/usr/share/pyshared/cogent/parse/tinyseq.py is in python-cogent 1.5.1-2.
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 | #!/usr/bin/env python
"""Parser for NCBI Tiny Seq XML format.
DOCTYPE TSeqSet PUBLIC "-//NCBI//NCBI TSeq/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_TSeq.dtd"
"""
import xml.dom.minidom
from cogent.core import annotation, moltype
__author__ = "Matthew Wakefield"
__copyright__ = "Copyright 2007-2011, The Cogent Project"
__credits__ = ["Matthew Wakefield", "Peter Maxwell", "Gavin Huttley",
"Rob Knight"]
__license__ = "GPL"
__version__ = "1.5.1"
__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 TinyseqParser(doc):
"""Parser for NCBI Tiny Seq XML format.
DOCTYPE TSeqSet PUBLIC "-//NCBI//NCBI TSeq/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_TSeq.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('TSeq'):
raw_seq = record.getElementsByTagName(
'TSeq_sequence')[0].childNodes[0].nodeValue
name = record.getElementsByTagName(
'TSeq_accver')[0].childNodes[0].nodeValue
#cast as string to de-unicode
raw_string = str(raw_seq).upper()
name=str(name)
if record.getElementsByTagName(
'TSeq_seqtype')[0].getAttribute('value') == u'protein':
alphabet = moltype.PROTEIN
else:
alphabet = moltype.DNA
seq = alphabet.makeSequence(raw_string, Name=name)
seq.addAnnotation(annotation.Feature, "genbank_id", name, [(0,len(seq))])
organism = str(record.getElementsByTagName(
'TSeq_orgname')[0].childNodes[0].nodeValue)
seq.addAnnotation(annotation.Feature, "organism", organism, [(0,len(seq))])
yield (name, seq)
def parse(*args):
return TinyseqParser(*args).next()[1]
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