RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode .....

[EricDeveaud]

Hello,

while runnin the test suite for pyseer-1.3.5 I got this warning

RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode

see

gensoft@06b71d9a76fe tests]$ annotate_hits_pyseer significant_kmers.txt references.txt /dev/null
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem -v 1 -k 8 Spn23F.fa /local/gensoft2/src/pyseer/pyseer-1.3.5/tests/remaining_kmers.fa
[main] Real time: 2.348 sec; CPU: 2.303 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[main] Version: 0.7.17-r1188
[main] CMD: bwa fastmap -l 9 Spn23F.fa /local/gensoft2/src/pyseer/pyseer-1.3.5/tests/remaining_kmers.fa
[main] Real time: 0.192 sec; CPU: 0.199 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[main] Version: 0.7.17-r1188
[main] CMD: bwa fastmap -l 9 6952_7#3.fa /local/gensoft2/src/pyseer/pyseer-1.3.5/tests/remaining_kmers.fa
[main] Real time: 0.200 sec; CPU: 0.207 sec
5348 kmers remain
Reference 1
/local/gensoft2/adm/Python/3.8/lib/python3.8/subprocess.py:849: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used
  self.stderr = io.open(errread, 'rb', bufsize)
/local/gensoft2/adm/Python/3.8/lib/python3.8/subprocess.py:844: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used
  self.stdout = io.open(c2pread, 'rb', bufsize)

[mgalardini]

Hi, thanks for reporting this; I think this warning has been introduced since python 3.8. I've checked and this warning is raised whenever pybedtools is called. I'll check to see if we can remove it from our side, otherwise I'll open an issue with them and wait for it to be resolved upstream.

[mgalardini]

This is the issue opened for pybedtools: daler/pybedtools#322