Spaces:
No application file
No application file
File size: 5,009 Bytes
b7731cd |
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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 |
# Copyright 2000 by Jeffrey Chang. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Code to work with the prosite.doc file from Prosite.
See https://www.expasy.org/prosite/
Tested with:
- Release 15.0, July 1998
- Release 16.0, July 1999
- Release 20.22, 13 November 2007
- Release 20.43, 10 February 2009
Functions:
- read Read a Prodoc file containing exactly one Prodoc entry.
- parse Iterates over entries in a Prodoc file.
Classes:
- Record Holds Prodoc data.
- Reference Holds data from a Prodoc reference.
"""
def read(handle):
"""Read in a record from a file with exactly one Prodoc record."""
record = __read(handle)
# We should have reached the end of the record by now
line = handle.readline()
if line:
raise ValueError("More than one Prodoc record found")
return record
def parse(handle):
"""Iterate over the records in a Prodoc file."""
while True:
record = __read(handle)
if not record:
return
yield record
class Record:
"""Holds information from a Prodoc record.
Attributes:
- accession Accession number of the record.
- prosite_refs List of tuples (prosite accession, prosite name).
- text Free format text.
- references List of reference objects.
"""
def __init__(self):
"""Initialize the class."""
self.accession = ""
self.prosite_refs = []
self.text = ""
self.references = []
class Reference:
"""Holds information from a Prodoc citation.
Attributes:
- number Number of the reference. (string)
- authors Names of the authors.
- citation Describes the citation.
"""
def __init__(self):
"""Initialize the class."""
self.number = ""
self.authors = ""
self.citation = ""
# Below are private functions
def __read_prosite_reference_line(record, line):
line = line.rstrip()
if line[-1] != "}":
raise ValueError(f"I don't understand the Prosite reference on line\n{line}")
acc, name = line[1:-1].split("; ")
record.prosite_refs.append((acc, name))
def __read_text_line(record, line):
record.text += line
return True
def __read_reference_start(record, line):
# Read the references
reference = Reference()
reference.number = line[1:3].strip()
if line[1] == "E":
# If it's an electronic reference, then the URL is on the
# line, instead of the author.
reference.citation = line[4:].strip()
else:
reference.authors = line[4:].strip()
record.references.append(reference)
def __read_reference_line(record, line):
if not line.strip():
return False
reference = record.references[-1]
if line.startswith(" "):
if reference.authors[-1] == ",":
reference.authors += line[4:].rstrip()
else:
reference.citation += line[5:]
return True
raise Exception(f"I don't understand the reference line\n{line}")
def __read_copyright_line(record, line):
# Skip the copyright statement
if line.startswith("+----"):
return False
return True
def __read(handle):
# Skip blank lines between records
for line in handle:
line = line.rstrip()
if line and not line.startswith("//"):
break
else:
return None
record = Record()
# Read the accession number
if not line.startswith("{PDOC"):
raise ValueError("Line does not start with '{PDOC':\n%s" % line)
if line[-1] != "}":
raise ValueError(f"I don't understand accession line\n{line}")
record.accession = line[1:-1]
# Read the Prosite references
for line in handle:
if line.startswith("{PS"):
__read_prosite_reference_line(record, line)
else:
break
else:
raise ValueError("Unexpected end of stream.")
# Read the actual text
if not line.startswith("{BEGIN"):
raise ValueError("Line does not start with '{BEGIN':\n%s" % line)
read_line = __read_text_line
for line in handle:
if line.startswith("{END}"):
# Clean up the record and return
for reference in record.references:
reference.citation = reference.citation.rstrip()
reference.authors = reference.authors.rstrip()
return record
elif line[0] == "[" and line[3] == "]" and line[4] == " ":
__read_reference_start(record, line)
read_line = __read_reference_line
elif line.startswith("+----"):
read_line = __read_copyright_line
elif read_line:
if not read_line(record, line):
read_line = None
raise ValueError("Unexpected end of stream.")
|