Description: Convert python2 syntax to python3 Author: Nilesh Patra Last-Update: 2021-10-15 --- a/docs/conf.py +++ b/docs/conf.py @@ -40,8 +40,8 @@ master_doc = 'index' # General information about the project. -project = u'PyVCF' -copyright = u'2012, James Casbon, @jdoughertyii' +project = 'PyVCF' +copyright = '2012, James Casbon, @jdoughertyii' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the @@ -179,8 +179,8 @@ # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, author, documentclass [howto/manual]). latex_documents = [ - ('index', 'PyVCF.tex', u'PyVCF Documentation', - u'James Casbon, @jdoughertyii', 'manual'), + ('index', 'PyVCF.tex', 'PyVCF Documentation', + 'James Casbon, @jdoughertyii', 'manual'), ] # The name of an image file (relative to this directory) to place at the top of @@ -212,6 +212,6 @@ # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). man_pages = [ - ('index', 'pyvcf', u'PyVCF Documentation', - [u'James Casbon, @jdoughertyii'], 1) + ('index', 'pyvcf', 'PyVCF Documentation', + ['James Casbon, @jdoughertyii'], 1) ] --- a/scripts/vcf_filter.py +++ b/scripts/vcf_filter.py @@ -108,7 +108,7 @@ while len(args.rest): filter_name = args.rest.pop(0) if filter_name not in filters: - sys.exit("%s is not a known filter (%s)" % (filter_name, str(filters.keys()))) + sys.exit("%s is not a known filter (%s)" % (filter_name, str(list(filters.keys())))) # create a parser only for arguments of current filter filt_parser = create_filt_parser(filter_name) --- a/scripts/vcf_sample_filter.py +++ b/scripts/vcf_sample_filter.py @@ -34,6 +34,6 @@ sf = SampleFilter(infile=args.file, outfile=args.o, filters=args.f, invert=args.invert) if args.f is None: - print "Samples:" + print("Samples:") for idx, val in enumerate(sf.samples): - print "{0}: {1}".format(idx, val) + print("{0}: {1}".format(idx, val)) --- a/vcf/model.py +++ b/vcf/model.py @@ -362,7 +362,7 @@ If there are i alleles with frequency p_i, H=1-sum_i(p_i^2) """ allele_freqs = [1-sum(self.aaf)] + self.aaf - return 1 - sum(map(lambda x: x**2, allele_freqs)) + return 1 - sum([x**2 for x in allele_freqs]) def get_hom_refs(self): """ The list of hom ref genotypes""" @@ -558,9 +558,8 @@ return True -class _AltRecord(object): +class _AltRecord(object, metaclass=ABCMeta): '''An alternative allele record: either replacement string, SV placeholder, or breakend''' - __metaclass__ = ABCMeta def __init__(self, type, **kwargs): super(_AltRecord, self).__init__(**kwargs) @@ -596,7 +595,7 @@ return len(self.sequence) def __eq__(self, other): - if isinstance(other, basestring): + if isinstance(other, str): return self.sequence == other elif not isinstance(other, self.__class__): return False --- a/vcf/parser.py +++ b/vcf/parser.py @@ -22,8 +22,8 @@ except ImportError: cparse = None -from model import _Call, _Record, make_calldata_tuple -from model import _Substitution, _Breakend, _SingleBreakend, _SV +from .model import _Call, _Record, make_calldata_tuple +from .model import _Substitution, _Breakend, _SingleBreakend, _SV # Metadata parsers/constants @@ -468,7 +468,7 @@ nfields = len(samp_fmt._fields) - for name, sample in itertools.izip(self.samples, samples): + for name, sample in zip(self.samples, samples): # parse the data for this sample sampdat = [None] * nfields @@ -548,7 +548,7 @@ else: return _Substitution(str) - def next(self): + def __next__(self): '''Return the next record in the file.''' line = next(self.reader) row = self._row_pattern.split(line.rstrip()) @@ -641,7 +641,7 @@ """VCF Writer. On Windows Python 2, open stream with 'wb'.""" # Reverse keys and values in header field count dictionary - counts = dict((v,k) for k,v in field_counts.iteritems()) + counts = dict((v,k) for k,v in field_counts.items()) def __init__(self, stream, template, lineterminator="\n"): self.writer = csv.writer(stream, delimiter="\t", @@ -654,30 +654,30 @@ # get a maximum key). self.info_order = collections.defaultdict( lambda: len(template.infos), - dict(zip(template.infos.iterkeys(), itertools.count()))) + dict(list(zip(iter(template.infos.keys()), itertools.count())))) two = '##{key}=\n' four = '##{key}=\n' _num = self._fix_field_count - for (key, vals) in