58f787640ea77f16c8f6d4481693a83ec9ef647b vsmalladi Tue May 8 10:29:52 2012 -0700 First step in python lib reogranization. Redmine #7029. diff --git python/lib/ucscGb/soft.py python/lib/ucscGb/soft.py deleted file mode 100644 index f2d26a5..0000000 --- python/lib/ucscGb/soft.py +++ /dev/null @@ -1,392 +0,0 @@ -import sys -import re -from ucscgenomics.ordereddict import OrderedDict - -class SoftFile(OrderedDict): - - """ - Stores an Ra file in a set of entries, one for each stanza in the file. - """ - - def __init__(self, filePath=''): - OrderedDict.__init__(self) - if filePath != '': - self.read(filePath) - - def read(self, filePath): - """ - Reads an SoftFile stanza by stanza, and internalizes it. - """ - - file = open(filePath, 'r') - - stanza = list() - - for line in file: - - line = line.strip() - - if line.startswith('^') and stanza != []: - name, entry = self.readStanza(stanza) - #print 'hit: ' + name - if entry != None: - if name in self: - raise KeyError('Duplicate Key ' + name) - self[name] = entry - - stanza = list() - - #print 'appending: ' + line - stanza.append(line) - - file.close() - - name, entry = self.readStanza(stanza) - #print 'hit: ' + name - if entry != None: - if name in self: - raise KeyError('Duplicate Key ' + name) - self[name] = entry - - - def readStanza(self, stanza): - - if stanza[0].startswith('^SAMPLE'): - entry = HighThroughputSampleStanza() #WILL HAVE TO CHANGE - elif stanza[0].startswith('^SERIES'): - entry = SeriesStanza() - elif stanza[0].startswith('^PLATFORM'): - entry = PlatformStanza() - else: - raise KeyError(stanza[0]) - - val = entry.readStanza(stanza) - return val, entry - - - def iter(self): - for item in self._OrderedDict__ordering: - yield item - - - def iterkeys(self): - for item in self._OrderedDict__ordering: - yield item - - - def itervalues(self): - for item in self._OrderedDict__ordering: - yield self[item] - - - def iteritems(self): - for item in self._OrderedDict__ordering: - yield [item] - - - def __str__(self): - str = '' - for item in self.iterkeys(): - str += self[item].__str__() - - return str - - -class HighThroughputSoftFile(SoftFile): - - def __init__(self, filePath=''): - SoftFile.__init__(self, filePath) - - def readStanza(self, stanza): - if stanza[0].startswith('^SAMPLE'): - entry = HighThroughputSampleStanza() - elif stanza[0].startswith('^SERIES'): - entry = SeriesStanza() - else: - raise KeyError(stanza[0]) - - val = entry.readStanza(stanza) - return val, entry - - -class MicroArraySoftFile(SoftFile): - - def __init__(self, filePath=''): - SoftFile.__init__(self, filePath) - - def readStanza(self, stanza): - if stanza[0].startswith('^SAMPLE'): - entry = MicroArraySampleStanza() - elif stanza[0].startswith('^SERIES'): - entry = SeriesStanza() - elif stanza[0].startswith('^PLATFORM'): - entry = PlatformStanza() - else: - raise KeyError(stanza[0]) - - val = entry.readStanza(stanza) - return val, entry - - -class KeyRequired(object): - pass - -class KeyOptional(object): - pass - -class KeyZeroPlus(object): - pass - -class KeyOnePlus(object): - pass - -class KeyZeroPlusNumbered(object): - pass - -class KeyOnePlusNumbered(object): - pass - -class KeyZeroPlusChannel(object): - pass - -class KeyOnePlusChannel(object): - pass - - -class SoftStanza(OrderedDict): - """ - Holds an individual entry in the RaFile. - """ - - def __init__(self, keys): - self._name = '' - self.keys = keys - OrderedDict.__init__(self) - - @property - def name(self): - return self._name - - def readStanza(self, stanza): - """ - Populates this entry from a single stanza - """ - - for line in stanza: - self.__readLine(line) - - return self.__readName(stanza[0]) - - - def __readName(self, line): - """ - Extracts the Stanza's name from the value of the first line of the - stanza. - """ - - if len(line.split('=', 1)) != 2: - raise ValueError() - - self._name = line.split('=', 1)[1].strip() - return self._name - - def __readLine(self, line): - """ - Reads a single line from the stanza, extracting the key-value pair - """ - key = line.split('=', 1)[0].strip() - val = '' - if (len(line.split('=', 1)) == 2): - val = line.split('=', 1)[1].strip() - - #split on the last underscore to determine if we're using a numbered key or not - splitkey = key.rsplit('_', 1)[0] - channelkey = splitkey + '_ch' - #if the key is a numbered key - if splitkey in self.keys and (self.keys[splitkey] == KeyZeroPlusNumbered or self.keys[splitkey] == KeyOnePlusNumbered): - self[key] = val - - #this is for channel data in MicroArraySamples - elif channelkey in self.keys and (self.keys[channelkey] == KeyZeroPlusChannel or self.keys[channelkey] == KeyOnePlusChannel): - self[key] = val - - #if its a single value (ie 0 or 1 allowed entries) - elif key in self.keys and (self.keys[key] == KeyRequired or self.keys[key] == KeyOptional): - self[key] = val - - else: - - if key not in self.keys: - print splitkey - raise