A Python tool to filter sam/bam files by percent identity or percent of matched sequence
Percent identity is computed as:
$$PI = 100 \frac{N_m}{N_m + N_i}$$
where $N_m$ is the number of matches and $N_i$ is the number of mismatches.
Percent of matched sequences is computed as:
$$PM = 100 \frac{N_m}{L}$$
where $L$ corresponds to query sequence length.
NOTE
BAM/SAM files must contain MD tags to be able to filter by percent identity. Aligners such as BWA add MD tags to each queried sequence in a BAM file. MD tags can also be generated with samtools.
Installation
pip install filtersam
Usage
You can find a jupyter notebook with usage examples here.
Citation
If you use this software, please cite it as below:
Robaina-Estévez, S. (2022). filterSAM: filter sam/bam files by percent identity or percent of matched sequence (Version 0.0.11)[Computer software]. https://doi.org/10.5281/zenodo.7056278.
1 maintainer
Release files for filtersam 0.0.11
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| filtersam-0.0.11.tar.gz | 11.2 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| filtersam-0.0.11-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 23.3 kB
Release files / filtersam-0.0.11.tar.gz
| Download URL | filtersam-0.0.11.tar.gz |
|---|---|
| Size | 11.2 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
75e9a381e749aef6c606459c4f59ff130209a0af35a03090541bbc474add854a
|
|
BLAKE2b-256 checksum How to use checksums |
51cd8b01e9af04d18f791dc8f943d1e12b104eec79c7f21d1a954abdc0870da1
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.1 CPython/3.9.7
|
Release files / filtersam-0.0.11-py3-none-any.whl
| Download URL | filtersam-0.0.11-py3-none-any.whl |
|---|---|
| Size | 12.1 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
8b963b392ce3cfc7c8521b205c00f69b52e428d4e2c0c91024dfae2eed235d1e
|
|
BLAKE2b-256 checksum How to use checksums |
ab00c3c2ffe65755801ece33b4044f6816eb5d4f1c6d83b146823d7dd86be571
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.1 CPython/3.9.7
|
