def mergeRa(self, other):
'''
Input:
Two RaFile objects
Output:
A merged RaFile
Common stanzas and key-val pairs are collapsed into
one with identical values being preserved,
differences are marked with a >>> and <<<
'''
mergedKeys = ucscUtils.mergeList(list(self), list(other))
selfKeys = set(self)
otherKeys = set(other)
newCommon = RaFile()
p = re.compile('^\s*#')
p2 = re.compile('^\s*$')
for i in mergedKeys:
if p.match(i) or p2.match(i):
newCommon.append(i)
continue
if i not in selfKeys:
newCommon[i] = other[i]
continue
if i not in otherKeys:
newCommon[i] = self[i]
continue
if i in otherKeys and i in selfKeys:
newStanza = RaStanza()
selfStanzaKeys = set(self[i].iterkeys())
otherStanzaKeys = set(other[i].iterkeys())
stanzaKeys = ucscUtils.mergeList(list(self[i]), list(other[i]))
for j in stanzaKeys:
if p.match(j):
newStanza.append(j)
continue
if j not in selfStanzaKeys:
newStanza[j] = other[i][j]
continue
if j not in otherStanzaKeys:
newStanza[j] = self[i][j]
continue
if j in selfStanzaKeys and j in otherStanzaKeys:
if self[i][j] == other[i][j]:
newStanza[j] = self[i][j]
else:
in_j = '>>>>>%s' % j
out_j = '<<<<<%s' % j
newStanza[out_j] = self[i][j]
newStanza[in_j] = other[i][j]
newCommon[i] = newStanza
return newCommon
def mergeRa(self, other):
'''
Input:
Two RaFile objects
Output:
A merged RaFile
Common stanzas and key-val pairs are collapsed into
one with identical values being preserved,
differences are marked with a >>> and <<<
'''
mergedKeys = ucscUtils.mergeList(list(self), list(other))
selfKeys = set(self)
otherKeys = set(other)
newCommon = RaFile()
p = re.compile('^\s*#')
p2 = re.compile('^\s*$')
for i in mergedKeys:
if p.match(i) or p2.match(i):
newCommon.append(i)
continue
if i not in selfKeys:
newCommon[i] = other[i]
continue
if i not in otherKeys:
newCommon[i] = self[i]
continue
if i in otherKeys and i in selfKeys:
newStanza = RaStanza()
selfStanzaKeys = set(self[i].iterkeys())
otherStanzaKeys = set(other[i].iterkeys())
stanzaKeys = ucscUtils.mergeList(list(self[i]), list(other[i]))
for j in stanzaKeys:
if p.match(j):
newStanza.append(j)
continue
if j not in selfStanzaKeys:
newStanza[j] = other[i][j]
continue
if j not in otherStanzaKeys:
newStanza[j] = self[i][j]
continue
if j in selfStanzaKeys and j in otherStanzaKeys:
if self[i][j] == other[i][j]:
newStanza[j] = self[i][j]
else:
in_j = '>>>>>%s' % j
out_j = '<<<<<%s' % j
newStanza[out_j] = self[i][j]
newStanza[in_j] = other[i][j]
newCommon[i] = newStanza
return newCommon
def processAntibodyEntry(entry, species, downloadsDirectory, noDownload,
username, password, wikiBaseUrl):
"""
For a single wiki table entry, generate an appropriate RA file stanza and
download any validation documents into the download directory, into a filename
that meets the naming convention for antibody documents. When finished, print
a new stanza to stdout.
"""
cells = entry.findAll("td")
#
# Skip over any example entries
if re.search("(Example)", getContents(cells[0])):
return ((None, False))
else:
stanza = RaStanza()
term = getContents(cells[0])
(vendorName, vendorId, orderUrl) = processSource(cells[3])
