the file1 has been fully compared with the file2

file1
HTML Code:
1    0.25    0.56    0.56   0   55 
5    0.99    0.44    0.89   0   89
7    0.77    0.45    0.75   0   100
file2

HTML Code:
1    0.25    0.56    0.56   0   6.565    6.555    1.589    7.892   70
2    0.88    0.25    0.77   0   6.458    4.215    1.588    7.222   80  
5    0.99    0.44    0.89   0   7.444    5.444    7.444    9.221   90
7    0.77    0.45    0.75   0   4.225    4.256    7.555    2.222   10
8    0.14    0.44    0.78   0   2.457    4.222    8.777    1.454   20
The required output file (file3) should look like:

HTML Code:
1    0.25    0.56    0.56   0   6.565    6.555    1.589    7.892   70
5    0.99    0.44    0.89   0   7.444    5.444    7.444    9.221   90
7    0.77    0.45    0.75   0   4.225    4.256    7.555    2.222   10
Last edited by begin_shell; 01-25-2013 at 11:38 AM..
 

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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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