def sff_filter(in_file, out_file, iterator_filter, inter): count = 0 try: from Bio.SeqIO.SffIO import ReadRocheXmlManifest except ImportError: # Prior to Biopython 1.56 this was a private function from Bio.SeqIO.SffIO import _sff_read_roche_index_xml as ReadRocheXmlManifest with open(in_file, "rb") as in_handle: try: manifest = ReadRocheXmlManifest(in_handle) except ValueError: manifest = None in_handle.seek(0) with open(out_file, "wb") as out_handle: writer = SffWriter(out_handle, xml=manifest) in_handle.seek(0) # start again after getting manifest if inter: from itertools import chain count = writer.write_file( chain.from_iterable( iterator_filter(pair(SffIterator(in_handle))))) assert count % 2 == 0, "Odd number of records? %i" % count count /= 2 else: count = writer.write_file( iterator_filter(SffIterator(in_handle))) return count
def test_no_manifest_xml(self): with open("Roche/E3MFGYR02_no_manifest.sff", "rb") as handle: try: xml = ReadRocheXmlManifest(handle) except ValueError as err: self.assertEqual(str(err), "No XML manifest found") else: self.assertTrue(False, "ReadRocheXmlManifest did not raise exception")
def sff_filter(in_file, pos_file, neg_file, wanted): """SFF filter.""" try: from Bio.SeqIO.SffIO import SffIterator, SffWriter except ImportError: sys.exit("SFF filtering requires Biopython 1.54 or later") try: from Bio.SeqIO.SffIO import ReadRocheXmlManifest except ImportError: # Prior to Biopython 1.56 this was a private function from Bio.SeqIO.SffIO import _sff_read_roche_index_xml as ReadRocheXmlManifest in_handle = open(in_file, "rb") # must be binary mode! try: manifest = ReadRocheXmlManifest(in_handle) except ValueError: manifest = None # This makes two passes though the SFF file with isn't so efficient, # but this makes the code simple. pos_count = neg_count = 0 if pos_file is not None: out_handle = open(pos_file, "wb") writer = SffWriter(out_handle, xml=manifest) in_handle.seek(0) # start again after getting manifest pos_count = writer.write_file(rec for rec in SffIterator(in_handle) if clean_name(rec.id) in wanted) out_handle.close() if neg_file is not None: out_handle = open(neg_file, "wb") writer = SffWriter(out_handle, xml=manifest) in_handle.seek(0) # start again neg_count = writer.write_file(rec for rec in SffIterator(in_handle) if clean_name(rec.id) not in wanted) out_handle.close() # And we're done in_handle.close() # At the time of writing, Galaxy doesn't show SFF file read counts, # so it is useful to put them in stdout and thus shown in job info. return pos_count, neg_count
def test_write(self): filename = "Roche/E3MFGYR02_random_10_reads.sff" with open(filename, "rb") as handle: metadata = ReadRocheXmlManifest(handle) with open(filename, "rb") as handle: sff = list(SffIterator(handle)) b_handle = BytesIO() w = SffWriter(b_handle, xml=metadata) w.write_file(sff) # list data = b_handle.getvalue() # And again with an iterator... handle = BytesIO() w = SffWriter(handle, xml=metadata) w.write_file(iter(sff)) self.assertEqual(data, handle.getvalue()) # Check 100% identical to the original: with open(filename, "rb") as handle: original = handle.read() self.assertEqual(len(data), len(original)) self.assertEqual(data, original) del data
def sff_filter(in_file, out_file, iterator_filter): count = 0 try: from Bio.SeqIO.SffIO import SffIterator, SffWriter except ImportError: stop_err("SFF filtering requires Biopython 1.54 or later") try: from Bio.SeqIO.SffIO import ReadRocheXmlManifest except ImportError: #Prior to Biopython 1.56 this was a private function from Bio.SeqIO.SffIO import _sff_read_roche_index_xml as ReadRocheXmlManifest with open(in_file, "rb") as in_handle: try: manifest = ReadRocheXmlManifest(in_handle) except ValueError: manifest = None in_handle.seek(0) with open(out_file, "wb") as out_handle: writer = SffWriter(out_handle, xml=manifest) in_handle.seek(0) #start again after getting manifest count = writer.write_file(iterator_filter(SffIterator(in_handle))) #count = writer.write_file(SffIterator(in_handle)) return count
