pysradb search error with specific search term

[jarrodscott]

• pysradb version: 0.9.0
• Python version: Python 3.7.3
• Operating System: Centos

Description

Searching for the term hypoxia worked fine but searching the term hypoxic produced the following error message:

This is most likely a bug, please report it upstream.
sample_attribute: investigation type: metagenome || project name: Landsort Depth 20090415 transect || sequencing method: 454 || collection date: 2009-04-15 || ammonium: 8.7: µM || chlorophyll: 0: µg/L || dissolved oxygen: -1.33: µmol/kg || nitrate: 0.02: µM || nitrogen: 0: µM || environmental package: water || geographic location (latitude): 58.6: DD || geographic location (longitude): 18.2: DD || geographic location (country and/or sea,region): Baltic Sea || environment (biome): 00002150 || environment (feature): 00002150 || environment (material): 00002150 || depth: 400: m || Phosphate:  || Total phosphorous:  || Silicon:
Traceback (most recent call last):
  File "/envs/pysradb/bin/pysradb", line 11, in <module>
    sys.exit(parse_args())
  File "/envs/pysradb/lib/python3.7/site-packages/pysradb/cli.py", line 944, in parse_args
    args.saveto,
  File "/envs/pysradb/lib/python3.7/site-packages/pysradb/cli.py", line 148, in search
    expand_sample_attributes=expand,
  File "/envs/pysradb/lib/python3.7/site-packages/pysradb/sradb.py", line 1044, in search_sra
    acc_is_searchstr=True,
  File "/envs/pysradb/lib/python3.7/site-packages/pysradb/sradb.py", line 316, in sra_metadata
    metadata_df = expand_sample_attribute_columns(metadata_df)
  File "/envs/pysradb/lib/python3.7/site-packages/pysradb/filter_attrs.py", line 75, in expand_sample_attribute_columns
    sample_attribute_keys, _ = _get_sample_attr_keys(sample_attribute)
  File "/envs/pysradb/lib/python3.7/site-packages/pysradb/filter_attrs.py", line 27, in _get_sample_attr_keys
    sample_attribute_dict = dict(split_by_colon)
ValueError: dictionary update sequence element #19 has length 1; 2 is required

What I Did

pysradb  search "hypoxic" --db SRAmetadb.sqlite   --assay --desc   --detailed --expand  --saveto hypoxic_search.txt

[jarrodscott]

FYI the above command works fine if I remove the --expand flag...

[saketkc]

Thanks @jarrodscott for reporting this! I am currently working on a partial rewrite of the core functionality. In the mean time, I have fixed this in 8b9cfa0 . You can install the latest version with pip install git+https://github.com/saketkc/pysradb

For search I would advise saving them to a tsv by passing the additional flag --saveto and then doing a head on the saved file. Using --expand mode can result in too many columns and the default printing on stdout is not optimized:

pysradb search hypoxic --desc --detailed --expand --saveto hypoxic_search.tsv

Let me know if you run into any issues.

[jarrodscott]

No problem @saketkc. Thank you for providing this awesome program. I will install latest version and follow your recommendation. Aside from this small hiccup everything else has worked beautifully