view gbk_to_five_col.py @ 1:1bdd481d5c25 draft

planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c

#!/usr/bin/env python
import BIO_FIX_TOPO  # NOQA
import argparse
import logging
from Bio import SeqIO

logging.basicConfig(level=logging.INFO)
log = logging.getLogger()


# Read in Genbank file and parse features
# Output features into Five Column format

"""
>Feature SeqID
Line 1
    Column 1: Start location (first nucleotide) of a feature
    Column 2: Stop location (last nucleotide) of a feature
    Column 3: Feature name (for example, 'CDS' or 'mRNA' or 'rRNA' or 'gene' or 'exon')
Line2:
    Column 4: Qualifier name (for example, 'product' or 'number' or 'gene' or 'note')
    Column 5: Qualifier value

Repeat for each feature in a seq
Repeat Line 2 for each qualifier in a feature
"""


def gbk_to_5col(genbank):
    """Converts genbank to BankIt five column format"""
    for record in SeqIO.parse(genbank, "genbank"):
        print(">Feature %s" % record.id)
        for feature in record.features:
            if feature.type == "source":
                continue
            else:
                for index, part in enumerate(feature.location.parts):
                    if part.strand > 0:
                        start = int(part.start) + 1
                        end = int(part.end)
                    else:
                        start = int(part.end)
                        end = int(part.start) + 1
                    if index == 0:
                        name = feature.type
                        print("%d\t%d\t%s" % (start, end, name))
                    else:
                        print("%d\t%d" % (start, end))
                for (qualifier, values) in feature.qualifiers.items():
                    for value in values:
                        print("\t\t\t%s\t%s" % (qualifier, value))


if __name__ == "__main__":
    parser = argparse.ArgumentParser(
        description="Convert a Genbank file into five column format"
    )
    parser.add_argument("genbank", type=argparse.FileType("r"), help="Genbank file")

    args = vars(parser.parse_args())
    gbk_to_5col(**args)