Transcription/Transcriptomic tools. Package of python tools facilitating bioinformatic analysis of RNA and nascent RNA sequencing data.
pip install trxtools
Documentation can be found here
Tomasz W. Turowski, Jan Mikołajczyk
Tools to study transcription
Home Page: https://turowskilab.github.io/trxtools/
License: Other
Transcription/Transcriptomic tools. Package of python tools facilitating bioinformatic analysis of RNA and nascent RNA sequencing data.
pip install trxtools
Documentation can be found here
Tomasz W. Turowski, Jan Mikołajczyk
Chiefly in nascent.py but could be elsewhere as well
~/anaconda3/lib/python3.9/site-packages/trxtools/go_enrichment.py in get_enrichment(query_genes, organism, use_reference_set, ref_genes, ref_organism, go_dataset, test_type, correction)
77 response = requests.post('http://pantherdb.org/services/oai/pantherdb/enrich/overrep', data=query)
78 ## extract data to a dataframe
---> 79 return pd.json_normalize(response.json()['results']['result'])
KeyError: 'results'
FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead.
While trying to run tt.nascent.Fold().RNAfold(df00)
Exception: b'/bin/sh: 1: tab2fasta.awk: Permission denied'. Code: 127
Ship awk script with repo or hardcode functionality in module
Currently using RNA folding functions seems to change python's (kernel's) working directory to ~ without telling the user.
Maybe it should be worth adding an option to specify the directory for temp files manually or set it automatically in the notebook's dir.
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