def parse(fileName):
from OpenSave import osOpen
f = osOpen(fileName, "r")
# skip header crap
inHeader = True
lineNum = 0
sequences = []
for line in f:
line = line.strip()
lineNum += 1
if not line:
continue
fields = line.split()
if inHeader:
if len(fields[0]) == 2:
continue
inHeader = False
if len(fields) != 2:
# since this format lacks mandatory headers,
# cannot be sure it _is_ a Pfam file and therefore
# cannot raise FormatSyntaxError
raise WrongFileTypeError()
seq = Sequence(makeReadable(fields[0]))
seq.extend(fields[1])
sequences.append(seq)
f.close()
if not sequences:
raise WrongFileTypeError()
return sequences, {}, {}
def parse(fileName):
from OpenSave import osOpen
f = osOpen(fileName, "r")
# skip header crap
inHeader = True
lineNum = 0
sequences = []
for line in f:
line = line.strip()
lineNum += 1
if not line:
continue
fields = line.split()
if inHeader:
if len(fields[0]) == 2:
continue
inHeader = False
if len(fields) != 2:
# since this format lacks mandatory headers,
# cannot be sure it _is_ a Pfam file and therefore
# cannot raise FormatSyntaxError
raise WrongFileTypeError()
seq = Sequence(makeReadable(fields[0]))
seq.extend(fields[1])
sequences.append(seq)
f.close()
if not sequences:
raise WrongFileTypeError()
return sequences, {}, {}
def parse(fileName):
from OpenSave import osOpen
f = osOpen(fileName, "r")
inSequence = 0
sequences = []
for line in f.readlines():
if inSequence:
if not line or line.isspace():
inSequence = 0
continue
if line[0] == '>':
inSequence = 0
# fall through
else:
sequences[-1].extend(line.strip())
if not inSequence:
if line[0] == '>':
if sequences and len(sequences[-1]) == 0:
raise FormatSyntaxError("No sequence"
" found for %s" % sequences[-1].name)
inSequence = 1
sequences.append(Sequence(makeReadable(
line[1:])))
f.close()
if not sequences:
raise WrongFileTypeError()
return sequences, {}, {}
def parse(fileName):
from OpenSave import osOpen
f = osOpen(fileName, "r")
inHeader = 1
sequences = []
lineNum = 0
for line in f.readlines():
lineNum += 1
if inHeader:
if line.startswith("CLUSTAL"):
inHeader = 0
firstBlock = 1
else:
if line.strip() !="":
raise WrongFileTypeError()
continue
if not line or line[0].isspace():
if sequences:
firstBlock = 0
expect = 0
continue
try:
seqName, seqBlock, numResidues = line.split()
except ValueError:
try:
seqName, seqBlock = line.split()
except ValueError:
raise FormatSyntaxError("Line %d is not "
"sequence name followed by sequence "
" contents and optional ungapped length"
% lineNum)
if firstBlock:
sequences.append(Sequence(makeReadable(seqName)))
sequences[-1].append(seqBlock)
continue
try:
seq = sequences[expect]
except IndexError:
raise FormatSyntaxError("Sequence on line %d not in"
" initial sequence block" % lineNum)
expect += 1
seq.append(seqBlock)
f.close()
if not sequences:
raise WrongFileTypeError()
return sequences, {}, {}
def parse(fileName):
from OpenSave import osOpen
f = osOpen(fileName, "r")
inHeader = 1
sequences = []
lineNum = 0
for line in f.readlines():
lineNum += 1
if inHeader:
if line.startswith("CLUSTAL"):
inHeader = 0
firstBlock = 1
else:
if line.strip() != "":
raise WrongFileTypeError()
continue
if not line or line[0].isspace():
if sequences:
firstBlock = 0
expect = 0
continue
try:
seqName, seqBlock, numResidues = line.split()
except ValueError:
try:
seqName, seqBlock = line.split()
except ValueError:
raise FormatSyntaxError(
"Line %d is not "
"sequence name followed by sequence "
" contents and optional ungapped length" % lineNum)
if firstBlock:
sequences.append(Sequence(makeReadable(seqName)))
sequences[-1].append(seqBlock)
continue
try:
seq = sequences[expect]
except IndexError:
raise FormatSyntaxError("Sequence on line %d not in"
" initial sequence block" % lineNum)
expect += 1
seq.append(seqBlock)
f.close()
if not sequences:
raise WrongFileTypeError()
return sequences, {}, {}
def parse(fileName):
from OpenSave import osOpen
f = osOpen(fileName, "r")
want = 'init'
sequences = []
for line in f.readlines():
line = line.strip()
if want == 'init':
if len(line) < 4:
continue
if line[0] != '>' or line[3] != ';':
continue
