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Merge pull request #250 from BuysDB/bamtagmultiome_unmapped
March 2022 update
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2 changes: 1 addition & 1 deletion
2
singlecellmultiomics/bamProcessing/bamFeatureDensityVisualisation.py
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,4 @@ | ||
| #!/usr/bin/env python3 | ||
| #!/usr/bin/env python | ||
| # -*- coding: utf-8 -*- | ||
| import os | ||
| import sys | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1 @@ | ||
| from .sample_sheet import SampleSheet |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,100 @@ | ||
| import json | ||
|
|
||
| def mark_autodetect(libname): | ||
| lib = libname.lower() | ||
| if 'k9me3' in lib: | ||
| return 'H3K9me3' | ||
| if 'k4me1' in lib: | ||
| return 'H3K4me1' | ||
| if 'k4me3' in lib: | ||
| return 'H3K4me3' | ||
| if 'k27me3' in lib: | ||
| return 'H3K27me3' | ||
| if 'k36me3' in lib: | ||
| return 'H3K36me3' | ||
|
|
||
| return 'NA' | ||
|
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|
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| class SampleSheet: | ||
| """ | ||
| Class for reading and writing sample sheet information | ||
| """ | ||
| def __init__(self, path=None): | ||
| self.data = {} | ||
| if path is not None: | ||
| self.load_json(path) | ||
|
|
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| def load_json(self,sample_sheet_location,merge=False): | ||
| """ | ||
| Load the data from the specified json file. | ||
| When merge=True the data will be added to the current data (used for merging sheets) | ||
| Duplicates will be overwritten by the last load file | ||
| """ | ||
| with open(sample_sheet_location) as f: | ||
| if merge: | ||
| for k,v in json.load(f).items(): | ||
| if k not in self.data: | ||
| self.data[k] = v | ||
| else: | ||
| self.data[k].update(v) | ||
| else: | ||
| self.data = json.load(f) | ||
| def get(self,key,default): | ||
| return self.data.get(key,default) | ||
|
|
||
| def __getitem__(self,k): | ||
| return self.data[k] | ||
|
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| def layout_well2index(self, layout_name): | ||
| """ Get the well to index mapping for the supplied layout """ | ||
| return {k:tuple(v) for k,v in self['well2coord'][self['layout_format'][layout_name]].items()} | ||
|
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| def index_to_condition(self, layout_name): | ||
| well_to_condition = self['layouts'][layout_name] | ||
| return {self['well2index'][self['layout_format'][layout_name]][k]:v for k,v in well_to_condition.items()} | ||
|
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|
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| def index2well(self, layout_name: str) -> dict: | ||
| """ | ||
| Returns a dictionary index->well | ||
| {1: 'A1', | ||
| 2: 'A2', | ||
| 3: 'A3', | ||
| 4: 'A4', | ||
| 5: 'A5', | ||
| """ | ||
| return {v:k for k,v in self['well2index'][self['layout_format'][layout_name]].items() } | ||
|
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||
| @property | ||
| def libraries(self): | ||
|
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| libraries = set() | ||
| for k in ['libtype','marks']: | ||
| libraries.update( set(self.get(k,dict()).keys())) | ||
| return libraries | ||
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| def drop_library(self, library): | ||
| if type(library) is list: | ||
| for l in library: | ||
| self.drop_library(l) | ||
| return | ||
| for main_key in ['marks','condition','libtype','library_layout']: | ||
| if main_key not in self.data: | ||
| continue | ||
| if library in self[main_key]: | ||
| del self[main_key][library] | ||
|
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||
| def drop_mark(self, mark): | ||
| """ Remove all libraries with the given mark """ | ||
| if type(mark) is list: | ||
| for m in mark: | ||
| self.drop_mark(m) | ||
| return | ||
| to_prune = [] | ||
| for sample, _mark in self['marks'].items(): | ||
| if mark==_mark: | ||
| to_prune.append(sample) | ||
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| self.drop_library(to_prune) |
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