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simon-anders / htseq

HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
https://htseq.readthedocs.io/en/release_0.11.1/
GNU General Public License v3.0
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Error when iterating FastqReader(fastq.gz) #32

Closed Puriney closed 7 years ago

Puriney commented 7 years ago 
File "foo_iter_fastqgz.py", line 9, in <module>
    for read in FastqReader(fpath):
  File "/ifs/home/yy1533/SHARED_APP/miniconda3/lib/python3.6/site-packages/HTSeq/__init__.py", line 392, in __iter__
    if not qual.endswith( "\n" ):
TypeError: endswith first arg must be bytes or a tuple of bytes, not str

There was no problem when running FastqReader(fastq) but error was reported when using fastq.gz file.

Py3.6 with HTseq installed by pip install HTSeq.

iosonofabio commented 7 years ago

Thx that's a bug will fix ASAP

On June 15, 2017 7:49:57 AM PDT, Yun YAN notifications@github.com wrote:

File "foo_iter_fastqgz.py", line 9, in <module>
   for read in FastqReader(fpath):
File
"/ifs/home/yy1533/SHARED_APP/miniconda3/lib/python3.6/site-packages/HTSeq/__init__.py",
line 392, in __iter__
   if not qual.endswith( "\n" ):
TypeError: endswith first arg must be bytes or a tuple of bytes, not
str

There was no problem when running FastqReader(fastq) but error was reported when using fastq.gz file.

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iosonofabio commented 7 years ago

fixed in 7fae5ea, will be in 0.9.0