Parsing prediction tool output

[HobnobMancer]

Notes:

• still need to add the unit tests
• development for these functions is within the Jupyter notebook 'parsing_prediction_tools_output', which is stored in HTML and .ipyn format within the directory ./notebooks/planning_parsing_prediction_tool_output, which additionally contains the output files from the tools that were used to develop the new functions
• have no added calls to these function from the main script (predict_cazymes.py)

Add the following new functions to pyrewton.cazymes.prediction.parse for the standardising/parsing the output from the prediction tools:

• parse_dbcan_output()
• add_hotpep_ec_predictions()
• parse_hmmer_output()
• parse_hotpep_output()
• parse_diamond_output()
• get_dbcan_consensus()
• add_hotpep_ec_predictions()
• parse_cupp_output()
• parse_ecami_output()

A dataframe of the output is created each for dbCAN (containing the consensus result, defined as all CAZy families that at least 2 tools predict for a query protein sequence), HMMER, Hotpep, DIAMOND, CUPP and eCAMI.

For each prediction tool the following data is retrieved:
dbCAN: CAZy family, CAZy subfamily (can predict multiple domains per protein)
HMMER: CAZy family, CAZy subfamily (can predict multiple domains per protein), domain ranges (the starting and end amino acid of the domain)
Hotpep: CAZy family, CAZy subfamily (can predict multiple domains per protein)
DIAMOND: CAZy family, CAZy subfamily (can predict multiple domains per protein)
CUPP: CAZy family, CAZy subfamily, predicated EC number and domain range
eCAMI: CAZy family, CAZy subfamily (can predict multiple domains per protein), EC number, here the best result is listed under the CAZy fam and subfam headings and additional domains under "additional_domains"

[codecov]

Codecov Report

Merging #45 (70891eb) into master (d2e7066) will decrease coverage by 17.06%.
The diff coverage is 1.73%.

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- Coverage   93.67%   76.60%   -17.07%     
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  Lines         759      932      +173     
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+ Hits          711      714        +3     
- Misses         48      218      +170