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
Metadata
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 | Provenance | Actions |
|---|---|---|---|---|
| filtersam-0.0.11.tar.gz | 11.2 kB | Without provenance | Details for filtersam-0.0.11.tar.gz |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Actions Reset |
|---|---|---|---|---|
| filtersam-0.0.11-py3-none-any.whl | Python 3 | none | any | Details for filtersam-0.0.11-py3-none-any.whl |
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 |
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BLAKE2b-256 checksum How to use checksums |
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|
| 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 |
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|
|
BLAKE2b-256 checksum How to use checksums |
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|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.1 CPython/3.9.7
|
Security for filtersam 0.0.11
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