#
# The naming standard (as of May 3, 2011) is to name antibodies as
# <target>_(<vendorId>), such as TAF7_(SC-101167). In the "term" cell,
# the antibody might already have that name, or (more likely) it might be
# named by just the target. If the vendor ID isn't in the name yet, add it.
# If the vendor ID is "missing" (the default value parsed if the field isn't
# filled in), then don't add it.
#
if re.search(vendorId, term):
stanza["term"] = term
elif vendorId == "missing":
stanza["term"] = term
else:
stanza["term"] = term + "_(" + vendorId + ")"
m = re.search("\s+", stanza['term'])
if m:
print "ERROR: term %s has spaces in the name" % stanza['term']
sys.exit()
stanza["tag"] = re.sub("[-_\(\)]", "", stanza["term"]).upper()
stanza["type"] = "Antibody"
stanza["antibodyDescription"] = getContents(cells[1])
stanza["target"] = re.split("_", stanza["term"])[0]
stanza["targetDescription"] = getContents(cells[2])
stanza["vendorName"] = vendorName
stanza["vendorId"] = vendorId
stanza["orderUrl"] = orderUrl
stanza["lab"] = getContents(cells[4])
stanza["lots"] = getContents(cells[5])
(stanza["targetId"], stanza["targetUrl"]) = processFactorId(cells[6])
stanza["validation"] = processValidation(cells[7], species,
stanza["term"], stanza["lab"],
downloadsDirectory,
noDownload, username,
password, wikiBaseUrl)
#
# Indicate whether or not the document (if any) is approved by the NHGRI
if re.search("^[Y|y]", getContents(cells[8])):
approved = True
else:
approved = False
return ((stanza, approved))
def updateDiffFilter(self, term, other):
'''
Replicates updateMetadata.
Input:
Term
Other raFile
Output:
Merged RaFile
Stanzas found in 'self' and 'other' that have the 'Term' in 'other'
are overwritten (or inserted if not found) into 'self'.
Final merged dictionary is returned.
'''
ret = self
common = set(self.iterkeys()) & set(other.iterkeys())
for stanza in common:
if term not in self[stanza] and term not in other[stanza]:
continue
if term in self[stanza] and term not in other[stanza]:
del ret[stanza][term]
continue
if term in other[stanza]:
#Remake stanza to keep order of terms
tempStanza = RaStanza()
tempStanza._name = stanza
selfKeys = list(self[stanza].iterkeys())
otherKeys = list(other[stanza].iterkeys())
newOther = list()
#filter out keys in other that aren't in self, or the term we're interested in
for i in otherKeys:
if not i in selfKeys and i != term:
continue
else:
newOther.append(i)
#merge self keylist and filtered other list
masterList = ucscUtils.mergeList(newOther, selfKeys)
for i in masterList:
if i == term:
tempStanza[i] = other[stanza][i]
else:
tempStanza[i] = self[stanza][i]
ret[stanza] = tempStanza
return ret
def updateDiffFilter(self, term, other):
'''
Replicates updateMetadata.
Input:
Term
Other raFile
Output:
Merged RaFile
Stanzas found in 'self' and 'other' that have the 'Term' in 'other'
are overwritten (or inserted if not found) into 'self'.
Final merged dictionary is returned.
'''
ret = self
common = set(self.iterkeys()) & set(other.iterkeys())
for stanza in common:
if term not in self[stanza] and term not in other[stanza]:
continue
if term in self[stanza] and term not in other[stanza]:
del ret[stanza][term]
continue
if term in other[stanza]:
#Remake stanza to keep order of terms
tempStanza = RaStanza()
tempStanza._name = stanza
selfKeys = list(self[stanza].iterkeys())
otherKeys = list(other[stanza].iterkeys())
newOther = list()
#filter out keys in other that aren't in self, or the term we're interested in
for i in otherKeys:
if not i in selfKeys and i != term:
continue
else:
newOther.append(i)
#merge self keylist and filtered other list
masterList = ucscUtils.mergeList(newOther, selfKeys)
for i in masterList:
if i == term:
tempStanza[i] = other[stanza][i]
else:
tempStanza[i] = self[stanza][i]
ret[stanza] = tempStanza
return ret
def readStanza(self, stanza, key=None, scopes=None):
'''
Override this to create custom stanza behavior in derived types.
IN
stanza: list of strings with keyval data
key: optional key for selective key filtering. Don't worry about it
OUT
namekey: the key of the stanza's name
nameval: the value of the stanza's name
entry: the stanza itself
'''
entry = RaStanza()
if entry.readStanza(stanza, key, scopes) == None:
return None, None, None
entry = RaStanza()
val1, val2 = entry.readStanza(stanza, key, scopes)
return val1, val2, entry
def readStanza(self, stanza, key=None):
'''
Override this to create custom stanza behavior in derived types.
IN
stanza: list of strings with keyval data
key: optional key for selective key filtering. Don't worry about it
OUT
namekey: the key of the stanza's name
nameval: the value of the stanza's name
entry: the stanza itself
'''
entry = RaStanza()
if entry.readStanza(stanza, key) == None:
return None, None, None
entry = RaStanza()
val1, val2 = entry.readStanza(stanza, key)
return val1, val2, entry
def __init__(self):
RaStanza.__init__(self)
def __init__(self, parent):
RaStanza.__init__(self)
self._parent = parent
def createStanza(self, key, value):
self[value] = RaStanza(key, value)
def __init__(self):
RaStanza.__init__(self)
def __init__(self, parent):
RaStanza.__init__(self)
self._parent = parent