template.metadata.iteritems(): + for (key, vals) in template.metadata.items(): if key in SINGULAR_METADATA: vals = [vals] for val in vals: if isinstance(val, dict): values = ','.join('{0}={1}'.format(key, value) - for key, value in val.items()) + for key, value in list(val.items())) stream.write('##{0}=<{1}>\n'.format(key, values)) else: stream.write('##{0}={1}\n'.format(key, val)) - for line in template.infos.itervalues(): + for line in template.infos.values(): stream.write(four.format(key="INFO", *line, num=_num(line.num))) - for line in template.formats.itervalues(): + for line in template.formats.values(): stream.write(four.format(key="FORMAT", *line, num=_num(line.num))) - for line in template.filters.itervalues(): + for line in template.filters.values(): stream.write(two.format(key="FILTER", *line)) - for line in template.alts.itervalues(): + for line in template.alts.values(): stream.write(two.format(key="ALT", *line)) - for line in template.contigs.itervalues(): + for line in template.contigs.values(): if line.length: stream.write('##contig=\n'.format(*line)) else: --- a/vcf/sample_filter.py +++ b/vcf/sample_filter.py @@ -7,7 +7,7 @@ import warnings -from parser import Reader, Writer +from .parser import Reader, Writer class SampleFilter(object): @@ -81,13 +81,13 @@ # is int, check if it's an idx if item < len(self.samples): return item - filters = set(filter(lambda x: x is not None, map(filt2idx, filt_s))) + filters = set([x for x in map(filt2idx, filt_s) if x is not None]) if len(filters) < len(filt_s): # TODO print the filters that were ignored warnings.warn("Invalid filters, ignoring", RuntimeWarning) if self.invert: - filters = set(xrange(len(self.samples))).difference(filters) + filters = set(range(len(self.samples))).difference(filters) # `sample_filter` setter updates `samples` self.parser.sample_filter = filters --- a/vcf/test/prof.py +++ b/vcf/test/prof.py @@ -19,7 +19,7 @@ elif sys.argv[1] == 'time': n = 1 t = timeit.timeit('parse_1kg()', "from __main__ import parse_1kg", number=n) - print t/n + print(t/n) elif sys.argv[1] == 'stat': import statprof @@ -30,4 +30,4 @@ statprof.stop() statprof.display() else: - print 'prof.py profile/time' + print('prof.py profile/time') --- a/vcf/test/test_vcf.py +++ b/vcf/test/test_vcf.py @@ -1,4 +1,4 @@ -from __future__ import print_function + import unittest try: unittest.skip @@ -6,9 +6,9 @@ import unittest2 as unittest import doctest import os -import commands -import cPickle -from StringIO import StringIO +import subprocess +import pickle +from io import StringIO import subprocess import sys @@ -137,7 +137,7 @@ """Test VCF inputs with ##contig inputs containing only IDs. produced by bcftools 1.2+ """ reader = vcf.Reader(fh("contig_idonly.vcf")) - for cid, contig in reader.contigs.items(): + for cid, contig in list(reader.contigs.items()): if cid == "1": assert contig.length is None elif cid == "2": @@ -390,24 +390,24 @@ reader2 = vcf.Reader(out) for l, r in zip(records, reader2): - self.assertEquals(l.INFO, r.INFO) + self.assertEqual(l.INFO, r.INFO) class TestBadInfoFields(unittest.TestCase): def test_parse(self): reader = vcf.Reader(fh('bad-info-character.vcf')) record = next(reader) - self.assertEquals(record.INFO['DOT_1'], None) - self.assertEquals(record.INFO['DOT_3'], [None, None, None]) - self.assertEquals(record.INFO['DOT_N'], [None]) - self.assertEquals(record.INFO['EMPTY_1'], None) + self.assertEqual(record.INFO['DOT_1'], None) + self.assertEqual(record.INFO['DOT_3'], [None, None, None]) + self.assertEqual(record.INFO['DOT_N'], [None]) + self.assertEqual(record.INFO['EMPTY_1'], None) # Perhaps EMPTY_3 should yield [None, None, None] but this is really a # cornercase of unspecified behaviour. - self.assertEquals(record.INFO['EMPTY_3'], [None]) - self.assertEquals(record.INFO['EMPTY_N'], [None]) - self.assertEquals(record.INFO['NOTEMPTY_1'], 1) - self.assertEquals(record.INFO['NOTEMPTY_3'], [1, 2, 3]) - self.assertEquals(record.INFO['NOTEMPTY_N'], [1]) + self.assertEqual(record.INFO['EMPTY_3'], [None]) + self.assertEqual(record.INFO['EMPTY_N'], [None]) + self.assertEqual(record.INFO['NOTEMPTY_1'], 1) + self.assertEqual(record.INFO['NOTEMPTY_3'], [1, 