sequences.append(Sequence(makeReadable(line[4:])))
pirType = line[1:3]
if pirType in ("P1", "F1"):
sequences[-1].nucleic = 0
else:
sequences[-1].nucleic = 1
sequences[-1].PIRtype = pirType
want = 'descript'
elif want == 'descript':
sequences[-1].descript = line
sequences[-1].PIRdescript = line
want = 'sequence'
elif want == 'sequence':
if not line:
continue
if line[-1] == '*':
want = 'init'
line = line[:-1]
sequences[-1].extend(filter(lambda c,
whsp=string.whitespace: not c in whsp, line))
f.close()
if not sequences:
raise WrongFileTypeError()
if want != 'init':
raise FormatSyntaxError("Could not find end of sequence '%s'"
% sequences[-1].name)
return sequences, {}, {}
def parse(fileName):
from OpenSave import osOpen
f = osOpen(fileName, "r")
want = 'init'
sequences = []
for line in f.readlines():
line = line.strip()
if want == 'init':
if len(line) < 4:
continue
if line[0] != '>' or line[3] != ';':
continue
sequences.append(Sequence(makeReadable(line[4:])))
pirType = line[1:3]
if pirType in ("P1", "F1"):
sequences[-1].nucleic = 0
else:
sequences[-1].nucleic = 1
sequences[-1].PIRtype = pirType
want = 'descript'
elif want == 'descript':
sequences[-1].descript = line
sequences[-1].PIRdescript = line
want = 'sequence'
elif want == 'sequence':
if not line:
continue
if line[-1] == '*':
want = 'init'
line = line[:-1]
sequences[-1].extend(
filter(lambda c, whsp=string.whitespace: not c in whsp, line))
f.close()
if not sequences:
raise WrongFileTypeError()
if want != 'init':
raise FormatSyntaxError("Could not find end of sequence '%s'" %
sequences[-1].name)
return sequences, {}, {}
def _readSequences(self, f):
#self.sequenceDict = {}
self.sequenceList = []
while 1:
line = f.readline()
if not line:
raise FormatSyntaxError('no alignment separator')
if line == '//\n' or line == '//\r\n':
break
m = MSF._Sum.match(line)
if m is not None:
name = m.group(1)
length = m.group(2)
check = m.group(3)
weight = m.group(4)
s = Sequence(makeReadable(name))
self.sequenceList.append(s)
s.attrs = {}
s.attrs['MSF length'] = length
s.attrs['MSF check'] = check
s.attrs['MSF weight'] = weight
if not self.sequenceList:
raise FormatSyntaxError('No sequences found in header')
def _readSequences(self, f):
#self.sequenceDict = {}
self.sequenceList = []
while 1:
line = f.readline()
if not line:
raise FormatSyntaxError(
'no alignment separator')
if line == '//\n' or line == '//\r\n':
break
m = MSF._Sum.match(line)
if m is not None:
name = m.group(1)
length = m.group(2)
check = m.group(3)
weight = m.group(4)
s = Sequence(makeReadable(name))
self.sequenceList.append(s)
s.attrs = {}
s.attrs['MSF length'] = length
s.attrs['MSF check'] = check
s.attrs['MSF weight'] = weight
if not self.sequenceList:
raise FormatSyntaxError('No sequences found in header')
def parse(fileName):
from OpenSave import osOpen
f = osOpen(fileName, "r")
doing = None
sequences = []
headerOK = False
lineNum = 0
alignStartIndex = None
for line in f:
if doing == 'alignments':
# don't strip() alignment section since it has significant
# leading spaces
line = line.rstrip()
else:
line = line.strip()
lineNum += 1
if not headerOK:
if line.lower().startswith('hssp'):
headerOK = True
continue
raise WrongFileTypeError("No initial HSSP header line")
if line.startswith('##'):
if doing == 'proteins' and not sequences:
raise FormatSyntaxError("No entries in PROTEINS section")
try:
doing = line.split()[1].lower()
except IndexError:
doing = None
if doing == 'alignments':
try:
hashes, alignments, begin, dash, end = line.strip().split()
begin = int(begin)
end = int(end)
except ValueError:
raise FormatSyntaxError(
"ALIGNMENTS line (line #%d) not of "
"the form: ## ALIGNMENTS (number) - (number)" %
lineNum)
continue
if doing == 'proteins':
if not line[0].isdigit():
continue
try:
seqName = line.split()[2]
except IndexError:
raise WrongFormatError(
"Line %d in PROTEINS section does not "
"start with [integer] : [sequence name]" % lineNum)
sequences.append(Sequence(makeReadable(seqName)))
elif doing == 'alignments':
if line.lstrip().lower().startswith('seqno'):
try:
alignStartIndex = line.index('.')
