def deprecated_map_to_precursors(seqs, names, loci, out_file, args):
with make_temp_directory() as temp:<EOL><INDENT>pre_fasta = os.path.join(temp, "<STR_LIT>")<EOL>seqs_fasta = os.path.join(temp, "<STR_LIT>")<EOL>out_sam = os.path.join(temp, "<STR_LIT>")<EOL>pre_fasta = get_loci_fasta(loci, pre_fasta, args.ref)<EOL>out_precursor_file = out_file.replace("<STR_LIT>", "<STR_LIT>")<EOL>seqs_fasta = get_seqs_fasta(seqs, names, seqs_fasta)<EOL>if find_cmd("<STR_LIT>"):<EOL><INDENT>cmd = "<STR_LIT>"<EOL>run(cmd.format(**locals()))<EOL>cmd = "<STR_LIT>"<EOL>run(cmd.format(**locals()))<EOL>out_file = read_alignment(out_sam, loci, seqs, out_file)<EOL>shutil.copy(pre_fasta, out_precursor_file)<EOL><DEDENT><DEDENT>return out_file<EOL>
map sequences to precursors with bowtie