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Ignore empty lines #73

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merged 2 commits into from
Sep 25, 2012
Merged

Ignore empty lines #73

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61c08ec
Skip lines with only whitespace
martijnvermaat Sep 23, 2012
9712355
Strip whitespace only once
martijnvermaat Sep 23, 2012
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17 changes: 9 additions & 8 deletions vcf/parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -185,18 +185,20 @@ def __init__(self, fsock=None, filename=None, compressed=False, prepend_chr=Fals
raise Exception('You must provide at least fsock or filename')

if fsock:
self.reader = fsock
self._reader = fsock
if filename is None and hasattr(fsock, 'name'):
filename = fsock.name
compressed = compressed or filename.endswith('.gz')
elif filename:
compressed = compressed or filename.endswith('.gz')
self.reader = open(filename, 'rb' if compressed else 'rt')
self._reader = open(filename, 'rb' if compressed else 'rt')
self.filename = filename
if compressed:
self.reader = gzip.GzipFile(fileobj=self.reader)
self._reader = gzip.GzipFile(fileobj=self._reader)
if sys.version > '3':
self.reader = codecs.getreader('ascii')(self.reader)
self._reader = codecs.getreader('ascii')(self._reader)

self.reader = (line.strip() for line in self._reader if line.strip())

#: metadata fields from header (string or hash, depending)
self.metadata = None
Expand Down Expand Up @@ -232,7 +234,6 @@ def _parse_metainfo(self):
line = self.reader.next()
while line.startswith('##'):
self._header_lines.append(line)
line = line.strip()

if line.startswith('##INFO'):
key, val = parser.read_info(line)
Expand All @@ -251,7 +252,7 @@ def _parse_metainfo(self):
self.formats[key] = val

else:
key, val = parser.read_meta(line.strip())
key, val = parser.read_meta(line)
if key in SINGULAR_METADATA:
self.metadata[key] = val
else:
Expand All @@ -261,7 +262,7 @@ def _parse_metainfo(self):

line = self.reader.next()

fields = re.split('\t| +', line.rstrip())
fields = re.split('\t| +', line)
self.samples = fields[9:]
self._sample_indexes = dict([(x,i) for (i,x) in enumerate(self.samples)])

Expand Down Expand Up @@ -436,7 +437,7 @@ def _parse_alt(self, str):
def next(self):
'''Return the next record in the file.'''
line = self.reader.next()
row = re.split('\t| +', line.strip())
row = re.split('\t| +', line)
chrom = row[0]
if self._prepend_chr:
chrom = 'chr' + chrom
Expand Down