except:
raise FormatSyntaxError(
"No indication of alignment "
" starting column ('.' character) in SeqNo line "
" in ALIGNMENTS section")
continue
if alignStartIndex == None:
raise FormatSyntaxError("No initial SeqNo line in "
"ALIGNMENTS section")
block = line[alignStartIndex:]
if not block:
raise FormatSyntaxError("No alignment block given on line %d" %
lineNum)
blockLen = end - begin + 1
if len(block) > blockLen:
raise FormatSyntaxError(
"Too many characters (%d, only %d "
" sequences) in alignment block given on line %d" %
(len(block), blockLen, lineNum))
block = block + ' ' * (blockLen - len(block))
for seq, c in zip(sequences[begin - 1:end], block):
seq.append(c)
f.close()
return sequences, {}, {}
def parse(fileName):
IN_HEADER = 0
START_ATTRS = 1
IN_ATTRS = 2
IN_FEATURES = 3
IN_SEQ = 4
state = IN_HEADER
from OpenSave import osOpen
f = osOpen(fileName, "r")
sequences = []
lineNum = 0
hasOffset = 0
longest = None
fileAttrs = {}
for line in f:
line = line.rstrip() # remove trailing whitespace/newline
lineNum += 1
if lineNum == 1:
if line.startswith("!!RICH_SEQUENCE"):
continue
raise WrongFileTypeError()
if state == IN_HEADER:
if line.strip() == "..":
state = START_ATTRS
continue
if "comments" in fileAttrs:
fileAttrs["comments"] += "\n" + line
else:
fileAttrs["comments"] = line
continue
if not line.strip():
continue
if state == START_ATTRS:
if line.strip() == "{":
state = IN_ATTRS
curAttr = None
attrs = {}
elif line:
raise FormatSyntaxError("Unexpected text before"
" start of sequence on line %d"
% lineNum)
continue
if state == IN_ATTRS or state == IN_FEATURES:
if line.strip() == "sequence" and line[0] == "s":
if "RSF name" not in attrs:
raise FormatSyntaxError("sequence on "
"line %d has no name" % lineNum)
state = IN_SEQ
seq = Sequence(makeReadable(attrs["RSF name"]))
del attrs["RSF name"]
seq.attrs = attrs
if "RSF descrip" in attrs:
attrs["description"] = attrs[
"RSF descrip"]
del attrs["RSF descrip"]
sequences.append(seq)
if "RSF offset" in attrs:
seq.extend("." * int(
attrs["RSF offset"]))
hasOffset = 1
del attrs["RSF offset"]
continue
if line.startswith("feature"):
if state == IN_ATTRS:
attrs["RSF features"] = [[line[8:]]]
else:
attrs["RSF features"].append([line[8:]])
state = IN_FEATURES
continue
if state == IN_ATTRS:
if line[0].isspace():
# continuation
if not curAttr:
raise FormatSyntaxError("Bogus "
"indentation at line %d"
% lineNum)
if attrs[curAttr]:
attrs[curAttr] += "\n" + line
else:
attrs[curAttr] = line
continue
if " " in line.strip():
curAttr, val = line.split(None, 1)
curAttr.replace("_", " ")
curAttr = "RSF " + curAttr
attrs[curAttr] = val.strip()
else:
curAttr = "RSF " + line.strip().replace("_", " ")
attrs[curAttr] = ""
continue
if state == IN_FEATURES:
attrs["RSF features"][-1].append(line)
continue
if line.strip() == "}":
state = START_ATTRS
if not longest:
longest = len(seq)
else:
if len(seq) < longest:
seq.extend("." * (longest - len(seq)))
elif len(seq) > longest:
longest = len(seq)
for s in sequences[:-1]:
s.extend("." *
(longest - len(s)))
continue
seq.extend(line.strip())
if not seq[0].isalpha():
hasOffset = 1
f.close()
if state == IN_HEADER:
raise FormatSyntaxError(
"No end to header (i.e. '..' line) found")
if state == IN_ATTRS or state == IN_FEATURES:
if "RSF name" in attrs:
raise FormatSyntaxError(
"No sequence data found for sequence %s"
% attrs["RSF name"])
raise FormatSyntaxError("Sequence without sequence data")
if state == IN_SEQ:
raise FormatSyntaxError("No terminating brace for sequence %s"
% attrs["RSF name"])
if not sequences:
raise FormatSyntaxError("No sequences found")
