more meaningful error in gsm.download_supplementary_files

[antonkulaga]

Whenever I try to use it it downloads everything, but in the end tells me:

Converting to /home/antonkulaga/rna-seq/containers/geoparse/GSM1696283/Supp_GSM1696283_Transgenic_Control_L4_A/SRR2040662_*.fasta.gz
Traceback (most recent call last):
  File "<input>", line 1, in <module>
  File "/home/antonkulaga/rna-seq/containers/geoparse/env/lib/python3.5/site-packages/GEOparse/GEOTypes.py", line 352, in download_supplementary_files
    self.download_SRA(email, filetype=sra_filetype, directory=directory)
  File "/home/antonkulaga/rna-seq/containers/geoparse/env/lib/python3.5/site-packages/GEOparse/GEOTypes.py", line 463, in download_SRA
    if "command not found" in perr:
TypeError: a bytes-like object is required, not 'str'

Probably it tries to find some SRA tools in the path. So, it is better just to say that SRA tools are not in the PATH

[guma44]

What python version do you use?

[antonkulaga]

python 3.5

[guma44]

I am looking at it.

[guma44]

Probably you do not have SRAToolkit but this you might know.

[antonkulaga]

Yes, just saw that there's a problem with the path, but it would be nice to have some meaningful error telling about it, not cryptic "TypeError: a bytes-like object is required, not 'str'"

[guma44]

The check procedure is giving error here. One line below there is a meaning full error returned :). Here is the problem described: https://stackoverflow.com/questions/606191/convert-bytes-to-a-python-string. As subprocess.cummunicate returns bytes not string in python 3.5.

[guma44]

I corrected this error.

[antonkulaga]

is the fix already in master?

On Jun 26, 2017 16:20, "Rafal Gumienny" notifications@github.com wrote:

I corrected this error.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/guma44/GEOparse/issues/24#issuecomment-311057088, or mute the thread https://github.com/notifications/unsubscribe-auth/AAzaxCOqu3OSyruf6bEnvFZ0-jjKMnhcks5sH7AegaJpZM4OFD75 .

[guma44]

yes