Renamed project
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bmlsa/aligner.py
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33
bmlsa/aligner.py
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from skbio.alignment import StripedSmithWaterman
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from datatypes import Annotation
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def generate_annotated_positions(sequence: str, annotations: dict[str, Annotation]):
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annotation_pairs = {}
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align = StripedSmithWaterman(sequence)
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for id, annot in annotations.items():
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alignment = align(annot.sequence)
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score, aligned_start, aligned_end = (
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alignment.optimal_alignment_score,
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alignment.query_begin,
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alignment.query_end,
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)
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annotation_pairs[id] = Annotation(
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id,
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annot.sequence,
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annot.name,
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annot.description,
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annot.start,
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annot.end,
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annot.score,
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), Annotation(
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id,
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alignment.aligned_target_sequence,
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annot.name,
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annot.description,
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aligned_start,
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aligned_end,
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score,
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)
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return annotation_pairs
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94
bmlsa/cli.py
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94
bmlsa/cli.py
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@ -0,0 +1,94 @@
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import os
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import argparse
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from Bio import SeqIO
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from aligner import generate_annotated_positions
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from persistence import read_annotations_from_csv, save_alignments_to_csv
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def main():
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argparser = argparse.ArgumentParser("blmsa")
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argparser.add_argument(
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"annotations",
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type=str,
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help=(
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"Path to CSV containing the sequences to align as well as the "
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"annotations for the respective sequences"
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),
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metavar="a",
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)
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argparser.add_argument(
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"sequence",
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type=str,
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help=(
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"Path to the sequence to annotate in FASTA format. "
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"If multiple sequences are present, annotations will be run on each"
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),
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metavar="s",
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)
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argparser.add_argument(
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"output", type=str, help="Path to output location", metavar="o"
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)
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argparser.add_argument(
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"-I", "--id-header", type=str, help="The header for the ID of the annotation"
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)
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argparser.add_argument(
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"-N",
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"--name-header",
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type=str,
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help="The header for the name of the annotation",
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required=False,
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)
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argparser.add_argument(
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"-D",
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"--desc-header",
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type=str,
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help="The header for the description of the annotation",
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required=False,
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)
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argparser.add_argument(
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"-T",
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"--start-header",
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type=str,
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help="The header for the start of the annotation",
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required=False,
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)
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argparser.add_argument(
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"-E",
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"--end-header",
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type=str,
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help="The header for the end of the annotation",
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required=False,
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)
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argparser.add_argument(
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"-S",
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"--seq-header",
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type=str,
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help="The header for the sequence of the annotation",
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)
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args = argparser.parse_args()
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given_annotations = read_annotations_from_csv(
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args.annotations,
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args.id_header,
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args.name_header,
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args.desc_header,
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args.start_header,
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args.end_header,
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args.seq_header,
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)
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with open(args.sequence, "r") as sequence_fd:
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for sequence in SeqIO.parse(sequence_fd, "fasta"):
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aligned_annotations = generate_annotated_positions(
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str(sequence.seq), given_annotations
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)
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save_alignments_to_csv(
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aligned_annotations,
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os.path.join(
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args.output,
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sequence.id.replace("|", "+").replace(".", "_") + ".csv",
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),
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)
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if __name__ == "__main__":
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main()
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70
bmlsa/persistence.py
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70
bmlsa/persistence.py
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import csv
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from datatypes import Annotation
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def read_annotations_from_csv(
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csv_path: str,
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id_header: str,
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name_header: str,
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desc_header: str,
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start_header: str,
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end_header: str,
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sequence_header: str,
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):
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annotations = {}
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with open(csv_path, "r") as csv_fd:
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reader = csv.reader(csv_fd)
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id_ind = None
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name_ind = None
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desc_ind = None
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start_ind = None
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end_ind = None
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sequence_ind = None
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headers_parsed = False
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for row in reader:
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if not headers_parsed:
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id_ind = row.index(id_header)
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name_ind = row.index(name_header) if name_header else None
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desc_ind = row.index(desc_header) if desc_header else None
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start_ind = row.index(start_header) if start_header else None
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end_ind = row.index(end_header) if end_header else None
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sequence_ind = row.index(sequence_header)
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headers_parsed = True
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continue
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id = row[id_ind]
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name = row[name_ind] if name_header else None
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desc = row[desc_ind] if desc_header else None
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start = row[start_ind] if start_header else None
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end = row[end_ind] if end_header else None
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sequence = row[sequence_ind]
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annotations[id] = Annotation(
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id,
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sequence,
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name,
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desc,
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int(start) if start else None,
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int(end) if end else None,
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)
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return annotations
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def save_alignments_to_csv(
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aligned_pairs: dict[str, tuple[Annotation, Annotation]], output_path: str
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):
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with open(output_path, "w") as output_fd:
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writer = csv.writer(output_fd)
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header_wrote = False
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header_order = None
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for id, annotations in aligned_pairs.items():
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original, aligned = annotations
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original_vars = vars(original)
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aligned_vars = vars(aligned)
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if not header_wrote:
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header_order = list(original_vars.keys())
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header = ["original" + key for key in header_order]
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header.extend(["aligned" + key for key in header_order])
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writer.writerow(header)
