<commit_before>from unittest import TestCase, main

from skbio.util import get_data_path

from microprot.scripts.pdb_search import is_overlapping, \
                                         _parse_hit_summary_line, \
                                         _parse_hit_block, parse_pdb_match, \
                                         select_hits, report_hits, \
                                         report_uncovered_subsequences


class ParsersTests(TestCase):
    def setUp(self):
        self.line_a = ('  3 2cdq_A Aspartokinase; aspartat 100.0 4.1E-58 '
                       '1.1E-62  453.8   0.0  458    1-473    28-496 (510)\n')
        self.true_a = {'No': 3,
                       'Hit': '2cdq_A Aspartokinase; aspartat',
                       'Prob': 100.0,
                       'E-value': 4.1e-58,
                       'P-value': 1.1e-62,
                       'Score': 453.8,
                       'SS': 0.0,
                       'Cols': 458,
                       'Query HMM': '1-473',
                       'Template HMM': '28-496',
                       '#match states': 510,
                       }
        self.line_b = ('    36 1gtm_A Glutamate dehydrogenase  98.8 2.9E-12 '
                       '7.9E-17  126.1   0.0  201  451-679   193-407 (419)\n')
        self.true_b = {'No': 36,
                       'Hit': '1gtm_A Glutamate dehydrogenase',
                       'Prob': 98.8,
                       'E-value': 2.9E-12,
                       'P-value': 7.9E-17,
                       'Score': 126.1,<commit_msg>syntax<commit_after>from unittest import TestCase, main

from skbio.util import get_data_path

from microprot.scripts.pdb_search import (is_overlapping,
                                          _parse_hit_summary_line,
                                          _parse_hit_block, parse_pdb_match,
                                          select_hits, report_hits,
                                          report_uncovered_subsequences)


class ParsersTests(TestCase):
    def setUp(self):
        self.line_a = ('  3 2cdq_A Aspartokinase; aspartat 100.0 4.1E-58 '
                       '1.1E-62  453.8   0.0  458    1-473    28-496 (510)\n')
        self.true_a = {'No': 3,
                       'Hit': '2cdq_A Aspartokinase; aspartat',
                       'Prob': 100.0,
                       'E-value': 4.1e-58,
                       'P-value': 1.1e-62,
                       'Score': 453.8,
                       'SS': 0.0,
                       'Cols': 458,
                       'Query HMM': '1-473',
                       'Template HMM': '28-496',
                       '#match states': 510,
                       }
        self.line_b = ('    36 1gtm_A Glutamate dehydrogenase  98.8 2.9E-12 '
                       '7.9E-17  126.1   0.0  201  451-679   193-407 (419)\n')
        self.true_b = {'No': 36,
                       'Hit': '1gtm_A Glutamate dehydrogenase',
                       'Prob': 98.8,
                       'E-value': 2.9E-12,
                       'P-value': 7.9E-17,
                       'Score': 126.1,
{'fraction_non_alphanumeric': 0.10722311396468699, 'fraction_numerical': 0.08089887640449438, 'mean_word_length': 0.9609817495280051, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 16, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '1538126', 'n_tokens_mistral': 1112, 'n_tokens_neox': 892, 'n_words': 187}