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How to use coverageValue method in fMBT
Best Python code snippet using fMBT_python
data.py
Source:data.py 
1import sys2import math3import readVCF4import fileinput5#Reads a tab file with name string given by toRead.6#Constructs a list of chromosome items, one per chromosome, and inserts7#chromosome name, start bp, end bp, coverage per 1000 bp in these items.8def readTab(toRead):9 totalReadLines = 010 tabFileName = toRead11 chromosomes = []12 coverageNorm = 013 coverageNormLog = 014 totalBP = 015 numChr = 016 with open(toRead, 'r') as tab:17 #Read the first line in the file, should start with #CHR.18 line = tab.readline()19 if (not line.startswith("#CHR")):20 print('TAB file is not in correct format')21 return None22 else:23 print('TAB file seems ok, continuing read')24 #Read the second line and create the first Chromosome object.25 #All following lines should be formatted as: chrName\tstart\tend\tcoverage26 line = tab.readline()27 fields = line.split('\t')28 if (not len(fields) == 4):29 print("TAB file not formatted correctly on line 2")30 return None31 else:32 curChrName = fields[0]33 chrom = Chromosome(curChrName)34 chrom.addCoverage(float(fields[3]))35 coverageNorm += float(fields[3])36 if(float(fields[3])) > 0:37 coverageNormLog += math.log(float(fields[3]),2)38 totalReadLines += 139 lastRead = line40 chromosomes.append(chrom)41 numChr += 142 #Iterate over the rest of the lines in the file43 for line in tab:44 fields = line.split('\t')45 if (not len(fields) == 4):46 print("TAB file not formatted correctly")47 return -148 #If we come across a new chromosome, assign end on current chromosome (contained in last read line)49 #Then create a new Chromosome object, assign name & start. Add to list.50 if fields[0] != curChrName:51 chrom.setEnd(lastRead.split('\t')[2])52 curChrName = fields[0]53 chrom = Chromosome(curChrName)54 chromosomes.append(chrom)55 numChr += 156 #Every line contains coverage data of interest, for current chromosome57 chrom.addCoverage(float(fields[3]))58 coverageNorm += float(fields[3])59 if(float(fields[3])) > 0:60 coverageNormLog += math.log(float(fields[3]),2)61 totalReadLines += 162 #Store last read line and go to next line63 lastRead = line64 chrom.setEnd(lastRead.split('\t')[2])65 coverageNorm = coverageNorm / totalReadLines66 coverageNormLog = coverageNormLog / totalReadLines67 #sum total read bp68 for chromo in chromosomes:69 totalBP += int(chromo.end)70 return (chromosomes,coverageNorm,coverageNormLog,totalBP)71def readCytoTab(toRead):72 cytoTabName = toRead73 cytoTabInfo = []74 with open(toRead, 'r') as tab:75 #Read the first line in the file, should start with #chromosome.76 line = tab.readline()77 if (not line.startswith("chr1")):78 print('TAB file is not in correct format')79 return None80 else:81 print('CytoBandTAB file seems ok, continuing read')82 #The fields are as following: #chromosome, startPos, endPos, cytoband, stain value83 fields = line.split('\t')84 fields[0] = fields[0].strip('chr')85 fields[4] = fields[4].strip('\n')86 cytoTab = [fields[0], fields[1], fields[2], fields[3], fields[4]]87 cytoTabInfo.append(cytoTab)88 for line in tab:89 fields = line.split('\t')90 fields[0] = fields[0].strip('chr')91 fields[4] = fields[4].strip('\n')92 cytoTab = [fields[0], fields[1], fields[2], fields[3], fields[4]]93 cytoTabInfo.append(cytoTab)94 return cytoTabInfo95def readVCFFile(toRead, chromosomes):96 vcfFileName = toRead97 vcfInfoLines = []98 with open(toRead, 'r') as vcf:99 #The first lines should be a number of meta-information lines, prepended by ##.100 #Should begin with fileformat. Store these. Check first line for correct format.101 line = vcf.readline()102 if (not line.startswith("##fileformat=")):103 print("VCF file is not in correct format")104 return None105 else:106 print("VCF file seems ok, continuing read")107 while (line.startswith("##")):108 vcfInfoLines.append(line)109 line = vcf.readline()110 #A header line prepended by # should follow containing 8 fields, tab-delimited.111 #These are in order CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO. Store in info line list.112 fields = line.split('\t')113 if (not (line.startswith('#') or len(fields) == 8) ):114 print("Header columns missing in VCF file")115 return None116 else:117 vcfInfoLines.append(line)118 #All following lines are tab-delmited data lines.119 #Store variant data in chromosome item corresponding to CHROM field120 numvars = 0121 for line in vcf:122 numvars += 1123 #Feed every data line into readVCF, returning: (chrA,posA,chrB,posB,event_type,description,format)124 (chrA,posA,chrB,posB,event_type,description,format) = readVCF.readVCFLine(line)125 #Iterate through chromosome list to find match to insert data into126 for chromo in chromosomes:127 if chromo.name == chrA:128 chromo.addVariant(chrA,posA,chrB,posB,event_type,description,format)129 break130 return (chromosomes,vcfInfoLines)131#Reads a general tab delimited file (such as a bed file)132def readGeneralTab(toRead):133 tabLines = []134 with open(toRead, 'r') as tab:135 #Skip first line136 line = tab.readline()137 for line in tab:138 #The fields are as following: #chromosome, startPos, endPos, text139 fields = line.split('\t')140 fields[0] = fields[0].replace("chr","").replace("Chr","").replace("CHR","")141 fields[-1] = fields[-1].strip('\n')142 tabLines.append(fields)143 return tabLines144def readConfig(toRead):145 circularConfig = {}146 coverageConfig = {}147 karyoConfig = {}148 heatmapConfig = {}149 colorConfig = {}150 with open(toRead, 'r') as config:151 activeSection = "CIRCULAR"152 for line in config:153 if line.startswith('#'):154 continue155 if line.startswith('['):156 if line.startswith('[CIRCULAR]'):157 activeSection = 'CIRCULAR'158 elif line.startswith('[COVERAGE]'):159 activeSection = 'COVERAGE'160 elif line.startswith('[KARYOGRAM]'):161 activeSection = 'KARYOGRAM'162 elif line.startswith('[HEATMAP]'):163 activeSection = 'HEATMAP'164 elif line.startswith('[COLORS]'):165 activeSection = 'COLORS'166 else:167 if activeSection == "CIRCULAR":168 fields = line.split('=')169 circularConfig[fields[0]] = fields[1].strip('\n')170 elif activeSection == "COVERAGE":171 fields = line.split('=')172 coverageConfig[fields[0]] = fields[1].strip('\n')173 elif activeSection == "KARYOGRAM":174 fields = line.split('=')175 karyoConfig[fields[0]] = fields[1].strip('\n')176 elif activeSection == "HEATMAP":177 fields = line.split('=')178 heatmapConfig[fields[0]] = fields[1].strip('\n')179 elif activeSection == 'COLORS':180 fields = line.split('=')181 fields[1] = fields[1]182 colorConfig[fields[0]] = fields[1].strip('\n')183 return (circularConfig,coverageConfig,karyoConfig,heatmapConfig,colorConfig)184def saveConfig(fileName,circularConfig,coverageConfig,karyoConfig,heatmapConfig,colorConfig):185 with open(fileName,'r+') as config:186 configData = config.readlines()187 activeSection = "CIRCULAR"188 newData = []189 for line in configData:190 if line.startswith('#'):191 line = line.strip('\n')192 newData.append(line)193 continue194 if line.startswith('['):195 if line.startswith('[CIRCULAR]'):196 activeSection = 'CIRCULAR'197 elif line.startswith('[COVERAGE]'):198 activeSection = 'COVERAGE'199 elif line.startswith('[KARYOGRAM]'):200 activeSection = 'KARYOGRAM'201 elif line.startswith('[HEATMAP]'):202 activeSection = 'HEATMAP'203 elif line.startswith('[COLORS]'):204 activeSection = 'COLORS'205 else:206 if activeSection == "CIRCULAR":207 fields = line.split('=')208 line = line.replace(fields[1],circularConfig[fields[0]])209 elif activeSection == "COVERAGE":210 fields = line.split('=')211 line = line.replace(fields[1],coverageConfig[fields[0]])212 elif activeSection == "KARYOGRAM":213 fields = line.split('=')214 line = line.replace(fields[1],karyoConfig[fields[0]])215 elif activeSection == "HEATMAP":216 fields = line.split('=')217 line = line.replace(fields[1],heatmapConfig[fields[0]])218 elif activeSection == 'COLORS':219 pass220 line = line.strip('\n')221 newData.append(line)222 config.seek(0)223 config.truncate()224 for line in newData:225 config.write(line + '\n')226class Chromosome():227 def __init__(self, name):228 self.name = name229 self.coverage = []230 self.coverageLog = []231 self.display = False232 self.variants = []233 self.connections = []234 self.display_connections = False235 self.display_cytoBandNames = False236 def addCoverage(self, coverageValue):237 self.coverage.append(coverageValue)238 if(coverageValue > 0):239 self.coverageLog.append(math.log(coverageValue,2))240 else:241 self.coverageLog.append(0)242 def setEnd(self,end):243 self.end = end244 def addVariant(self,chrA,posA,chrB,posB,event_type,description,format):245 #The variants are by default set to be shown246 display_variant = True247 marked = False248 #For every variant we would like the genes in CSQ, if this exists249 if "CSQ" in description:250 csqField = description["CSQ"]251 #The CSQ field has several sub-fields, each separated with ','252 subList = csqField.split(',')253 geneList = []254 for subIndex in range(len(subList)):255 #The gene name field is always the fourth element in the CSQ field separated with '|'256 subSubList = subList[subIndex].split('|')257 geneList.append(subSubList[3])258 #Convert the list to a set to remove any duplicates259 geneSet = set(geneList)260 s = ', '261 allGenes = s.join(geneSet)262 else:263 allGenes = ""264 #We would also like the CYTOBAND field, if this exists265 if "CYTOBAND" in description:266 cband = description["CYTOBAND"]267 else:268 cband = None269 if "RankScore" in description:270 rankScore = description["RankScore"]271 else:272 rankScore = None273 #Add the variant data to this chromosome274 variant = [chrA,posA,chrB,posB,event_type,description,format,allGenes,cband,display_variant,rankScore, marked]275 self.variants.append(variant)276 def createConnections(self):277 #These corresponding values for the variant are added to the list: CHRA,CHRB,WINA,WINB,CYTOBAND278 self.connections = []279 for variant in self.variants:280 if not variant[9]:281 continue282 else:283 description = variant[5]284 if "CYTOBAND" in description:285 cband = description["CYTOBAND"]286 else:287 cband = None288 if variant[0] is not variant[2]:289 connection = [variant[0],variant[2],description["WINA"],description["WINB"],cband]290 self.connections.append(connection)291 else:292 connection = [variant[0], variant[2], str(variant[1]) + "," + str(variant[1]), str(variant[3]) + "," + str(variant[3]), cband]...
coverage_data.py
Source:coverage_data.py
1from __future__ import annotations2from typing import List, Set3from dataclasses import dataclass, field, asdict4import enum5from pathlib import Path6import json7from ros_metrics_reporter.color import Color8import pandas as pd9from datetime import datetime10class CoverageKeys(enum.Enum):11 Lines = "Lines"12 Functions = "Functions"13 Branches = "Branches"14@dataclass15class CoverageValue:16 label: str = ""17 line: float = 0.018 function: float = 0.019 branch: float = 0.020 def get(self, coverage_key: CoverageKeys):21 if coverage_key == CoverageKeys.Lines:22 return self.line23 elif coverage_key == CoverageKeys.Functions:24 return self.function25 elif coverage_key == CoverageKeys.Branches:26 return self.branch27 else:28 raise Exception("Unknown coverage key")29@dataclass30class Coverage:31 package: str = ""32 value: List[CoverageValue] = field(default_factory=list)33 def write(self, file: Path):34 with open(file, "w") as f:35 json.dump(asdict(self), f, indent=2)36 def read(self, file: Path) -> Coverage:37 with open(file, "r") as f:38 data = json.load(f)39 self.package = data["package"]40 self.value = [CoverageValue(**value) for value in data["value"]]41 return self42 def get_label_value(self, label: str) -> CoverageValue:43 for value in self.value:44 if value.label == label:45 return value46 return