KeyError(self._name + ': invalid key: ' + key) - - if (self.keys[key] == KeyRequired or self.keys[key] == KeyOptional) and key in self: - raise KeyError(self._name + ': too many of key: ' + key) - - if key not in self: - self[key] = list() - self[key].append(val) - - - def iter(self): - yield iterkeys(self) - - - def iterkeys(self): - for item in self._OrderedDict__ordering: - yield item - - - def itervalues(self): - for item in self._OrderedDict__ordering: - yield self[item] - - - def iteritems(self): - for item in self._OrderedDict__ordering: - yield item, self[item] - - - def __str__(self): - str = '' - for key in self: - if isinstance(self[key], basestring): - str += key + ' = ' + self[key] + '\n' - else: - for val in self[key]: - str += key + ' = ' + val + '\n' - - return str - - def write(self, filename): - #check for absence of required vars - file = open(filename, 'r') - file.write(self.__str__()) - file.close() - - -class MicroArrayPlatformStanza(SoftStanza): - - def __init__(self): - - keys = { - '^PLATFORM': KeyRequired, - '!Platform_title': KeyRequired, - '!Platform_distribution': KeyRequired, - '!Platform_technology': KeyRequired, - '!Platform_organism': KeyOnePlus, - '!Platform_manufacturer': KeyRequired, - '!Platform_manufacture_protocol': KeyOnePlus, - '!Platform_catalog_number': KeyZeroPlus, - '!Platform_web_link': KeyZeroPlus, - '!Platform_support': KeyOptional, - '!Platform_coating': KeyOptional, - '!Platform_description': KeyZeroPlus, - '!Platform_contributor': KeyZeroPlus, - '!Platform_pubmed_id': KeyZeroPlus, - '!Platform_geo_accession': KeyOptional, - '!Platform_table_begin': KeyRequired, - '!Platform_table_end': KeyRequired - } - - SoftStanza.__init__(self, keys) - - -class MicroArraySampleStanza(SoftStanza): - - def __init__(self): - - keys = { - '^SAMPLE': KeyRequired, - '!Sample_title': KeyRequired, - '!Sample_supplementary_file': KeyOnePlus, - '!Sample_table': KeyOptional, - '!Sample_source_name_ch': KeyOnePlusNumbered, - '!Sample_organism_ch': KeyOnePlusNumbered, - '!Sample_characteristics_ch': KeyOnePlusNumbered, - '!Sample_biomaterial_provider_ch': KeyZeroPlusNumbered, - '!Sample_treatment_protocol_ch': KeyZeroPlusNumbered, - '!Sample_growth_protocol_ch': KeyZeroPlusNumbered, - '!Sample_molecule_ch': KeyOnePlusNumbered, - '!Sample_extract_protocol_ch': KeyOnePlusNumbered, - '!Sample_label_ch': KeyOnePlusNumbered, - '!Sample_label_protocol_ch': KeyOnePlusNumbered, - '!Sample_hyb_protocol': KeyOnePlus, - '!Sample_scan_protocol': KeyOnePlus, - '!Sample_data_processing': KeyOnePlus, - '!Sample_description': KeyZeroPlus, - '!Sample_platform_id': KeyRequired, - '!Sample_geo_accession': KeyOptional, - '!Sample_anchor': KeyRequired, - '!Sample_type': KeyRequired, - '!Sample_tag_count': KeyRequired, - '!Sample_tag_length': KeyRequired, - '!Sample_table_begin': KeyRequired, - '!Sample_table_end': KeyRequired - } - - SoftStanza.__init__(self, keys) - - -class SeriesStanza(SoftStanza): - - def __init__(self): - - keys = { - '^SERIES': KeyRequired, - '!Series_title': KeyRequired, - '!Series_summary': KeyOnePlus, - '!Series_overall_design': KeyRequired, - '!Series_pubmed_id': KeyZeroPlus, - '!Series_web_link': KeyZeroPlus, - '!Series_contributor': KeyZeroPlus, - '!Series_variable': KeyZeroPlusNumbered, - '!Series_variable_description': KeyZeroPlusNumbered, - '!Series_variable_sample_list': KeyZeroPlusNumbered, - '!Series_repeats': KeyZeroPlusNumbered, - '!Series_repeats_sample_list': KeyZeroPlusNumbered, - '!Series_sample_id': KeyOnePlus, - '!Series_geo_accession': KeyOptional, - '!Series_gp_id': KeyOptional - } - - SoftStanza.__init__(self, keys) - - -class HighThroughputSampleStanza(SoftStanza): - - def __init__(self): - - keys = { - '^SAMPLE': KeyRequired, - '!Sample_type': KeyRequired, - '!Sample_title': KeyRequired, - '!Sample_supplementary_file': KeyOnePlusNumbered, - '!Sample_supplementary_file_checksum': KeyZeroPlusNumbered, - '!Sample_supplementary_file_build': KeyZeroPlusNumbered, - '!Sample_raw_file': KeyOnePlusNumbered, - '!Sample_raw_file_type': KeyOnePlusNumbered, - '!Sample_raw_file_checksum': KeyZeroPlusNumbered, - '!Sample_source_name': KeyRequired, - '!Sample_organism': KeyOnePlus, - '!Sample_characteristics': KeyOnePlus, - '!Sample_biomaterial_provider': KeyZeroPlus, - '!Sample_treatment_protocol': KeyZeroPlus, - '!Sample_growth_protocol': KeyZeroPlus, - '!Sample_molecule': KeyRequired, - '!Sample_extract_protocol': KeyOnePlus, - '!Sample_library_strategy': KeyOnePlus, - '!Sample_library_source': KeyOnePlus, - '!Sample_library_selection': KeyOnePlus, - '!Sample_instrument_model': KeyOnePlus, - '!Sample_data_processing': KeyRequired, - '!Sample_barcode': KeyOptional, - '!Sample_description': KeyZeroPlus, - '!Sample_geo_accession': KeyOptional, - '!Sample_table_begin': KeyOptional, - '!Sample_table': KeyOptional, - '!Sample_table_end': KeyOptional - } - - SoftStanza.__init__(self, keys) -