ca1f73bcb5983fb36199f9bb09f5fd75b27f4ac4 Merge parents e14a4cf 438ca3f mmaddren Mon Jan 30 10:50:53 2012 -0800 fixed merge conflict with ra.py diff --cc python/lib/ucscgenomics/ra.py index 04abb68,2595548..fd32b73 --- python/lib/ucscgenomics/ra.py +++ python/lib/ucscgenomics/ra.py @@@ -1,550 -1,592 +1,603 @@@ import sys, string import re from ucscgenomics.ordereddict import OrderedDict from ucscgenomics import ucscUtils import collections class RaFile(OrderedDict): ''' Stores a Ra file in a set of entries, one for each stanza in the file. To make a RaFile, it is usually easiest to just pass it's path: rafile = ra.RaFile('kent/src/hg/.../wgEncodeSomeRaFile.ra') The data is read in and organized as a collection of stanzas. Ra files store the stanza by it's name, so to access a specific stanza, say: somestanza = rafile['wgEncodeSomeStanzaName'] Once you have a stanza, you may want specific data about that stanza. Stanzas are, as ra files, organized as a collection of terms. Therefore to get the description of the stanza, we can say: somedescription = somestanza['description'] You can also access a stanza's name from the stanza itself, since by the nature of ra files, the first key is it's name. Therefore for most ra files the following holds true: somestanza.name = somestanza['metaObject'] = 'wgEncodeSomeStanzaName' Although the above is useful if you want one thing, it's usually more helpful to be able to loop and query on the stanza. To add a term named 'foobar' to every stanza in a ra file: for stanza in rafile.values(): stanza['foobar'] = 'some value' Note that I iterated over values. It can also be useful to iterate over a stanza's keys: for key in rafile.keys(): print key Note that ra files are order preserving. Added entries are appended to the end of the file. This allows you to print out a ra file easily: print rafile Most of the time you don't want to do something with all stanzas though, instead you want to filter them. The included filter method allows you to specify two functions (or lambda expressions). The first is the 'where' predicate, which must take in one stanza, and return true/false depending on whether you want to take that stanza. The second is the 'select' predicate, which takes in the stanza, and returns some subset or superset of the stanza as a list. Using filter is preferable to for loops where there are no side effects, or to filter data before iterating over it as opposed to using if statements in the loop. To get all stanzas with one experiment ID for instance, we would do something like this: stanzas = rafile.filter(lambda s: s['expId'] == '123', lambda s: s) Note that you don't have to ensure 'expId' is in the stanza, it will silently fail. Let's look at another example, say you want to find all stanza's with an geoSampleAccession that are also fastq's submittedfastqs = rafile.filter( lambda s: 'geoSampleAccession' in s and s['fileName'].endswith('.fastq'), lambda s: s) We don't always have to just return the stanza in the second parameter however. If we wanted to, for each stanza, return the file associated with that stanza, we could easily do that as well. This would return a simple list of the string filenames in a ra file: files = rafile.filter(lambda s: 1, lambda s: s['fileName']) Note that once again, we don't have to ensure 'fileName' exists. Also note that lambda s: 1 means always return true. Lambda expressions are always preferable to functions unless the expression would need to be reused multiple times. It is also best to reduce the set of stanzas as much as possible before operating over them. Filtering allows you to eliminate a lot of code. ''' def __init__(self, filePath=None, key=None): OrderedDict.__init__(self) if filePath != None: self.read(filePath, key) def read(self, filePath, key=None): ''' - Reads an rafile stanza by stanza, and internalizes it. + Reads an rafile stanza by stanza, and internalizes it. Don't override + this for derived types, instead override readStanza. ''' file = open(filePath, 'r') #entry = None stanza = list() keyValue = '' reading = 1 while reading: line = file.readline() if line == '': reading = 0 line = line.strip() if len(stanza) == 0 and (line.startswith('#') or (line == '' and reading)): OrderedDict.append(self, line) continue if line != '': stanza.append(line) elif len(stanza) > 0: if keyValue == '': keyValue, name, entry = self.readStanza(stanza, key) else: testKey, name, entry = self.readStanza(stanza, key) if entry != None and keyValue != testKey: raise KeyError('Inconsistent Key ' + testKey) if entry != None: if name != None or key == None: if name in self: raise KeyError('Duplicate Key ' + name) self[name] = entry stanza = list() file.close() 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 iter(self): pass def iterkeys(self): for item in self._OrderedDict__ordering: if not(item.startswith('#') or item == ''): yield item def itervalues(self): for item in self._OrderedDict__ordering: if not (item.startswith('#') or item == ''): yield self[item] def iteritems(self): for item in self._OrderedDict__ordering: if not (item.startswith('#') or item == ''): yield item, self[item] else: yield [item] def append(self, item): OrderedDict.append(self, item) def filter(self, where, select): ''' select useful data from matching criteria where: the conditional function that must be met. Where takes one argument, the stanza and should return true or false select: the data to return. Takes in stanza, should return whatever to be added to the list for that stanza. For each stanza, if where(stanza) holds, it will add select(stanza) to the list of returned entities. Also forces silent failure of key errors, so you don't have to check that a value is or is not in the stanza. ''' ret = list() for stanza in self.itervalues(): try: if where(stanza): ret.append(select(stanza)) except KeyError: continue return ret def filter2(self, where): ''' select useful data from matching criteria Filter2 returns a Ra dictionary. Easier to use but more memory intensive. where: the conditional function that must be met. Where takes one argument, the stanza and should return true or false select: the data to return. Takes in stanza, should return whatever to be added to the list for that stanza. For each stanza, if where(stanza) holds, it will add select(stanza) to the list of returned entities. Also forces silent failure of key errors, so you don't have to check that a value is or is not in the stanza. ''' ret = RaFile() for stanza in self.itervalues(): try: if where(stanza): ret[stanza.name] = stanza except KeyError: continue return ret 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 + newCommon.append(other[i]) if i not in otherKeys: - newCommon[i] = self[i] - continue + newCommon.append(self[i]) 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])) + stanzaKeys = ucscUtils.mergeList(list(self[i].iterkeys()), list(other[i].iterkeys())) 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 + newCommon.append(newStanza) return newCommon def summaryDiff(self, other): ''' Input: RaFile object being compared. Output: RaFile with differences. Returns ***partial*** stanzas of ***anything*** different from the self dictionary compared to the other dictionary. For versatility, it only returns stanzas from the self Ra file. In other words, it returns the self dictionary lines that are either not present in or different from the other dictionary. To obtain full set of differences, run summaryDiff twice ra1 = this.summaryDiff(that) and ra2 = that.summaryDiff(this) ''' this = RaFile() RetThis = RaFile() for stanza in self.itervalues(): if stanza.name not in other.keys(): RetThis[stanza.name] = stanza else: if stanza.difference(other[stanza.name]): RetThis[stanza.name] = stanza.difference(other[stanza.name]) return RetThis def changeSummary(self, otherRa): ''' Input: Two RaFile objects Output: Dictionary showing differences between stanzas, list of added and dropeed stanzas ''' retDict = collections.defaultdict(list) - addList = set(self.iterkeys()) - set(otherRa.iterkeys()) - dropList = set(otherRa.iterkeys()) - set(self.iterkeys()) + dropList = set(self.iterkeys()) - set(otherRa.iterkeys()) + addList = set(otherRa.iterkeys()) - set(self.iterkeys()) common = set(self.iterkeys()) & set(otherRa.iterkeys()) p = re.compile('^\s*#') for stanza in common: if p.match(stanza): continue for key in self[stanza]: if p.match(key): continue if key in otherRa[stanza]: if self[stanza][key] != otherRa[stanza][key]: - retDict[stanza].append("Changed %s from %s -> %s" %(key, otherRa[stanza][key], self[stanza][key])) + retDict[stanza].append("Changed %s from %s -> %s" %(key, otherRa[stanza][key], self[stanza][key])) else: retDict[stanza].append("Added %s -> %s" %(key, self[stanza][key])) for key in otherRa[stanza]: if p.match(key): continue if key not in self[stanza]: retDict[stanza].append("Dropped %s -> %s" %(key, otherRa[stanza][key])) - return retDict, addList, dropList + return retDict, dropList, addList def diffFilter(self, select, other): ''' Input: Lambda function of desired comparison term RaFile object being compared. Output: RaFile with differences. Filter returns ***full*** stanzas of a ***select function*** from the self dictionary compared to the other dictionary. For versatility, it only returns stanzas from the self Ra file. In other words, it only returns self dictionary stanzas with the function term that are either not found in or different from the other dictionary. To obtain full set of differences, run diffFilter twice ra1 = this.diffFilter(select function, that) and ra2 = that.diffFilter(select function, this) ''' this = RaFile() RetThis = RaFile() thisSelectDict = dict() thatSelectDict = dict() #Build 2 dict of stanzas to later compare line-by-line for stanza in self.itervalues(): try: if select(stanza): this[stanza.name] = stanza #'this' only records stanzas of the self dict thisSelectDict[stanza.name] = select(stanza) except