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stdlibStandard Library Python modules in the Lib/ directoryStandard Library Python modules in the Lib/ directorytype-featureA feature request or enhancementA feature request or enhancement
Description
Bug report
csv file:
sample,is_nc,fastq_1,fastq_2
5B7822-M1-U055G,False,data/5B7822-M1-U055G_S12_R1_001.fastq.gz,
5B7822-M1-U042G,False,data/5B7822-M1-U042G_S3_R1_001.fastq.gz,
5B7821-M1-U054G,False,data/5B7821-M1-U054G_S11_R1_001.fastq.gz,
5B7821-M1-U041G,False,data/5B7821-M1-U041G_S2_R1_001.fastq.gz,
5M26799-M1-U043G,False,data/5M26799-M1-U043G_S4_R1_001.fastq.gz,
5M26799-M1-U056G,False,data/5M26799-M1-U056G_S13_R1_001.fastq.gz,
5M26800-M1-U044G,False,data/5M26800-M1-U044G_S5_R1_001.fastq.gz,
5M26800-M1-U057G,False,data/5M26800-M1-U057G_S14_R1_001.fastq.gz,
5M26802-M1-U046G,False,data/5M26802-M1-U046G_S6_R1_001.fastq.gz,
code:
def read_head(handle, num_lines=2):
"""Read the specified number of lines from the current position in the file."""
lines = []
for idx, line in enumerate(handle):
if idx == num_lines:
break
lines.append(line)
return "".join(lines)
def sniff_format(handle):
"""
Detect the tabular format.
Args:
handle (text file): A handle to a `text file`_ object. The read position is
expected to be at the beginning (index 0).
Returns:
csv.Dialect: The detected tabular format.
.. _text file:
https://docs.python.org/3/glossary.html#term-text-file
"""
peek = read_head(handle)
handle.seek(0)
sniffer = csv.Sniffer()
if not sniffer.has_header(peek):
logger.critical("The given sample sheet does not appear to contain a header.")
sys.exit(1)
dialect = sniffer.sniff(peek)
return dialectYour environment
- CPython versions tested on: 3.8.3
- Operating system and architecture: Ubuntu 20.04.3 LTS
Comments
This bug does not only occur with v3.8.3, it occurs also with version 3.11.3.
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stdlibStandard Library Python modules in the Lib/ directoryStandard Library Python modules in the Lib/ directorytype-featureA feature request or enhancementA feature request or enhancement
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