/usr/lib/python2.7/dist-packages/cogent/parse/gbseq.py is in python-cogent 1.9-9.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 | #!/usr/bin/env python
"""Parser for NCBI Sequence Set XML format.
DOCTYPE Bioseq-set PUBLIC "-//NCBI//NCBI Seqset/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_Seqset.dtd"
"""
import xml.dom.minidom
from cogent.core import annotation, moltype
__author__ = "Matthew Wakefield"
__copyright__ = "Copyright 2007-2016, The Cogent Project"
__credits__ = ["Matthew Wakefield", "Peter Maxwell", "Gavin Huttley",
"Rob Knight"]
__license__ = "GPL"
__version__ = "1.9"
__maintainer__ = "Matthew Wakefield"
__email__ = "wakefield@wehi.edu.au"
__status__ = "Production"
"""
CAUTION:
This XML PARSER uses minidom. This means a bad performance for
big files (>5MB), and huge XML files will for sure crash the program!
"""
def GbSeqXmlParser(doc):
"""Parser for NCBI Sequence Set XML format.
DOCTYPE Bioseq-set PUBLIC "-//NCBI//NCBI Seqset/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_Seqset.dtd"
Arguments:
- doc: An xml.dom.minidom.Document, file object of string
Yields:
- name, cogent sequence
CAUTION:
This XML PARSER uses minidom. This means a bad performance for
big files (>5MB), and huge XML files will for sure crash the program!
"""
if isinstance(doc,xml.dom.minidom.Document):
dom_obj = doc
elif isinstance(doc,file):
dom_obj = xml.dom.minidom.parse(doc)
elif isinstance(doc,str):
dom_obj = xml.dom.minidom.parseString(doc)
else:
raise TypeError
for record in dom_obj.getElementsByTagName('GBSeq'):
raw_seq = record.getElementsByTagName(
'GBSeq_sequence')[0].childNodes[0].nodeValue
name = record.getElementsByTagName(
'GBSeq_accession-version')[0].childNodes[0].nodeValue
#cast as string to de-unicode
raw_string = str(raw_seq).upper()
name=str(name)
if record.getElementsByTagName(
'GBSeq_moltype')[0].childNodes[0].nodeValue == u'9':
alphabet = moltype.PROTEIN
else:
alphabet = moltype.DNA
seq = alphabet.makeSequence(raw_string, Name=name)
all = annotation.Map([(0,len(seq))], parent_length=len(seq))
seq.addAnnotation(annotation.Source, all, name, all)
organism = str(record.getElementsByTagName(
'GBSeq_organism')[0].childNodes[0].nodeValue)
seq.addAnnotation(annotation.Feature, "organism", organism, [(0,len(seq))])
features = record.getElementsByTagName('GBFeature')
for feature in features:
key = str(feature.getElementsByTagName(
'GBFeature_key')[0].childNodes[0].nodeValue)
if key == 'source':
continue
spans = []
feature_name = ""
for interval in feature.getElementsByTagName("GBInterval"):
try:
start = int(interval.getElementsByTagName(
"GBInterval_from")[0].childNodes[0].nodeValue)
end= int(interval.getElementsByTagName(
"GBInterval_to")[0].childNodes[0].nodeValue)
spans.append((start-1, end))
except IndexError:
point = int(interval.getElementsByTagName(
"GBInterval_point")[0].childNodes[0].nodeValue)
spans.append((point-1, point))
if spans == []:
spans = [(0,len(seq))]
for qualifier in feature.getElementsByTagName("GBQualifier"):
qname = qualifier.getElementsByTagName(
"GBQualifier_name")[0].childNodes[0].nodeValue
if qname == u'gene':
feature_name = qualifier.getElementsByTagName(
"GBQualifier_value")[0].childNodes[0].nodeValue
seq.addAnnotation(annotation.Feature, key, feature_name, spans)
yield (name, seq)
def parse(*args):
return GbSeqXmlParser(*args).next()[1]
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