4.1.2. join_pairs.py¶
This script reads two pairs files (the left one and the right one) made with make_pairs.py and join them based on a list of orthologs.
The result is a data set with 5 columns:
- (str) gene name 1 in species left
- (str) gene name 2 in species left
- (str) gene name 1 in species right
- (str) gene name 2 in species right
- (float) Hi-C value for gene 1 and 2 in species left
- (float) Hi-C value for gene 1 and 2 in species right
This table is written as TSV with no header row, in a Gzipped file.
| created: | May 2018 |
|---|---|
| last modified: | July 2018 |
4.1.2.1. Usage¶
Reads two pairs files (the left one and the right one) and join them based on a list of orthologs.
usage: join_pairs.py [-h] [-t THRESHOLD] [-x] [-a {all,none,and,or,xor}] [-v]
orthos left right outfile
4.1.2.1.1. Positional Arguments¶
| orthos | the orthologs file, can be a pair of species or not (see doc) |
| left | the left pairs file, optionally Gzipped |
| right | the right pairs file, optionally Gzipped |
| outfile | the output file, optionally Gzipped |
4.1.2.1.2. Named Arguments¶
| -t, --threshold | |
| the threshold to apply | |
| -x, --exclude | exclude the pairs with both values lesser than or equal to the threshold Default: False |
| -a, --adjacencies | |
Possible choices: all, none, and, or, xor the adjacencies status to keep Default: “all” | |
| -v, --verbose | be verbose Default: False |