record.annotations[ "clip_qual_right"] = left_clip + new_len clipped += 1 yield record else: short_clipped += 1 elif keep_negatives: if len(seq) >= min_len: negs += 1 yield record else: short_neg += 1 in_handle = open(in_file, "rb") try: manifest = ReadRocheXmlManifest(in_handle) except ValueError: manifest = None in_handle.seek(0) out_handle = open(out_file, "wb") writer = SffWriter(out_handle, xml=manifest) writer.write_file(process(SffIterator(in_handle))) #End of SFF code elif seq_format.lower().startswith("fastq"): in_handle = open(in_file, "rU") out_handle = open(out_file, "w") reader = fastqReader(in_handle) writer = fastqWriter(out_handle) if forward: for record in reader: seq = record.sequence.upper()
def test_manifest(self): filename = "Roche/E3MFGYR02_random_10_reads.sff" with open(filename, "rb") as handle: metadata = ReadRocheXmlManifest(handle)
def test_no_manifest_xml(self): with open("Roche/E3MFGYR02_no_manifest.sff", "rb") as handle: with self.assertRaises(ValueError) as cm: xml = ReadRocheXmlManifest(handle) self.assertEqual(str(cm.exception), "No XML manifest found")
# Ugly bit of code to make a fake index at end with open("Roche/E3MFGYR02_random_10_reads.sff", "rb") as handle: records = list(SffIterator(handle)) with open("Roche/E3MFGYR02_alt_index_at_end.sff", "w") as out_handle: w = SffWriter(out_handle, index=False, xml=None) # Fake the header... w._number_of_reads = len(records) w._index_start = 0 w._index_length = 0 w._key_sequence = records[0].annotations["flow_key"] w._flow_chars = records[0].annotations["flow_chars"] w._number_of_flows_per_read = len(w._flow_chars) w.write_header() for record in records: w.write_record(record) w._index_start = out_handle.tell() w._index_length = len(index) out_handle.write(index) out_handle.seek(0) w.write_header() # this time with index info with open("Roche/E3MFGYR02_alt_index_at_end.sff", "rb") as handle: records2 = list(SffIterator(handle)) for old, new in zip(records, records2): assert old.seq == new.seq with unittest.TestCase.assertRaises(None, ValueError): with open("Roche/E3MFGYR02_alt_index_at_end.sff", "rb") as handle: print(ReadRocheXmlManifest(handle)) with open("Roche/E3MFGYR02_alt_index_at_end.sff", "rb") as handle: k = list(_sff_do_slow_index(handle)) print("Done")
records = list( SffIterator(open("Roche/E3MFGYR02_random_10_reads.sff", "rb"))) with open("Roche/E3MFGYR02_alt_index_at_end.sff", "w") as out_handle: w = SffWriter(out_handle, index=False, xml=None) # Fake the header... w._number_of_reads = len(records) w._index_start = 0 w._index_length = 0 w._key_sequence = records[0].annotations["flow_key"] w._flow_chars = records[0].annotations["flow_chars"] w._number_of_flows_per_read = len(w._flow_chars) w.write_header() for record in records: w.write_record(record) w._index_start = out_handle.tell() w._index_length = len(index) out_handle.write(index) out_handle.seek(0) w.write_header() # this time with index info records2 = list( SffIterator(open("Roche/E3MFGYR02_alt_index_at_end.sff", "rb"))) for old, new in zip(records, records2): assert str(old.seq) == str(new.seq) with unittest.TestCase.assertRaises(None, ValueError): print( ReadRocheXmlManifest( open("Roche/E3MFGYR02_alt_index_at_end.sff", "rb"))) k = list( _sff_do_slow_index(open("Roche/E3MFGYR02_alt_index_at_end.sff", "rb"))) print("Done")