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/singlecellmultiomics/libraryProcessing/sample_sheet.py
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| a | b/singlecellmultiomics/libraryProcessing/sample_sheet.py | ||
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| 1 | import json |
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| 2 | |||
| 3 | def mark_autodetect(libname): |
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| 4 | lib = libname.lower() |
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| 5 | if 'k9me3' in lib: |
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| 6 | return 'H3K9me3' |
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| 7 | if 'k4me1' in lib: |
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| 8 | return 'H3K4me1' |
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| 9 | if 'k4me3' in lib: |
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| 10 | return 'H3K4me3' |
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| 11 | if 'k27me3' in lib: |
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| 12 | return 'H3K27me3' |
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| 13 | if 'k36me3' in lib: |
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| 14 | return 'H3K36me3' |
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| 15 | |||
| 16 | return 'NA' |
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| 17 | |||
| 18 | |||
| 19 | class SampleSheet: |
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| 20 | """ |
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| 21 | Class for reading and writing sample sheet information |
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| 22 | """ |
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| 23 | def __init__(self, path=None): |
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| 24 | self.data = {} |
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| 25 | if path is not None: |
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| 26 | self.load_json(path) |
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| 27 | |||
| 28 | def load_json(self,sample_sheet_location,merge=False): |
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| 29 | """ |
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| 30 | Load the data from the specified json file. |
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| 31 | When merge=True the data will be added to the current data (used for merging sheets) |
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| 32 | Duplicates will be overwritten by the last load file |
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| 33 | """ |
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| 34 | with open(sample_sheet_location) as f: |
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| 35 | if merge: |
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| 36 | for k,v in json.load(f).items(): |
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| 37 | if k not in self.data: |
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| 38 | self.data[k] = v |
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| 39 | else: |
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| 40 | self.data[k].update(v) |
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| 41 | else: |
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| 42 | self.data = json.load(f) |
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| 43 | def get(self,key,default): |
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| 44 | return self.data.get(key,default) |
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| 45 | |||
| 46 | def __getitem__(self,k): |
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| 47 | return self.data[k] |
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| 48 | |||
| 49 | def layout_well2index(self, layout_name): |
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| 50 | """ Get the well to index mapping for the supplied layout """ |
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| 51 | return {k:tuple(v) for k,v in self['well2coord'][self['layout_format'][layout_name]].items()} |
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| 52 | |||
| 53 | def index_to_condition(self, layout_name): |
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| 54 | well_to_condition = self['layouts'][layout_name] |
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| 55 | return {self['well2index'][self['layout_format'][layout_name]][k]:v for k,v in well_to_condition.items()} |
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| 56 | |||
| 57 | |||
| 58 | def index2well(self, layout_name: str) -> dict: |
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| 59 | """ |
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| 60 | Returns a dictionary index->well |
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| 61 | {1: 'A1', |
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| 62 | 2: 'A2', |
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| 63 | 3: 'A3', |
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| 64 | 4: 'A4', |
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| 65 | 5: 'A5', |
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| 66 | """ |
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| 67 | return {v:k for k,v in self['well2index'][self['layout_format'][layout_name]].items() } |
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| 68 | |||
| 69 | @property |
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| 70 | def libraries(self): |
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| 71 | |||
| 72 | libraries = set() |
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| 73 | for k in ['libtype','marks']: |
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| 74 | libraries.update( set(self.get(k,dict()).keys())) |
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| 75 | return libraries |
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| 76 | |||
| 77 | |||
| 78 | def drop_library(self, library): |
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| 79 | if type(library) is list: |
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| 80 | for l in library: |
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| 81 | self.drop_library(l) |
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| 82 | return |
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| 83 | for main_key in ['marks','condition','libtype','library_layout']: |
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| 84 | if main_key not in self.data: |
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| 85 | continue |
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| 86 | if library in self[main_key]: |
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| 87 | del self[main_key][library] |
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| 88 | |||
| 89 | def drop_mark(self, mark): |
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| 90 | """ Remove all libraries with the given mark """ |
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| 91 | if type(mark) is list: |
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| 92 | for m in mark: |
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| 93 | self.drop_mark(m) |
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| 94 | return |
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| 95 | to_prune = [] |
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| 96 | for sample, _mark in self['marks'].items(): |
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| 97 | if mark==_mark: |
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| 98 | to_prune.append(sample) |
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| 99 | |||
| 100 | self.drop_library(to_prune) |