4.1.1. make_pairs.py¶
Make the pairs of genes for a species.
For each pair, fetch the Hi-C values for two bins where the TSS are located. Also check the adjacency of the genes. If wanted, the Hi-C matrices can be scrambled in-memory before use. This feature uses two functions written by Krister SWENSON for the locality program.
The result is a TSV file, optionally Gzipped (if the file name has the extension .gz). The file has no header and the following columns:
- gene 1 name (string)
- gene 2 name (string)
- Hi-C value (64 bits float)
- Adjacency status (either True or False, case-insensitive)
| created: | May 2018 |
|---|---|
| last modified: | July 2018 |
4.1.1.1. Usage¶
Make the pairs of genes for a species.
usage: make_pairs.py [-h] [-N] [-i] [-s] [-v] [--debug] genes hic output
4.1.1.1.1. Positional Arguments¶
| genes | the genes, in BED |
| hic | the directory with the Hi-C sparses matrices |
| output | explicit enough; can be gzipped |
4.1.1.1.2. Named Arguments¶
| -N, --no-nan | skip the pair if the Hi-C value is Not-a-Number Default: False |
| -i, --intra | only look at genes on the same chromosomes; if not set and there is no interchromosomal values, Not-a-Number is used Default: False |
| -s, --scramble | Scramble in-memory the Hi-C matrices before use Default: False |
| -v, --verbose | be verbose Default: False |
| --debug | print debug information Default: False |