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compomics / psm_utils

Common utilities for parsing and handling peptide-spectrum matches and search engine results in Python
https://psm-utils.readthedocs.io
Apache License 2.0
25 stars 7 forks source link

Add score_key argument to XTandemReader #57

Closed RalfG closed 1 year ago

RalfG commented 1 year ago

Added

Adds new argument to XTandemReader:

Key of score to use as PSM score. One of "expect", "hyperscore", "delta", or "nextscore". Default: "expect". The "expect" score e-value) is converted to its negative natural logarithm to facilitate downstream analysis.

Addresses #55

codecov-commenter commented 1 year ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Comparison is base (90dafe0) 58.49% compared to head (0357d5b) 58.51%.

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Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #57 +/- ## ========================================== + Coverage 58.49% 58.51% +0.01% ========================================== Files 23 23 Lines 2159 2160 +1 ========================================== + Hits 1263 1264 +1 Misses 896 896 ``` | [Files](https://app.codecov.io/gh/compomics/psm_utils/pull/57?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=compomics) | Coverage Δ | | |---|---|---| | [psm\_utils/io/xtandem.py](https://app.codecov.io/gh/compomics/psm_utils/pull/57?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=compomics#diff-cHNtX3V0aWxzL2lvL3h0YW5kZW0ucHk=) | `81.81% <100.00%> (+0.42%)` | :arrow_up: |

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