KeyError: continue for stanza in other.itervalues(): #Exact code as filter2 but kept for clarity. try: if select(stanza): thatSelectDict[stanza.name] = select(stanza) except KeyError: continue #Compare this and that dict for stanza in this.itervalues(): if stanza.name not in thatSelectDict: RetThis[stanza.name] = stanza elif thisSelectDict[stanza.name] != thatSelectDict[stanza.name]: RetThis[stanza.name] = stanza return RetThis 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. + 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] + try: + tempStanza['metaObject'] = self[stanza]['metaObject'] + tempStanza['objType'] = self[stanza]['objType'] + termList = self[stanza].keys() + termList.remove('metaObject') + termList.remove('objType') + except KeyError: + termList = self[stanza].keys() + if term not in termList: + termList.append(term) + for t in sorted(termList, key=str.lower): + if t == term: + if t not in self[stanza]: + tempStanza[t] = other[stanza][t] + elif self[stanza][t] != other[stanza][t]: + tempStanza[t] = other[stanza][t] + else: + tempStanza[t] = self[stanza][t] else: - tempStanza[i] = self[stanza][i] - ret[stanza] = tempStanza + tempStanza[t] = self[stanza][t] + ret[stanza] = tempStanza + return ret + def printTrackDbFormat(self): + ''' + Converts a .ra file into TrackDb format. + Returns a printable string. + ''' + retstring = "" + parentTrack = "" + tier = 0 + commentList = [] + p = re.compile('^.*parent') + p2 = re.compile('^.*subTrack') + for stanza in self: + if stanza == "": + if commentList: + for line in commentList: + for i in range(tier): + retstring += " " + retstring += line + "\n" + commentList = [] + retstring += "\n" + continue + if stanza.startswith("#"): + commentList.append(stanza) + continue + keys = self[stanza].keys() + parentKey = "NOKEYFOUND" + for key in keys: + if p.search(key): + parentKey = key + if p2.search(key): + parentKey = key + if parentKey in keys: + if parentTrack not in self[stanza][parentKey] or parentTrack == "": + parentTrack = self[stanza]['track'] + tier = 1 + else: + tier = 2 + if commentList: + for line in commentList: + for i in range(tier): + retstring += " " + retstring += line + "\n" + commentList = [] + for line in self[stanza]: + for i in range(tier): + retstring += " " + if line.startswith("#"): + retstring += line + "\n" + else: + retstring += line + " " + self[stanza][line] + "\n" + retstring += "\n" + return retstring + def __str__(self): str = '' for item in self.iteritems(): if len(item) == 1: str += item[0].__str__() + '\n' else: str += item[1].__str__() + '\n' return str #.rsplit('\n', 1)[0] class RaStanza(OrderedDict): ''' Holds an individual entry in the RaFile. ''' + @property + def name(self): + return self._name + def __init__(self): self._name = '' self._nametype = '' OrderedDict.__init__(self) - @property - def name(self): - return self._name - - def readStanza(self, stanza, key=None): ''' - Populates this entry from a single stanza + Populates this entry from a single stanza. Override this to create + custom behavior in derived classes ''' for line in stanza: self.readLine(line) return self.readName(stanza, key) def readName(self, stanza, key=None): ''' Extracts the Stanza's name from the value of the first line of the stanza. ''' if key == None: line = stanza[0] else: line = None for s in stanza: if s.split(' ', 1)[0] == key: line = s break if line == None: return None if len(line.split(' ', 1)) != 2: raise ValueError() names = map(str.strip, line.split(' ', 1)) self._nametype = names[0] self._name = names[1] return names def readLine(self, line): ''' Reads a single line from the stanza, extracting the key-value pair ''' if line.startswith('#') or line == '': OrderedDict.append(self, line) else: raKey = line.split(' ', 1)[0] raVal = '' if (len(line.split(' ', 1)) == 2): raVal = line.split(' ', 1)[1] #if raKey in self: #raise KeyError(raKey + ' already exists') self[raKey] = raVal def difference(self, other): ''' Complement function to summaryDiff. Takes in self and a comparison Stanza. Returns new stanza with terms from 'self' that are different from 'other' Like the summaryDiff, to get the other terms, this needs to be run again with self and other switched. ''' retRa = RaStanza() retRa._name = self.name for key in other.keys(): try: if other[key] != self[key] and not key.startswith('#'): retRa[key] = self[key] except KeyError: continue #maybe add empty keys return retRa def iterkeys(self): for item in self._OrderedDict__ordering: if not (item.startswith('#') or item == ''): yield item def itervalues(self): for item in self._OrderedDict__ordering: if not (item.startswith('#') or item == ''): yield self[item] def iteritems(self): for item in self._OrderedDict__ordering: if not (item.startswith('#') or item == ''): yield item, self[item] def iter(self): iterkeys(self) def __str__(self): str = '' for key in self: if key.startswith('#'): str += key + '\n' else: str += key + ' ' + self[key] + '\n' return str