`libgunshotmatch.utils`¶

Utility functions.

Functions:

`create_alignment`(peakpos, expr_code[, …])	Create a new `pyms.DPA.Alignment.Alignment` object.
`get_rt_range`(project)	Returns the minimum and maximum retention times (in minutes) across the repeats.
`get_truncated_normal`(mean, sd[, low, upp, …])	Returns `count` values from a truncated normal distrubition.
`ms_comparison`(top_ms, bottom_ms)	Performs a Mass Spectrum similarity calculation two mass spectra.
`round_rt`(rt)	Truncate precision of retention time to 10 decimal places.

create_alignment(peakpos, expr_code, similarity=0)[source]¶

Parameters

peakpos (Sequence[Sequence[Optional[Peak]]]) – Nested list of aligned peaks. Top level list contains lists of peaks for each experiment in expr_code.
expr_code (List[str]) – Experiment names. Order must match peakpos.
similarity (float) – Default 0.

Return type

Alignment

New in version 0.8.0.

get_rt_range(project)[source]¶

Returns the minimum and maximum retention times (in minutes) across the repeats.

New in version 0.7.0.

get_truncated_normal(mean, sd, low=0, upp=10, count=10, random_state=None)[source]¶

Returns count values from a truncated normal distrubition.

Parameters

mean (float) – The midpoint of the normal distribution.
sd (float) – The spread of the normal distribution (the standard deviation).
low (float) – The lower bound. Default 0.
upp (float) – The upper bound. Default 10.
count (int) – Default 10.
random_state (Optional[int]) – Optional seed for the random number generator. Default None.

Return type

Sequence[float]

ms_comparison(top_ms, bottom_ms)[source]¶

Performs a Mass Spectrum similarity calculation two mass spectra.

Parameters

If either of top_ms or bottom_ms is None then None is returned, otherwise a comparison score is returned.

round_rt(rt)[source]¶

Truncate precision of retention time to 10 decimal places.

libgunshotmatch.utils¶