mirror of
https://github.com/biopython/biopython.git
synced 2025-10-20 13:43:47 +08:00
Kozo Nishida
Peter Cock
147
Bio/KEGG/Gene/__init__.py
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147
Bio/KEGG/Gene/__init__.py
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# Copyright 2017 by Kozo Nishida. All rights reserved.
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# This code is part of the Biopython distribution and governed by its
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# license. Please see the LICENSE file that should have been included
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# as part of this package.
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"""Code to work with the KEGG Gene database.
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Functions:
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parse - Returns an iterator giving Record objects.
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Classes:
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Record - A representation of a KEGG Gene.
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"""
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# other Biopython stuff
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from __future__ import print_function
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from Bio.KEGG import _write_kegg
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from Bio.KEGG import _wrap_kegg
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# Set up line wrapping rules (see Bio.KEGG._wrap_kegg)
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name_wrap = [0, "",
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(" ", "$", 1, 1),
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("-", "$", 1, 1)]
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id_wrap = lambda indent: [indent, "", (" ", "", 1, 0)]
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class Record(object):
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"""Holds info from a KEGG Gene record.
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Attributes:
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- entry The entry identifier.
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- name A list of the gene names.
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- definition The definition for the gene.
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- orthology A list of 2-tuples: (orthology id, role)
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- organism A tuple: (organism id, organism)
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- position The position for the gene
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- motif A list of 2-tuples: (database, list of link ids)
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- dblinks A list of 2-tuples: (database, list of link ids)
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"""
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def __init__(self):
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"""Initialize new record."""
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self.entry = ""
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self.name = []
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self.definition = ""
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self.orthology = []
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self.organism = ""
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self.position = ""
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self.motif = []
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self.dblinks = []
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def __str__(self):
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"""Return a string representation of this Record."""
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return self._entry() + \
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self._name() + \
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self._dblinks() + \
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"///"
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def _entry(self):
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return _write_kegg("ENTRY",
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[self.entry])
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def _name(self):
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return _write_kegg("NAME",
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[_wrap_kegg(l, wrap_rule=name_wrap)
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for l in self.name])
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def _definition(self):
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return _write_kegg("DEFINITION",
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[self.definition])
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def _dblinks(self):
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s = []
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for entry in self.dblinks:
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s.append(entry[0] + ": " + " ".join(entry[1]))
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return _write_kegg("DBLINKS",
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[_wrap_kegg(l, wrap_rule=id_wrap(9))
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for l in s])
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def parse(handle):
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"""Parse a KEGG Gene file, returning Record objects.
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This is an iterator function, typically used in a for loop. For
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example, using one of the example KEGG files in the Biopython
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test suite,
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>>> with open("KEGG/gene.sample") as handle:
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... for record in parse(handle):
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... print("%s %s" % (record.entry, record.name[0]))
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...
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b1174 minE
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b1175 minD
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"""
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record = Record()
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for line in handle:
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if line[:3] == "///":
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yield record
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record = Record()
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continue
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if line[:12] != " ":
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keyword = line[:12]
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data = line[12:].strip()
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if keyword == "ENTRY ":
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words = data.split()
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record.entry = words[0]
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elif keyword == "NAME ":
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data = data.strip(";")
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record.name.append(data)
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elif keyword == "DEFINITION ":
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record.definition = data
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elif keyword == "ORTHOLOGY ":
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id, name = data.split(" ")
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orthology = (id, name)
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record.orthology.append(orthology)
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elif keyword == "ORGANISM ":
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id, name = data.split(" ")
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organism = (id, name)
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record.organism = organism
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elif keyword == "POSITION ":
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record.position = data
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elif keyword == "MOTIF ":
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key, values = data.split(": ")
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values = values.split()
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row = (key, values)
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record.motif.append(row)
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elif keyword == "DBLINKS ":
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if ":" in data:
