X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=blobdiff_plain;f=htsworkflow%2Fpipelines%2Feland.py;fp=htsworkflow%2Fpipelines%2Feland.py;h=feb7ff7c066ea070b836f47ce4d03536b8416095;hp=a508a494c8c24900e8574c75f43c3616bf309814;hb=53ebb47e86e81ce349d4ef4e16aef94be93486ea;hpb=4262586d10cc0cc227390873b301b55244204c11 diff --git a/htsworkflow/pipelines/eland.py b/htsworkflow/pipelines/eland.py index a508a49..feb7ff7 100644 --- a/htsworkflow/pipelines/eland.py +++ b/htsworkflow/pipelines/eland.py @@ -376,7 +376,7 @@ class ElandLane(ResultLane): def get_elements(self): lane = ElementTree.Element(ElandLane.LANE, {'version': - unicode(ElandLane.XML_VERSION)}) + str(ElandLane.XML_VERSION)}) sample_tag = ElementTree.SubElement(lane, SAMPLE_NAME) sample_tag.text = self.sample_name lane_tag = ElementTree.SubElement(lane, LANE_ID) @@ -385,22 +385,22 @@ class ElandLane(ResultLane): end_tag = ElementTree.SubElement(lane, END) end_tag.text = str(self.end) genome_map = ElementTree.SubElement(lane, GENOME_MAP) - for k, v in self.genome_map.items(): + for k, v in list(self.genome_map.items()): item = ElementTree.SubElement( genome_map, GENOME_ITEM, - {'name':k, 'value':unicode(v)}) + {'name':k, 'value':str(v)}) mapped_reads = ElementTree.SubElement(lane, MAPPED_READS) - for k, v in self.mapped_reads.items(): + for k, v in list(self.mapped_reads.items()): item = ElementTree.SubElement( mapped_reads, MAPPED_ITEM, - {'name':k, 'value':unicode(v)}) + {'name':k, 'value':str(v)}) match_codes = ElementTree.SubElement(lane, MATCH_CODES) - for k, v in self.match_codes.items(): + for k, v in list(self.match_codes.items()): item = ElementTree.SubElement( match_codes, MATCH_ITEM, - {'name':k, 'value':unicode(v)}) + {'name':k, 'value':str(v)}) reads = ElementTree.SubElement(lane, READS) - reads.text = unicode(self.reads) + reads.text = str(self.reads) return lane @@ -457,7 +457,7 @@ class MatchCodes(collections.MutableMapping): for key in initializer: if key not in self.match_codes: errmsg = "Initializer can only contain: %s" - raise ValueError(errmsg % (",".join(self.match_codes.keys()))) + raise ValueError(errmsg % (",".join(list(self.match_codes.keys())))) self.match_codes[key] += initializer[key] def __iter__(self): @@ -472,7 +472,7 @@ class MatchCodes(collections.MutableMapping): def __setitem__(self, key, value): if key not in self.match_codes: errmsg = "Unrecognized key, allowed values are: %s" - raise ValueError(errmsg % (",".join(self.match_codes.keys()))) + raise ValueError(errmsg % (",".join(list(self.match_codes.keys())))) self.match_codes[key] = value def __len__(self): @@ -483,7 +483,7 @@ class MatchCodes(collections.MutableMapping): raise ValueError("Expected a MatchCodes, got %s", str(type(other))) newobj = MatchCodes(self) - for key, value in other.items(): + for key, value in list(other.items()): newobj[key] = self.get(key, 0) + other[key] return newobj @@ -574,7 +574,7 @@ class SequenceLane(ResultLane): LOGGER.info("summarizing results for %s" % (pathname)) lines = 0 f = open(pathname) - for l in f.xreadlines(): + for l in f: lines += 1 f.close() @@ -589,7 +589,7 @@ class SequenceLane(ResultLane): def get_elements(self): lane = ElementTree.Element(SequenceLane.LANE, {'version': - unicode(SequenceLane.XML_VERSION)}) + str(SequenceLane.XML_VERSION)}) sample_tag = ElementTree.SubElement(lane, SAMPLE_NAME) sample_tag.text = self.sample_name lane_tag = ElementTree.SubElement(lane, LANE_ID) @@ -598,16 +598,16 @@ class SequenceLane(ResultLane): end_tag = ElementTree.SubElement(lane, END) end_tag.text = str(self.end) reads = ElementTree.SubElement(lane, READS) - reads.text = unicode(self.reads) + reads.text = str(self.reads) sequence_type = ElementTree.SubElement(lane, SequenceLane.SEQUENCE_TYPE) - sequence_type.text = unicode(SequenceLane.SEQUENCE_DESCRIPTION[self.sequence_type]) + sequence_type.text = str(SequenceLane.SEQUENCE_DESCRIPTION[self.sequence_type]) return lane def set_elements(self, tree): if tree.tag != SequenceLane.LANE: raise ValueError('Exptecting %s' % (SequenceLane.LANE,)) - lookup_sequence_type = dict([ (v,k) for k,v in SequenceLane.SEQUENCE_DESCRIPTION.items()]) + lookup_sequence_type = dict([ (v,k) for k,v in list(SequenceLane.SEQUENCE_DESCRIPTION.items())]) for element in tree: tag = element.tag.lower() @@ -657,7 +657,7 @@ class ELAND(collections.MutableMapping): del self.result[key] def __iter__(self): - keys = self.results.iterkeys() + keys = iter(self.results.keys()) for k in sorted(keys): yield k @@ -670,18 +670,18 @@ class ELAND(collections.MutableMapping): raise ValueError("Key must be a %s" % (str(type(SampleKey)))) if not search.iswild: yield self[search] - for key in self.keys(): + for key in list(self.keys()): if key.matches(search): yield key def get_elements(self): root = ElementTree.Element(ELAND.ELAND, - {'version': unicode(ELAND.XML_VERSION)}) + {'version': str(ELAND.XML_VERSION)}) for key in self: eland_lane = self[key].get_elements() - eland_lane.attrib[ELAND.END] = unicode(self[key].end-1) - eland_lane.attrib[ELAND.LANE_ID] = unicode(self[key].lane_id) - eland_lane.attrib[ELAND.SAMPLE] = unicode(self[key].sample_name) + eland_lane.attrib[ELAND.END] = str(self[key].end-1) + eland_lane.attrib[ELAND.LANE_ID] = str(self[key].lane_id) + eland_lane.attrib[ELAND.SAMPLE] = str(self[key].sample_name) root.append(eland_lane) return root return root @@ -895,7 +895,7 @@ def main(cmdline=None): for a in args: LOGGER.info("Starting scan of %s" % (a,)) e = eland(a) - print ElementTree.tostring(e.get_elements()) + print(ElementTree.tostring(e.get_elements())) return