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Reader compatible with files opened in bytes mode #305

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Reader compatible with files opened in bytes mode #305

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3ee5a93
Added support for bytes read files (ie. for remote files)
jkoestinger Oct 2, 2018
8df5301
Rectified error in implementation
jkoestinger Oct 2, 2018
46c1c8a
Fixed typo
jkoestinger Oct 2, 2018
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18 changes: 17 additions & 1 deletion vcf/parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -297,9 +297,9 @@ def __init__(self, fsock=None, filename=None, compressed=None, prepend_chr=False
self._column_headers = []
self._tabix = None
self._prepend_chr = prepend_chr
self.encoding = encoding
self._parse_metainfo()
self._format_cache = {}
self.encoding = encoding

def __iter__(self):
return self
Expand All @@ -315,6 +315,12 @@ def _parse_metainfo(self):
parser = _vcf_metadata_parser()

line = next(self.reader)

try:
line = line.decode(self.encoding)
except AttributeError:
pass

while line.startswith('##'):
self._header_lines.append(line)

Expand Down Expand Up @@ -348,6 +354,10 @@ def _parse_metainfo(self):
self.metadata[key].append(val)

line = next(self.reader)
try:
line = line.decode(self.encoding)
except AttributeError:
pass

fields = self._row_pattern.split(line[1:])
self._column_headers = fields[:9]
Expand Down Expand Up @@ -551,6 +561,12 @@ def _parse_alt(self, str):
def next(self):
'''Return the next record in the file.'''
line = next(self.reader)

try:
line = line.decode(self.encoding)
except AttributeError:
pass

row = self._row_pattern.split(line.rstrip())
chrom = row[0]
if self._prepend_chr:
Expand Down