<commit_before>#!/usr/bin/env python3
# -*- coding: utf-8 -*-

import os
import sys
import argparse
import statistics
import subprocess
import time
import logging


# Create logger
logger = logging.getLogger(__name__)

# Get program filename
program_filename = os.path.basename(sys.argv[0])

# Get MATAM root dir absolute path
matam_assembly_bin = os.path.realpath(sys.argv[0])
matam_bin_dir = os.path.dirname(matam_assembly_bin)
matam_root_dir = os.path.dirname(matam_bin_dir)
matam_db_dir = os.path.join(matam_root_dir, 'db')

# Set default ref db
default_ref_db = os.path.join(matam_db_dir, 'SILVA_128_SSURef_rdNs_NR95')

# Get all dependencies bin
matam_script_dir = os.path.join(matam_root_dir, 'scripts')
clean_name_bin = os.path.join(matam_script_dir, 'fasta_clean_name.py')
filter_sam_cov_bin = os.path.join(matam_script_dir, 'fasta_clean_name.py')
filter_score_bin = os.path.join(matam_script_dir, 'filter_score_multialign.py')
compute_lca_bin = os.path.join(matam_script_dir, 'compute_lca_from_tab.py')
compute_compressed_graph_stats_bin = os.path.join(matam_script_dir, 'compute_compressed_graph_stats.py')
sga_assemble_bin = os.path.join(matam_script_dir, 'sga_assemble.py')
remove_redundant_bin = os.path.join(matam_script_dir, 'remove_redundant_sequences.py')
fastq_name_filter_bin = os.path.join(matam_script_dir, 'fastq_name_filter.py')
evaluate_assembly_bin = os.path.join(matam_script_dir, 'evaluate_assembly.py')
get_best_matches_bin = os.path.join(matam_script_dir, 'get_best_matches_from_blast.py')
gener_scaff_blast_bin = os.path.join(matam_script_dir, 'generate_scaffolding_blast.py')
filter_sam_blast_bin = os.path.join(matam_script_dir, 'filter_sam_based_on_blast.py')
compute_contigs_compatibility_bin = os.path.join(matam_script_dir, 'compute_contigs_compatibility.py')
scaffold_contigs_bin = os.path.join(matam_script_dir, 'scaffold_contigs.py')
fasta_length_filter_bin = os.path.join(matam_script_dir, 'fasta_length_filter.py')
<commit_msg>Corrected small bug<commit_after>#!/usr/bin/env python3
# -*- coding: utf-8 -*-

import os
import sys
import argparse
import statistics
import subprocess
import time
import logging


# Create logger
logger = logging.getLogger(__name__)

# Get program filename
program_filename = os.path.basename(sys.argv[0])

# Get MATAM root dir absolute path
matam_assembly_bin = os.path.realpath(sys.argv[0])
matam_bin_dir = os.path.dirname(matam_assembly_bin)
matam_root_dir = os.path.dirname(matam_bin_dir)
matam_db_dir = os.path.join(matam_root_dir, 'db')

# Set default ref db
default_ref_db = os.path.join(matam_db_dir, 'SILVA_128_SSURef_rdNs_NR95')

# Get all dependencies bin
matam_script_dir = os.path.join(matam_root_dir, 'scripts')
clean_name_bin = os.path.join(matam_script_dir, 'fasta_clean_name.py')
filter_sam_cov_bin = os.path.join(matam_script_dir, 'filter_sam_by_coverage.py')
filter_score_bin = os.path.join(matam_script_dir, 'filter_score_multialign.py')
compute_lca_bin = os.path.join(matam_script_dir, 'compute_lca_from_tab.py')
compute_compressed_graph_stats_bin = os.path.join(matam_script_dir, 'compute_compressed_graph_stats.py')
sga_assemble_bin = os.path.join(matam_script_dir, 'sga_assemble.py')
remove_redundant_bin = os.path.join(matam_script_dir, 'remove_redundant_sequences.py')
fastq_name_filter_bin = os.path.join(matam_script_dir, 'fastq_name_filter.py')
evaluate_assembly_bin = os.path.join(matam_script_dir, 'evaluate_assembly.py')
get_best_matches_bin = os.path.join(matam_script_dir, 'get_best_matches_from_blast.py')
gener_scaff_blast_bin = os.path.join(matam_script_dir, 'generate_scaffolding_blast.py')
filter_sam_blast_bin = os.path.join(matam_script_dir, 'filter_sam_based_on_blast.py')
compute_contigs_compatibility_bin = os.path.join(matam_script_dir, 'compute_contigs_compatibility.py')
scaffold_contigs_bin = os.path.join(matam_script_dir, 'scaffold_contigs.py')
fasta_length_filter_bin = os.path.join(matam_script_dir, 'fasta_length_filter.py')

{'fraction_non_alphanumeric': 0.10683544303797468, 'fraction_numerical': 0.004556962025316456, 'mean_word_length': 8.38479809976247, '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': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '1847266', 'n_tokens_mistral': 1543, 'n_tokens_neox': 1513, 'n_words': 204}