[BUG] - Githubissues

Describe the bug Example command from the README.rst is not working on a fresh install.

To Reproduce Steps to reproduce the behavior:

pip install pysradb;
pysradb metadata SRP000941 --detailed | grep 'study\|RNA-Seq' | pysradb download

Desktop (please complete the following information):

OS:

Linux 5.19.0-35-generic #36~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Fri Feb 17 15:17:25 UTC 2 x86_64 x86_64 x86_64 GNU/Linux

Python version:

$ pip --version
pip 22.0.2 from /usr/lib/python3/dist-packages/pip (python 3.10)
$ python
sh: 5: python: not found
$ python3 --version
Python 3.10.6

Additional context Output to terminal looks like this:


No URL column is found.
You may wish to re-run your query with either
pysradb metadata --detailed 
or 
pysradb search -v 3
Generating default download URL for each run accession...

The supplied url column "None" cannot be found.

Using recommended_url instead.

Checking download URLs Key error for: ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR020/SRR020285 SRP000941 UCSD Human Reference Epigenome Mapping Project SRX007166/SRR020285 SRP000941 UCSD Human Reference Epigenome Mapping Project SRX007166.sra Key error for: ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR020/SRR020286 SRP000941 UCSD Human Reference Epigenome Mapping Project SRX007168/SRR020286 SRP000941 UCSD Human Reference Epigenome Mapping Project SRX007168.sra Key error for: ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR020/SRR020287 SRP000941 UCSD Human Reference Epigenome Mapping Project SRX007165/SRR020287 SRP000941 UCSD Human Reference Epigenome Mapping Project SRX007165.sra Key error for: ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR020/SRR020288 SRP000941 UCSD Human Reference Epigenome Mapping Project SRX007165/SRR020288 SRP000941 UCSD Human Reference Epigenome Mapping Project SRX007165.sra Key error for: ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR020/SRR020289 SRP000941 UCSD Human Reference Epigenome Mapping Project SRX007165/SRR020289 SRP000941 UCSD Human Reference Epigenome Mapping Project SRX007165.sra Key error for: ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR020/SRR020290 SRP000941 UCSD Human Reference Epigenome Mapping Project SRX007165/SRR020290 SRP000941 UCSD Human Reference Epigenome Mapping Project SRX007165.sra Key error for: ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR020/SRR020291 SRP000941 UCSD Human Reference Epigenome Mapping Project SRX007165/SRR020291 SRP000941 UCSD Human Reference Epigenome Mapping Project SRX007165.sra Key error for: ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR020/SRR020292 SRP000941 UCSD Human Reference Epigenome Mapping Project SRX007167/SRR020292 SRP000941 UCSD Human Reference Epigenome Mapping Project SRX007167.sra

saketkc / pysradb

[BUG] #192