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header_wrote = True
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row_data = [original_vars[header] for header in header_order]
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row_data.extend([aligned_vars[header] for header in header_order])
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writer.writerow(row_data)
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@ -1,193 +0,0 @@
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import csv
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import os
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from skbio.alignment import StripedSmithWaterman
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import argparse
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from Bio import SeqIO
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from Datatypes import Annotation
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def read_annotations_from_csv(
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csv_path: str,
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id_header: str,
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name_header: str,
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desc_header: str,
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start_header: str,
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end_header: str,
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sequence_header: str,
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):
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annotations = {}
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with open(csv_path, "r") as csv_fd:
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reader = csv.reader(csv_fd)
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id_ind = None
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name_ind = None
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desc_ind = None
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start_ind = None
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end_ind = None
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sequence_ind = None
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headers_parsed = False
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for row in reader:
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if not headers_parsed:
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id_ind = row.index(id_header)
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name_ind = row.index(name_header) if name_header else None
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desc_ind = row.index(desc_header) if desc_header else None
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start_ind = row.index(start_header) if start_header else None
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end_ind = row.index(end_header) if end_header else None
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sequence_ind = row.index(sequence_header)
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headers_parsed = True
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continue
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id = row[id_ind]
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name = row[name_ind] if name_header else None
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desc = row[desc_ind] if desc_header else None
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start = row[start_ind] if start_header else None
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end = row[end_ind] if end_header else None
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sequence = row[sequence_ind]
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annotations[id] = Annotation(
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id,
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sequence,
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name,
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desc,
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int(start) if start else None,
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int(end) if end else None,
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)
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return annotations
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def generate_annotated_positions(sequence: str, annotations: dict[str, Annotation]):
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annotation_pairs = {}
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align = StripedSmithWaterman(sequence)
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for id, annot in annotations.items():
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alignment = align(annot.sequence)
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score, aligned_start, aligned_end = (
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alignment.optimal_alignment_score,
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alignment.query_begin,
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alignment.query_end,
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)
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annotation_pairs[id] = Annotation(
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id,
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annot.sequence,
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annot.name,
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annot.description,
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annot.start,
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annot.end,
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annot.score,
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), Annotation(
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id,
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alignment.aligned_target_sequence,
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annot.name,
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annot.description,
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aligned_start,
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aligned_end,
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score,
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)
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return annotation_pairs
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def save_alignments_to_csv(
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aligned_pairs: dict[str, tuple[Annotation, Annotation]], output_path: str
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):
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with open(output_path, "w") as output_fd:
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writer = csv.writer(output_fd)
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header_wrote = False
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header_order = None
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for id, annotations in aligned_pairs.items():
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original, aligned = annotations
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original_vars = vars(original)
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aligned_vars = vars(aligned)
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if not header_wrote:
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header_order = list(original_vars.keys())
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header = ["original" + key for key in header_order]
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header.extend(["aligned" + key for key in header_order])
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writer.writerow(header)
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header_wrote = True
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row_data = [original_vars[header] for header in header_order]
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row_data.extend([aligned_vars[header] for header in header_order])
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writer.writerow(row_data)
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def main():
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argparser = argparse.ArgumentParser("protannot")
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argparser.add_argument(
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"annotations",
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type=str,
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help=(
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"Path to CSV containing the sequences to align as well as the "
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"annotations for the respective sequences"
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),
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metavar="a",
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)
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argparser.add_argument(
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"sequence",
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type=str,
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help=(
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"Path to the sequence to annotate in FASTA format. "
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"If multiple sequences are present, annotations will be run on each"
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),
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metavar="s",
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)
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argparser.add_argument(
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"output", type=str, help="Path to output location", metavar="o"
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)
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argparser.add_argument(
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"-I", "--id-header", type=str, help="The header for the ID of the annotation"
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)
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argparser.add_argument(
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"-N",
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"--name-header",
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type=str,
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help="The header for the name of the annotation",
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required=False,
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)
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argparser.add_argument(
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"-D",
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"--desc-header",
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type=str,
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help="The header for the description of the annotation",
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required=False,
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)
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argparser.add_argument(
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"-T",
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"--start-header",
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type=str,
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help="The header for the start of the annotation",
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required=False,
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)
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argparser.add_argument(
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"-E",
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"--end-header",
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type=str,
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help="The header for the end of the annotation",
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required=False,
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)
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argparser.add_argument(
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"-S",
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"--seq-header",
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type=str,
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help="The header for the sequence of the annotation",
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)
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args = argparser.parse_args()
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given_annotations = read_annotations_from_csv(
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args.annotations,
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args.id_header,
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args.name_header,
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args.desc_header,
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args.start_header,
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args.end_header,
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args.seq_header,
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)
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with open(args.sequence, "r") as sequence_fd:
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for sequence in SeqIO.parse(sequence_fd, "fasta"):
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aligned_annotations = generate_annotated_positions(
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str(sequence.seq), given_annotations
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)
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save_alignments_to_csv(
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aligned_annotations,
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os.path.join(
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args.output,
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sequence.id.replace("|", "+").replace(".", "_") + ".csv",
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),
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)
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if __name__ == "__main__":
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main()
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