gunshotmatch_pipeline.excluded_peaks

Report excluded peaks from various pipeline steps.

New in version 0.10.0.

Classes:

ExcludedPeaks(alignment, small_peaks, ...)	Represents the excluded peaks in a project.
PeakCounts(found_peaks, alignment_peaks, ...)	Counts of peaks at different steps of the pipeline.

Functions:

get_excluded_peaks(project, ...)

Determine excluded peaks in a project.

class ExcludedPeaks(alignment, small_peaks, filtered_out_consolidated_peaks, debug_stdout)

Bases: object

Represents the excluded peaks in a project.

Parameters

• alignment (Alignment) – Partial alignment of peaks.

• small_peaks (List[Peak]) – Small peaks

• filtered_out_consolidated_peaks (List[ConsolidatedPeak]) – Peaks filtered during the consolidate process

• debug_stdout (StringIO) – Stdout from alignment and peak identification process, for debugging.

Attributes:

alignment	Partial alignment of peaks.
debug_stdout	Stdout from alignment and peak identification process, for debugging.
filtered_out_consolidated_peaks	Peaks filtered during the consolidate process
small_peaks	Small peaks

alignment

Type:    Alignment

Partial alignment of peaks.

debug_stdout

Type:    StringIO

Stdout from alignment and peak identification process, for debugging.

filtered_out_consolidated_peaks

Type:    List[ConsolidatedPeak]

Peaks filtered during the consolidate process

small_peaks

Type:    List[Peak]

Small peaks

namedtuple PeakCounts(found_peaks, alignment_peaks, unaligned_peaks, small_peaks)

Bases: NamedTuple

Counts of peaks at different steps of the pipeline.

Fields

0.  found_peaks (int) – Peak list after Biller-Biemann peak detection and subsequent noise and base peak filtering.

1.  alignment_peaks (int) – Peaks for which partners were found during alignment (after filtering to min_peaks).

2.  unaligned_peaks (int) – Peaks which didn’t survive alignment step (no/insufficient matching peaks in other datafiles).

3.  small_peaks (int) – Peaks filtered after alignment due to size (top_n_peaks and min_peak_area).

get_excluded_peaks(project, pyms_nist_search_config, peak_filter)

Determine excluded peaks in a project.

Parameters

• project (Project)

• pyms_nist_search_config (PyMSNISTSearchCfg)

• peak_filter (InvertedFilter)

Return type

ExcludedPeaks