if not hasOffset:
from chimera import replyobj
replyobj.warning("No offset fields in RSF file;"
" assuming zero offset\n")
return sequences, fileAttrs, {}
def parse(fileName):
from OpenSave import osOpen
from chimera import replyobj
f = osOpen(fileName, "r")
lineNum = 0
fileAttrs = {}
fileMarkups = {}
seqAttrs = {}
seqMarkups = {}
sequences = {}
seqSequence = []
for line in f:
line = line[:-1] # drop newline
lineNum += 1
if lineNum == 1:
if line.startswith("# STOCKHOLM"):
continue
raise WrongFileTypeError()
if not line:
continue
if line.startswith('#='):
markupType = line[2:4]
markup = line[5:].strip()
def trySplit(numSplit):
fields = markup.split(None, numSplit)
if len(fields) == numSplit:
# value is empty
fields.append("")
if len(fields) != numSplit + 1:
raise FormatSyntaxError("Not enough"
" arguments after #=%s markup"
" on line %d" %
(markupType, lineNum))
return fields
if markupType == "GF":
tag, val = trySplit(1)
tag = tag.replace("_", " ")
tag = genericFileAttrs.get(tag, "Stockholm " + tag)
if tag in fileAttrs:
fileAttrs[tag] += '\n' + val
else:
fileAttrs[tag] = val
elif markupType == "GS":
seqName, tag, val = trySplit(2)
tag = tag.replace("_", " ")
attrs = seqAttrs.setdefault(seqName, {})
tag = genericSeqAttrs.get(tag, "Stockholm " + tag)
if tag in attrs:
attrs[tag] += '\n' + val
else:
attrs[tag] = val
elif markupType == "GC":
tag, val = trySplit(1)
tag = tag.replace("_", " ")
fileMarkups[tag] = fileMarkups.get(tag, "") + val
elif markupType == "GR":
seqName, tag, val = trySplit(2)
tag = tag.replace("_", " ")
seqMarkups.setdefault(seqName, {}).setdefault(tag, "")
seqMarkups[seqName][tag] += val
# ignore other types
continue
elif line.startswith('#'):
# unstructured comment
if 'comments' in fileAttrs:
fileAttrs['comments'] += "\n" + line[1:]
else:
fileAttrs['comments'] = line[1:]
continue
elif line.strip() == "//":
# end of sequence alignment blocks, but comments
# may follow this, so keep going...
continue
# sequence info...
try:
seqName, block = line.split(None, 1)
except ValueError:
raise FormatSyntaxError("Sequence info not in name/"
"contents format on line %d" % lineNum)
if seqName not in sequences:
sequences[seqName] = Sequence(makeReadable(seqName))
seqSequence.append(seqName)
sequences[seqName].extend(block)
f.close()
if not sequences:
raise FormatSyntaxError("No sequences found")
for seqName, seq in sequences.items():
if seqName in seqAttrs:
seq.attrs = seqAttrs[seqName]
if seqName in seqMarkups:
seq.markups = seqMarkups[seqName]
for tag, markup in seq.markups.items():
if len(markup) != len(seq):
replyobj.warning("Markup %s for"
" sequence %s is wrong length;"
" ignoring\n" % (tag, seqName))
del seq.markups[tag]
for seqInfo, label in [(seqAttrs, "sequence"), (seqMarkups, "residue")]:
for seqName in seqInfo.keys():
if seqName in sequences:
continue
# might be sequence name without trailing '/start-end'
for fullName in sequences.keys():
if fullName.startswith(seqName) \
and fullName[len(seqName)] == '/' \
and '/' not in fullName[len(seqName)+1:]:
break
else:
raise FormatSyntaxError(
"%s annotations "
"provided for non-existent sequence %s" %
(label.capitalize(), seqName))
replyobj.info("Updating %s %s annotions with %s "
"annotations\n" % (fullName, label, seqName))
seqInfo[fullName].update(seqInfo[seqName])
del seqInfo[seqName]
for tag, markup in fileMarkups.items():
if len(markup) != len(sequences[seqSequence[0]]):
raise FormatSyntaxError("Column annotation %s is"
" wrong length" % tag)
return map(lambda name: sequences[name], seqSequence), \
fileAttrs, fileMarkups