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| # Copyright 2015 by Gert Hulselmans. All rights reserved. | |
| # This file is part of the Biopython distribution and governed by your | |
| # choice of the "Biopython License Agreement" or the "BSD 3-Clause License". | |
| # Please see the LICENSE file that should have been included as part of this | |
| # package. | |
| """Parse Cluster Buster position frequency matrix files.""" | |
| from Bio import motifs | |
| class Record(list): | |
| """Class to store the information in a Cluster Buster matrix table. | |
| The record inherits from a list containing the individual motifs. | |
| """ | |
| def __str__(self): | |
| """Return a string representation of the motifs in the Record object.""" | |
| return "\n".join(str(motif) for motif in self) | |
| def read(handle): | |
| """Read motifs in Cluster Buster position frequency matrix format from a file handle. | |
| Cluster Buster motif format: http://zlab.bu.edu/cluster-buster/help/cis-format.html | |
| """ | |
| motif_nbr = 0 | |
| record = Record() | |
| nucleotide_counts = {"A": [], "C": [], "G": [], "T": []} | |
| motif_name = "" | |
| for line in handle: | |
| line = line.strip() | |
| if line: | |
| if line.startswith(">"): | |
| if motif_nbr != 0: | |
| motif = motifs.Motif(alphabet="GATC", counts=nucleotide_counts) | |
| motif.name = motif_name | |
| record.append(motif) | |
| motif_name = line[1:].strip() | |
| nucleotide_counts = {"A": [], "C": [], "G": [], "T": []} | |
| motif_nbr += 1 | |
| else: | |
| if line.startswith("#"): | |
| continue | |
| matrix_columns = line.split() | |
| if len(matrix_columns) == 4: | |
| [ | |
| nucleotide_counts[nucleotide].append(float(nucleotide_count)) | |
| for nucleotide, nucleotide_count in zip( | |
| ["A", "C", "G", "T"], matrix_columns | |
| ) | |
| ] | |
| motif = motifs.Motif(alphabet="GATC", counts=nucleotide_counts) | |
| motif.name = motif_name | |
| record.append(motif) | |
| return record | |
| def write(motifs): | |
| """Return the representation of motifs in Cluster Buster position frequency matrix format.""" | |
| lines = [] | |
| for m in motifs: | |
| line = f">{m.name}\n" | |
| lines.append(line) | |
| for ACGT_counts in zip( | |
| m.counts["A"], m.counts["C"], m.counts["G"], m.counts["T"] | |
| ): | |
| lines.append("{:0.0f}\t{:0.0f}\t{:0.0f}\t{:0.0f}\n".format(*ACGT_counts)) | |
| # Finished; glue the lines together. | |
| text = "".join(lines) | |
| return text | |