2, 3]) + self.assertEqual(record.INFO['NOTEMPTY_N'], [1]) pass @@ -440,7 +440,7 @@ self.assertEqual(f['Options'], '"< 4 and > 3"') for l, r in zip(records, reader2): - self.assertEquals(l.INFO, r.INFO) + self.assertEqual(l.INFO, r.INFO) class TestGatkOutputWriter(unittest.TestCase): @@ -463,13 +463,13 @@ print (out_str) reader2 = vcf.Reader(out) - self.assertEquals(reader.samples, reader2.samples) - self.assertEquals(reader.formats, reader2.formats) - self.assertEquals(reader.infos, reader2.infos) - self.assertEquals(reader.contigs, reader2.contigs) + self.assertEqual(reader.samples, reader2.samples) + self.assertEqual(reader.formats, reader2.formats) + self.assertEqual(reader.infos, reader2.infos) + self.assertEqual(reader.contigs, reader2.contigs) for l, r in zip(records, reader2): - self.assertEquals(l.samples, r.samples) + self.assertEqual(l.samples, r.samples) # test for call data equality, since equality on the sample calls # may not always mean their data are all equal @@ -493,12 +493,12 @@ print (out.getvalue()) reader2 = vcf.Reader(out) - self.assertEquals(reader.samples, reader2.samples) - self.assertEquals(reader.formats, reader2.formats) - self.assertEquals(reader.infos, reader2.infos) + self.assertEqual(reader.samples, reader2.samples) + self.assertEqual(reader.formats, reader2.formats) + self.assertEqual(reader.infos, reader2.infos) for l, r in zip(records, reader2): - self.assertEquals(l.samples, r.samples) + self.assertEqual(l.samples, r.samples) # test for call data equality, since equality on the sample calls # may not always mean their data are all equal @@ -522,7 +522,7 @@ out_str = out.getvalue() for line in out_str.split("\n"): if line.startswith("##PEDIGREE"): - self.assertEquals(line, '##PEDIGREE=') + self.assertEqual(line, '##PEDIGREE=') if line.startswith("##SAMPLE"): assert line.startswith('##SAMPLE=<'), "Found dictionary in meta line: {0}".format(line) @@ -955,7 +955,7 @@ def test_pickle(self): reader = vcf.Reader(fh('example-4.0.vcf')) for var in reader: - self.assertEqual(cPickle.loads(cPickle.dumps(var)), var) + self.assertEqual(pickle.loads(pickle.dumps(var)), var) def assert_has_expected_coordinates( @@ -1498,7 +1498,7 @@ @unittest.skip("test currently broken") def testApplyFilter(self): # FIXME: broken with distribute - s, out = commands.getstatusoutput('python scripts/vcf_filter.py --site-quality 30 test/example-4.0.vcf sq') + s, out = subprocess.getstatusoutput('python scripts/vcf_filter.py --site-quality 30 test/example-4.0.vcf sq') #print(out) self.assertEqual(s, 0) buf = StringIO() @@ -1528,7 +1528,7 @@ @unittest.skip("test currently broken") def testApplyMultipleFilters(self): # FIXME: broken with distribute - s, out = commands.getstatusoutput('python scripts/vcf_filter.py --site-quality 30 ' + s, out = subprocess.getstatusoutput('python scripts/vcf_filter.py --site-quality 30 ' '--genotype-quality 50 test/example-4.0.vcf sq mgq') self.assertEqual(s, 0) #print(out) @@ -1599,7 +1599,7 @@ assert recs[1] is not None # test files with many chromosomes, set 'vcf_record_sort_key' to define chromosome order - chr_order = map(str, range(1, 30)) + ['X', 'Y', 'M'] + chr_order = list(map(str, list(range(1, 30)))) + ['X', 'Y', 'M'] get_key = lambda r: (chr_order.index(r.CHROM.replace('chr','')), r.POS) reader1 = vcf.Reader(fh('issue-140-file1.vcf')) reader2 = vcf.Reader(fh('issue-140-file2.vcf')) --- a/vcf/utils.py +++ b/vcf/utils.py @@ -37,19 +37,19 @@ next_idx_to_k = dict( (i, get_key(r)) for i, r in enumerate(nexts) if r is not None) keys_with_prev_contig = [ - k for k in next_idx_to_k.values() if k[0] == min_k[0]] + k for k in list(next_idx_to_k.values()) if k[0] == min_k[0]] if any(keys_with_prev_contig): min_k = min(keys_with_prev_contig) # finish previous contig else: min_k = min(next_idx_to_k.values()) # move on to next contig - min_k_idxs = set([i for i, k in next_idx_to_k.items() if k == min_k]) + min_k_idxs = set([i for i, k in list(next_idx_to_k.items()) if k == min_k]) yield [nexts[i] if i in min_k_idxs else None for i in range(len(nexts))] for i in min_k_idxs: try: - nexts[i] = readers[i].next() + nexts[i] = next(readers[i]) except StopIteration: nexts[i] = None