def create_features(bam_in, loci_file, reference, out_dir):
lenvec_plus = op.join(out_dir, '<STR_LIT>')<EOL>lenvec_minus = op.join(out_dir, '<STR_LIT>')<EOL>compute_genomic_cmd = ("<STR_LIT>"<EOL>"<STR_LIT>"<EOL>"<STR_LIT>"<EOL>"<STR_LIT>"<EOL>"<STR_LIT>")<EOL>index_genomic_cmd = ("<STR_LIT>"<EOL>"<STR_LIT>")<EOL>genomic_lenvec = op.join(out_dir, '<STR_LIT>')<EOL>feat_len_file = op.join(out_dir, '<STR_LIT>')<EOL>compute_locus_cmd = ("<STR_LIT>"<EOL>"<STR_LIT>"<EOL>"<STR_LIT>"<EOL>"<STR_LIT>"<EOL>"<STR_LIT>"<EOL>"<STR_LIT>")<EOL>cov_S_file = op.join(out_dir, '<STR_LIT>')<EOL>coverage_anti_cmd = ("<STR_LIT>"<EOL>"<STR_LIT>"<EOL>"<STR_LIT>")<EOL>feat_posentropy = op.join(out_dir, '<STR_LIT>')<EOL>entropy_cmd = ("<STR_LIT>"<EOL>"<STR_LIT>"<EOL>"<STR_LIT>")<EOL>with utils.chdir(out_dir):<EOL><INDENT>run(compute_genomic_cmd.format(min_len=min_trimmed_read_len, max_len=max_trimmed_read_len, **locals()), "<STR_LIT>")<EOL>run(index_genomic_cmd.format(lenvec=lenvec_plus), "<STR_LIT>")<EOL>run(index_genomic_cmd.format(lenvec=lenvec_minus), "<STR_LIT>")<EOL>run(compute_locus_cmd.format(min_len=min_trimmed_read_len, max_len=max_trimmed_read_len, **locals()), "<STR_LIT>")<EOL>run(coverage_anti_cmd.format(**locals()), "<STR_LIT>")<EOL>feat_antisense = _order_antisense_column(cov_S_file, min_trimmed_read_len)<EOL>counts_reads = _reads_per_position(bam_in, loci_file, out_dir)<EOL>run(entropy_cmd.format(**locals()), "<STR_LIT>")<EOL>rnafold = calculate_structure(loci_file, reference)<EOL><DEDENT>
Use feature extraction module from CoRaL