zoophy / geoboost2 Goto Github PK

Installed geonames and geoboost2 as instructed. Renamed zodo/settings_template.py to zodo/settings.py and made the following changes: 1) added personal API key; 2) changed USE_REDIS value from "True" to "False". Attempted to implement demo code (with custom newline delimited accession file):

python run.py genbank examples/ebola_accessions.txt out/ebola/

Encountered the following error:

Traceback (most recent call last): File "run.py", line 191, in <module> main() File "run.py", line 184, in main extract_genbank_loih(args) File "run.py", line 87, in extract_genbank_loih write_genbank_run_results(gb_req, args.outdir) File "run.py", line 52, in write_genbank_run_results df.to_csv(out_dir, sep='\t') File "/home/firstname_lastname/.local/lib/python3.7/site-packages/pandas/core/generic.py", line 3204, in to_csv formatter.save() File "/home/firstname_lastname/.local/lib/python3.7/site-packages/pandas/io/formats/csvs.py", line 188, in save compression=dict(self.compression_args, method=self.compression), File "/home/firstname_lastname/.local/lib/python3.7/site-packages/pandas/io/common.py", line 455, in get_handle f = open(path_or_buf, mode, encoding=encoding, newline="") FileNotFoundError: [Errno 2] No such file or directory: 'out/PRRSV-Austria/Confidence.tsv'

Edit1 - target files/directories were full read/write accessible (777)
Edit2 - Identified user error. Closing...

Installed geonames and geoboost2 as instructed. Renamed zodo/settings_template.py to zodo/settings.py and made the following changes: 1) added personal API key; 2) changed USE_REDIS value from "True" to "False". Attempted to run unit test:

pytest tests/

Encountered the following error:

ImportError while importing test module '/mnt/c/Users/firstname lastname/Documents/geoboost2-master/tests/test_accessions.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: tests/test_accessions.py:6: in <module> from geopy.distance import geodesic E ImportError: cannot import name 'geodesic' from 'geopy.distance' (/home/firstname_lastname/.local/lib/python3.7/site-packages/geopy/distance.py)

Python version == 3.7.9
geopy version == 1.12.0