gunshotmatch_reports.alignment

CSV reports of alignment between reference projects and unknown samples.

New in version 0.5.0.

Classes:

CSVRow([peak_no, name, rt, area, …])

Represents data for a peak in a CSV report.

Functions:

csv_two_projects(p1, padded_p1_cp, p2, …)	Returns CSV report for the alignment between the given projects.
csv_two_projects_and_unknown(p1, …[, …])	Returns CSV report for the alignment between the given projects and unknown.
get_csv_data(project, cp, max_area)	Return data for the CSV report for given peak in the given project.

namedtuple CSVRow(peak_no='', name='', rt='', area='', area_percentage='', match_factor='')

Bases: NamedTuple

Represents data for a peak in a CSV report.

Fields

0.  peak_no (str) – Alias for field number 0

1.  name (str) – Alias for field number 1

2.  rt (str) – Alias for field number 2

3.  area (str) – Alias for field number 3

4.  area_percentage (str) – Alias for field number 4

5.  match_factor (str) – Alias for field number 5

__repr__()

Return a nicely formatted representation string

classmethod header()

Returns the CSV column headers.

Return type

Tuple[str, str, str, str, str, str]

csv_two_projects(p1, padded_p1_cp, p2, padded_p2_cp)

Returns CSV report for the alignment between the given projects.

Parameters

• p1 (Project) – The first project.

• padded_p1_cp (MutableSequence[Optional[ConsolidatedPeak]]) – Padded consolidated peak list for the first project.

• p2 (Project) – The second project.

• padded_p2_cp (MutableSequence[Optional[ConsolidatedPeak]]) – Padded consolidated peak list for the second project.

Return type

str

csv_two_projects_and_unknown(p1, padded_p1_cp, p2, padded_p2_cp, u, padded_u_cp, *, pair_only=False)

Returns CSV report for the alignment between the given projects and unknown.

Parameters

• p1 (Project) – The first project.

• padded_p1_cp (MutableSequence[Optional[ConsolidatedPeak]]) – Padded consolidated peak list for the first project.

• p2 (Project) – The second project.

• padded_p2_cp (MutableSequence[Optional[ConsolidatedPeak]]) – Padded consolidated peak list for the second project.

• u (Project) – The unknown sample.

• padded_u_cp (MutableSequence[Optional[ConsolidatedPeak]]) – Padded consolidated peak list for the unknown sample.

• pair_only (bool) – Only show peaks in common between two or more of the projects/unknown. Default False.

Return type

str

get_csv_data(project, cp, max_area)

Return data for the CSV report for given peak in the given project.

Parameters

• project (Project)

• cp (Optional[ConsolidatedPeak])

• max_area (float) – The maximum peak area in the project.

Return type

CSVRow