CoverageValue(label=label)47 def get_labels(self) -> Set[str]:48 return {value.label for value in self.value}49@dataclass50class CoverageStamped(Coverage):51 date: datetime = field(default_factory=datetime.now)52@dataclass53class Threshold:54 high: float = 0.055 med: float = 0.056 def write(self, file: Path):57 with open(file, "w") as f:58 json.dump(asdict(self), f, indent=2)59@dataclass60class CoverageData:61 coverage: List[Coverage] = field(default_factory=list)62 threshold: Threshold = field(default_factory=Threshold)63 def add_threshold(self, high, med):64 self.threshold.high = high65 self.threshold.med = med66 def add_coverage(self, coverage: Coverage):67 for i, item in enumerate(self.coverage):68 if item.package == coverage.package:69 self.coverage[i].value.extend(coverage.value)70 return71 self.coverage.append(coverage)72 def add_coverages(self, coverages: List[Coverage]):73 for coverage in coverages:74 self.add_coverage(coverage)75 def save_coverage(self, output_dir: Path):76 for item in self.coverage:77 output_json_dir = output_dir / item.package78 output_json_dir.mkdir(parents=True, exist_ok=True)79 item.write(output_json_dir / "coverage.json")80 def save_threshold_value(self, output_path: Path):81 self.threshold.write(output_path)82 def get_coverage(self, package: str) -> Coverage:83 for item in self.coverage:84 if item.package == package:85 return item86 return Coverage(package=package)87 def get_color(self, value: str, coverage_key: CoverageKeys) -> Color:88 if coverage_key == CoverageKeys.Lines:89 if value >= self.threshold.high:90 return Color.GREEN91 elif value >= self.threshold.med:92 return Color.YELLOW93 else:94 return Color.RED95 elif coverage_key == CoverageKeys.Functions:96 if value >= self.threshold.high:97 return Color.GREEN98 elif value >= self.threshold.med:99 return Color.YELLOW100 else:101 return Color.RED102 elif coverage_key == CoverageKeys.Branches:103 if value >= self.threshold.high:104 return Color.GREEN105 elif value >= self.threshold.med:106 return Color.YELLOW107 else:108 return Color.RED109 else:...
makeCoverageDB.py
Source:makeCoverageDB.py
1# -*- coding: utf-8 -*-2"""3Created on Fri Oct 23 21:58:09 20154@author: jiun5"""6import os7import re8import sys9from pymongo import MongoClient10# main function11# get list of txt.gz files, extract, parse and print to screen12# input main directory13def main():14 dirName = sys.argv[1]15 db = connecttomongo()16 filenames = next(os.walk(dirName))[2]17 for iF in filenames:18 if iF.endswith(".gz"):19 fName = os.path.join(dirName, iF)20 fObj = unzipCoverageFile(fName)21 22 uid = os.path.splitext(os.path.splitext(iF)[0])[0]23 parselines_insert(db, fObj, uid)24 25# function to parse coverage text file26# takes in the file object and prints the each coverage value to screen27# in the following format:28# chromosomeName GeneName Location CoverageValue29def parselines_insert(db, fileObj, uid):30 31 for line in fileObj:32 bits = re.split("\t", line)33 #coverage = re.split(",", re.sub("\n","",bits[3]))34 coverage = [int(i) for i in re.sub("\n", "", bits[3]).split(",")]35 startPos = int(bits[2])36 endPos = int(startPos) + len(coverage) 37 # seqLen = len(coverage)38 # seqIdx = range(startPos,startPos + seqLen)39 40 content = {"UID": uid, "chr": bits[0], "genename": bits[1], "startpos": startPos, "endpos": endPos, "coverage": coverage}41 42 #print content # print it43 insertrecord(db, content) # insert it44# files are stored in gz format, so unzip and get unique id 45# based on the filename 46def unzipCoverageFile(fileName):47 import gzip48 fileObj = gzip.open(fileName, 'rb')49 50 return fileObj51def insertrecord(db, r):52 db.insert(r)53 54def connecttomongo():55 #connection = MongoClient("mongodb://localhost:27017")56 connection = MongoClient("mongodb://146.118.98.44:27017")57 db_test = connection.healthhack.testcoverage58 return db_test59if __name__ == '__main__':...
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