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key, values = data.split(": ")
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values = values.split()
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row = (key, values)
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record.dblinks.append(row)
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else:
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row = record.dblinks[-1]
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key, values = row
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values.extend(data.split())
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row = key, values
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record.dblinks[-1] = row
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if __name__ == "__main__":
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from Bio._utils import run_doctest
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run_doctest()
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80
Tests/KEGG/gene.sample
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80
Tests/KEGG/gene.sample
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@ -0,0 +1,80 @@
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ENTRY b1174 CDS T00007
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NAME minE
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DEFINITION (RefSeq) cell division topological specificity factor
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ORTHOLOGY K03608 cell division topological specificity factor
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ORGANISM eco Escherichia coli K-12 MG1655
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BRITE Chromosome [BR:eco03036]
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Prokaryotic Type
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Chromosome partitioning proteins
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Inhibitors of FtsZ assembly
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b1174 (minE)
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Cytoskeleton proteins [BR:eco04812]
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Prokaryotic cytoskeleton proteins
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MinD / ParA class of bacterial cytoskeletal proteins
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b1174 (minE)
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POSITION complement(1224279..1224545)
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MOTIF Pfam: MinE DUF4364
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DBLINKS NCBI-ProteinID: NP_415692
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NCBI-GeneID: 945740
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Pasteur: minE
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RegulonDB: ECK120000591
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ECOCYC: EG10598
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ASAP: ABE-0003935
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UniProt: P0A734
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STRUCTURE PDB: 3R9I 3R9J 1EV0
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AASEQ 88
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MALLDFFLSRKKNTANIAKERLQIIVAERRRSDAEPHYLPQLRKDILEVICKYVQIDPEM
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VTVQLEQKDGDISILELNVTLPEAEELK
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NTSEQ 267
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atggcattactcgatttctttctctcgcggaagaaaaacacagccaacattgcaaaagaa
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cggctgcagattattgttgctgaacgccgtcgcagcgatgcagaaccgcattatctgccg
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cagttgcgtaaagatattcttgaggtcatttgtaaatacgtacaaattgatcctgagatg
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gtaaccgtacagcttgagcaaaaagatggcgatatttctattcttgagctgaacgtgacc
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ttaccggaagcagaagagctgaaataa
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///
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ENTRY b1175 CDS T00007
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NAME minD
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DEFINITION (RefSeq) inhibitor of FtsZ ring polymerization; chromosome-membrane tethering protein; membrane ATPase of the MinCDEE system
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ORTHOLOGY K03609 septum site-determining protein MinD
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ORGANISM eco Escherichia coli K-12 MG1655
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BRITE Chromosome [BR:eco03036]
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Prokaryotic Type
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Chromosome partitioning proteins
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Inhibitors of FtsZ assembly
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b1175 (minD)
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Cytoskeleton proteins [BR:eco04812]
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Prokaryotic cytoskeleton proteins
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MinD / ParA class of bacterial cytoskeletal proteins
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b1175 (minD)
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POSITION complement(1224549..1225361)
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MOTIF Pfam: CbiA AAA_31 ParA ArsA_ATPase MipZ CBP_BcsQ Fer4_NifH AAA_24 CLP1_P SRP54 VirC1 DUF87
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DBLINKS NCBI-ProteinID: NP_415693
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NCBI-GeneID: 945741
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Pasteur: minD
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RegulonDB: ECK120000590
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ECOCYC: EG10597
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ASAP: ABE-0003938
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UniProt: P0AEZ3
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STRUCTURE PDB: 3Q9L 3R9I 3R9J
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AASEQ 270
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MARIIVVTSGKGGVGKTTSSAAIATGLAQKGKKTVVIDFDIGLRNLDLIMGCERRVVYDF
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VNVIQGDATLNQALIKDKRTENLYILPASQTRDKDALTREGVAKVLDDLKAMDFEFIVCD
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SPAGIETGALMALYFADEAIITTNPEVSSVRDSDRILGILASKSRRAENGEEPIKEHLLL
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TRYNPGRVSRGDMLSMEDVLEILRIKLVGVIPEDQSVLRASNQGEPVILDINADAGKAYA
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DTVERLLGEERPFRFIEEEKKGFLKRLFGG
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NTSEQ 813
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atggcacgcattattgttgttacttcgggcaaagggggtgttggtaagacaacctccagc
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gcggccatcgccactggtttggcccagaagggaaagaaaactgtcgtgatagattttgat
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atcggcctgcgtaatctcgacctgattatgggttgtgaacgccgggtcgtttacgatttc
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gtcaacgtcattcagggcgatgcaacgctaaatcaggcgttaattaaagataagcgtact
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gaaaatctctatattctgccggcatcgcaaacacgcgataaagatgccctcacccgtgaa
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ggggtcgccaaagttcttgatgatctgaaagcgatggattttgaatttatcgtttgtgac
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tccccggcagggattgaaaccggtgcgttaatggcactctattttgcagacgaagccatt
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attaccaccaacccggaagtctcctcagtacgcgactctgaccgtattttaggcattctg
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gcgtcgaaatcacgccgcgcagaaaatggcgaagagcctattaaagagcacctgctgtta
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acgcgctataacccaggccgcgtaagcagaggtgacatgctgagcatggaagatgtgctg
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gagatcctgcgcatcaaactcgtcggcgtgatcccagaggatcaatcagtattgcgcgcc
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tctaaccagggtgaaccggtcattctcgacattaacgccgatgcgggtaaagcctacgca
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gataccgtagaacgtctgttgggagaagaacgtcctttccgcttcattgaagaagagaag
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aaaggcttcctcaaacgcttgttcggaggataa
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///
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@ -102,6 +102,7 @@ DOCTEST_MODULES = [
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"Bio.Graphics.GenomeDiagram._Colors",
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"Bio.KEGG.Compound",
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"Bio.KEGG.Enzyme",
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"Bio.KEGG.Gene",
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"Bio.KEGG.KGML.KGML_parser",
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"Bio.NMR.xpktools",
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"Bio.motifs",
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