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        "author": "Kent Kawashima",
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        "description": "# alignmentrs\n\nQuickly read and manipulate multiple sequence alignments in Python\n\n## Installation\n\n    pip install alignmentrs\n\n## Quickstart\n\n### Import alignment into Python\n```python\n>>> import alignmentrs as rs\n>>> aln = rs.Alignment.from_fasta('hiv.fna', 'HIV_alignment')\n>>> aln\nAlignment(nsamples=10, nsites=120, nmarkers=0)\n>>> aln.sample_ids\n['sample01', 'sample02', 'sample03', 'sample04', 'sample05', 'sample06'\n 'sample07', 'sample08', 'sample09', 'sample10']\n```\n\n### Select sites to remove from the alignment\n```python\n>>> sites_to_remove = [i for i in range(120) if (i-2) % 3 != 0]  # remove 1st and 2nd position in codon triplet\n>>> aln.remove_sites(sites_to_remove, copy=False)  # manipulate inplace, copy=True returns a new copy\nAlignment(nsamples=10, nsites=40, nmarkers=0)\n```\n\n### Select sites to retain in the alignment\n```python\n>>> sites_to_retain = list(range(2, 3, 120))  # third position in codon triplet\n>>> aln.retain_sites(sites_to_retain, copy=False)  # manipulate inplace, copy=True returns a new copy\nAlignment(nsamples=10, nsites=40, nmarkers=0)\n```\n\n### Get a subset of samples and sites\n```python\n>>> sub_aln = aln.subset(samples=['sample01', 'sample03', 'sample05'], sites=list(range(2, 3, 120)))\n>>> sub_aln\nAlignment(nsamples=3, nsites=40, nmarkers=0)\n```\n\n## License\n\n[MIT License](https://github.com/kentwait/alignmentrs/blob/master/LICENSE)\n\n\n\n",
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