33 lines
1.7 KiB
Markdown
33 lines
1.7 KiB
Markdown
[](https://ci.reslate.systems/job/ydeng/job/bmlsa/job/master/)
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# BMLSA
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A Basic multi local sequence alignment tool using the Biopython implementation of the Smith-Waterman alignment algorithm. May be used as a python library, or as a full command line interface.
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## Features
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- Aligns a CSV of short sequences locally to a given reference sequence
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- Outputs in a CSV with old and new positions
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- Selectable parameters for alignment
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- Compatible with broad-range of input CSV formats
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- Automatically align with all sequences in reference FASTA
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- All produced output is human readable!
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## Install via `pip`
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Just run `pip install --index-url https://git.reslate.systems/api/packages/ydeng/pypi/simple/ bmlsa` in a console that is capable of running `pip`!
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## CLI Demo from Git Repo
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Resources have been provided in this package for CI purposes, but you may use them to try out the program yourself!
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1. Install the program
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2. clone this repository
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3. Change into the cloned repository directory
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4. Run `bmlsa -I id -S sequence -B BLASTp tests/resources/SARS_CoV-2_genes.csv tests/resources/NC_045512_coding.fasta ./output/`
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The results will show up in a `output` folder (which will be generated if it doesn't exist). Use `bmlsa -h` to see what each part of the above command does!
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## More Information
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For all live downloadable artifacts, build statuses, unit test results, and documentation, check out the continuous integration page for the [master branch](https://ci.reslate.systems/job/ydeng/job/bmlsa/job/master/) ([development branch](https://ci.reslate.systems/job/ydeng/job/bmlsa/job/develop/)). |