Best Python code snippet using lisa_python
inventory.py
Source: inventory.py
...21 'placeholders': devices.placeholders()22 }23 return jsonify(response)24class InventoryAggregation(Aggregation):25 def _aggregate_count(self, pipeline, value_if_none=0) -> int:26 response = self._aggregate(pipeline)27 try:28 return response[0]['count']29 except IndexError:30 return value_if_none31class InventoryDeviceAggregation(InventoryAggregation):32 FINAL_EVENTS = ['devices:Ready', 'devices:Dispose']33 def __init__(self):34 super().__init__('devices')35 def devices_not_fully_processed(self):36 pipeline = [37 {38 '$match': {39 '@type': {'$nin': list(Component.types)},40 }41 }42 ]43 pipeline += self._not_containing_events(self.FINAL_EVENTS)44 pipeline += [45 {46 '$group': {47 '_id': None,48 'count': {'$sum': 1}49 }50 },51 {52 '$project': {53 '_id': False,54 'count': True55 }56 }57 ]58 return self._aggregate_count(pipeline)59 def devices_more_than_without_being_processed(self, more_than: timedelta = timedelta(weeks=1)):60 EVENTS = map_(DeviceEventDomain.GENERIC_TYPES, lambda _, key: Naming.new_type(key, 'devices'))61 EVENTS += ['devices:Add', 'devices:Migrate']62 pipeline = [63 {64 '$match': {65 '@type': {'$nin': list(Component.types)},66 '_created': {'$lte': datetime.today() - more_than}67 }68 },69 ]70 pipeline += self._not_containing_events(EVENTS)71 pipeline += [72 {73 '$group': {74 '_id': None,75 'count': {'$sum': 1}76 }77 },78 {79 '$project': {80 '_id': False,81 'count': True82 }83 }84 ]85 return self._aggregate_count(pipeline)86 def hard_drives_with_errors(self) -> int:87 pipeline = [88 {89 '$match': {90 '@type': 'HardDrive'91 }92 },93 {94 '$project': {95 'erased': {96 '$filter': {97 'input': '$events',98 'as': 'event',99 'cond': {'$in': ['$$event.@type', ['devices:EraseBasic', 'devices:EraseSectors']]}100 }101 },102 'disposed': {103 '$filter': {104 'input': '$events',105 'as': 'event',106 'cond': {'$in': ['$$event.@type', ['devices:Dispose']]}107 }108 }109 }110 },111 {112 '$match': {113 'erased': {'$gte': ['$size', 1]},114 'disposed': {'$size': 0},115 }116 },117 {118 '$group': {119 '_id': None,120 'count': {'$sum': 1}121 }122 }123 ]124 return self._aggregate_count(pipeline)125 def placeholders(self) -> int:126 pipeline = [127 {128 '$match': {129 'placeholder': True130 }131 },132 {133 '$group': {134 '_id': None,135 'count': {'$sum': 1}136 }137 }138 ]139 return self._aggregate_count(pipeline)140 @staticmethod141 def _not_containing_events(events_type: list):142 return [143 {144 '$project': {145 'contains': {146 '$filter': {147 'input': '$events',148 'as': 'event',149 'cond': {'$in': ['$$event.@type', events_type]}150 }151 }152 }153 },...
get_ligation_efficiency.py
Source: get_ligation_efficiency.py
1from collections import Counter2import gzip3import operator4import pysam5import re6import sys7# Program for checking barcoding success rate8def main():9 lig = LigationEfficiency()10 lig.count_barcodes(sys.argv[1])11 lig.print_to_stdout()12class LigationEfficiency:13 def __init__(self):14 self._aggregate_count = Counter()15 self._position_count = Counter()16 self._pattern = re.compile('\[([a-zA-Z0-9_\-]+)\]')17 self._total = 018 def count_barcodes(self, filename):19 if filename.lower().endswith(".bam"):20 self.count_barcodes_in_bam_file(filename)21 elif filename.lower().endswith((".fastq", ".fq")):22 self.count_barcodes_in_fastq_file(filename)23 elif filename.lower().endswith((".fastq.gz", ".fq.gz")):24 self.count_barcodes_in_fastqgz_file(filename)25 def count_barcodes_in_bam_file(self, bamfile):26 with pysam.AlignmentFile(bamfile, "rb") as f:27 for read in f.fetch(until_eof=True):28 self.count_barcodes_in_name(read.query_name)29 self._total += 130 def count_barcodes_in_fastq_file(self, fastqfile):31 with open(fastqfile, "r") as f:32 for line in f:33 self.count_barcodes_in_name(line)34 next(f)35 next(f)36 next(f)37 self._total += 138 def count_barcodes_in_fastqgz_file(self, fastqgzfile):39 with gzip.open(fastqgzfile, "r") as f:40 for line in f:41 self.count_barcodes_in_name(line)42 next(f)43 next(f)44 next(f)45 self._total += 146 def count_barcodes_in_name(self, name):47 barcodes = self._pattern.findall(name)48 num_found = 049 pos = 050 for barcode in barcodes:51 if barcode != "NOT_FOUND":52 num_found += 153 self._position_count[pos] += 154 pos += 155 self._aggregate_count[num_found] += 156 def print_to_stdout(self):57 counts = sorted(self._aggregate_count.items(),58 key=operator.itemgetter(0))59 for num_barcodes, count in counts:60 pct = "{0:.1f}%".format(100.0 * count / self._total)61 barcode = "barcode" if num_barcodes == 1 else "barcodes"62 print (str(count) + " (" + pct + ") reads found with " +63 str(num_barcodes) + " " + barcode + ".")64 print65 counts = sorted(self._position_count.items(),66 key=operator.itemgetter(0))67 for position, count in counts:68 pct = "{0:.1f}%".format(100.0 * count / self._total)69 print (str(count) + " (" + pct + ") barcodes found in position " +70 str(position + 1) + ".")71if __name__ == "__main__":...
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