<commit_before>#!/usr/bin/env python3

"""

Put some general, high-level documentation here

"""

import argparse
import biocodegff
import biocodeutils
import os
import sys


def main():
    parser = argparse.ArgumentParser( description='Extracts the protein or CDS seqeunces from a GFF3 file')

    ## output file to be written<commit_msg>Added basic documentation<commit_after>#!/usr/bin/env python3

"""

This utility reads an annotated GFF3 file and writes FASTA of different feature types,
either the CDS or protein sequences (protein seqs are translated from the CDS).  In
either case, the genomic FASTA must be available, either embedded at the end of the
GFF3 or as a separate file (passed via -f).

The exported IDs will be the ID attributes of the mRNA features unless these have
locus_tag values in the 9th column.  Also, if the polypeptides associated with each
mRNA have product_name values, that will also be written to the FASTA header.

Author:  <NAME> (jorvis AT gmail)
"""

import argparse
import biocodegff
import biocodeutils
import os
import sys


def main():
    parser = argparse.ArgumentParser( description='Extracts the protein or CDS seqeunces from a GFF3 file')

    ## output file to be written
{'fraction_non_alphanumeric': 0.05973813420621931, 'fraction_numerical': 0.0057283142389525366, 'mean_word_length': 4.484304932735426, 'pattern_counts': {'":': 0, '<': 4, '<?xml version=': 0, '>': 4, 'https://': 0, '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': '4122070', 'n_tokens_mistral': 366, 'n_tokens_neox': 343, 'n_words': 167}