Biodiff
A bioinformatics program to compare two data files and output
Program:
This program can find differences between two files containing bioinformatics data.
If provided two files A (from-file) and B (to-file), program will generate all lines
in A-B, A&B_A, A&B_B and B-A in terms of the criteria given. The file format of
file A and B can be different.
There will be two styles for comparison: one is coordinate based (option –c ) and
the other is name based (option –n). The default style is option -c.
The two styles were described as follows.
1) Coordinate-based diff. Two or more columns from file A and B will be selected and
compared to check if the two regions overlap. If two regions from the two files overlap,
then these two regions will be put into to A&B_A and A&B_B; those regions in A but not
in A&B will be put into A-B; and those in B but not in A&B will be put into B-A.
2) Name-based diff. Two columns from file A and B will be selected and compared in terms
of string comparison. Users need to specify the column numbers in two files to be compared.
If their names “overlap”, it should generate 4 result files corresponding to A&B_A, A&B_B,
A-B, and B-A, where A&B_A contains those lines from file A and overlapping with some entries
in file B; A&B_B contains lines from file B and overlapping with entries in file A; A-B
contains those lines from file A and with no overlapping entries in B; and B-A stands for
those lines from file B but with no overlapping entries in A.
Usage:
This program can be used by following code when execute:
./Biodiff [options] from-file to-file
In which,
option --- the option you choose. See also OPTION in Reference
from-file, to-file --- the absolute or relative path to the two files
Reference:
OPTION:
-c output according to coordinate-based diff
-n output according to name-based diff
-a specify the criteria of from-file(following by the criteria)
-b specify the criteria of to-file(following by the criteria)
-h get the help of this program
Example:
./Biodiff -a 3,4 -b 3,4 geneA.gtf geneB.gtf
./Biodiff -c -a 3,4 -b 3,4 geneA.gtf geneB.gtf
./Biodiff -n -a 0 -b 8 geneA.gtf geneB.gtf
Author:
Zhang