<commit_before>#MSAOnt Population Software
------
This software generates an instance of the multiple sequence alignment ontology
(MSAOnt) from an aligned fasta or cma file.

Requires Python version 2.7

License: MIT

#Python dependencies
------
Please ensure the following Python packages are installed via ``pip``:
- `Biopython <http://biopython.org/wiki/Main_Page>`
- `RDFLib <https://github.com/RDFLib/rdflib>`
- `progress <https://pypi.python.org/pypi/progress>`
- `biocma <https://github.com/etal/biocma>`

#Note
------
If you are populating MSAOnt with a cma file, the first sequence must be an 
aligned consensus (with no deletions).
<commit_msg>Edited README for clarity.<commit_after>#MSAOnt Population Software
------
This software generates an instance of the multiple sequence alignment ontology
(MSAOnt) from an aligned fasta or cma file.

Requires Python version 2.7

License: MIT

#Python dependencies
------
Please ensure the following Python packages are installed via ``pip``:
- `Biopython <http://biopython.org/wiki/Main_Page>`
- `RDFLib <https://github.com/RDFLib/rdflib>`
- `progress <https://pypi.python.org/pypi/progress>`
- `biocma <https://github.com/etal/biocma>`

#Note
------
If you are populating MSAOnt with a cma file, the first entry must be an 
aligned gapless consensus sequence.

{'fraction_non_alphanumeric': 0.12547528517110265, 'fraction_numerical': 0.003041825095057034, 'mean_word_length': 4.10077519379845, 'pattern_counts': {'":': 0, '<': 11, '<?xml version=': 0, '>': 11, 'https://': 6, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6754840', 'n_tokens_mistral': 428, 'n_tokens_neox': 402, 'n_words': 140}