07-02-2012
Printing lines with non-redundant itens in the output
Hi all,
I'm trying to select lines of a file and at the end do not have redundant itens:
Input
A_B
K_A
C_T
A_O
U_B
P_C
D_F
Z_G
W_U
Output
A_B
C_T
D_F
Z_G
W_U
Note: You can see that the output does not have the itens K_A, A_O, U_B and P_C because A, B and C were present at least one time in output. Moreover, the W_U is present because U is combined with W and B, but in the later case the letter B was alread present in the output. In other words, each item must be present just one time in the output.
I tried a lot of things, but I was not able to rigth this script.
Regards
V
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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)