https://github.com/deprekate/breseq_tools
A script to count the number of SPSs per gene
https://github.com/deprekate/breseq_tools
breseq snps
Last synced: about 2 months ago
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A script to count the number of SPSs per gene
- Host: GitHub
- URL: https://github.com/deprekate/breseq_tools
- Owner: deprekate
- License: gpl-3.0
- Created: 2020-04-24T21:27:14.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2020-05-30T01:59:24.000Z (over 5 years ago)
- Last Synced: 2025-03-23T00:41:17.111Z (7 months ago)
- Topics: breseq, snps
- Language: Python
- Size: 68.4 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
e breseq_tools
## snp_count
A script to count the number of SPSs per gene
Example
Run on included sample data:
```sh
$ python3 count_snps.py index.html | head
GENE SNPS
AMNIBMGE_00001 28.0
intergenic 335
AMNIBMGE_00003 11.0
AMNIBMGE_00004 6.0
AMNIBMGE_00006 13.0
AMNIBMGE_00007 1.0
AMNIBMGE_00008 10.0
AMNIBMGE_00009 44.0
AMNIBMGE_00010 3.0
```
## mask_false_positives
A script to remove the SNPs already present at timepoint zero from subsequent later timepoints
Example
Run on included sample data:
```sh
$ python3 mask_false_positves.py FALSE_POSITVE_DIR TO_BE_MASKED_DIR
```