本文整理汇总了Python中tools.Tools.getChromosomeOfFile方法的典型用法代码示例。如果您正苦于以下问题：Python Tools.getChromosomeOfFile方法的具体用法？Python Tools.getChromosomeOfFile怎么用？Python Tools.getChromosomeOfFile使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类tools.Tools的用法示例。
在下文中一共展示了Tools.getChromosomeOfFile方法的1个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: findFastqFiles
# 需要导入模块: from tools import Tools [as 别名]
# 或者: from tools.Tools import getChromosomeOfFile [as 别名]
def findFastqFiles(self, directory, inFormat):
"""The method findFastqFiles finds all fastq files recursively in a directory, from each directory with fastq files a sample is created.
:param directory: the directory where the user hid his fastq files
:type directory: str -- path to the directory
"""
fastqFiles = []
for fileName in os.listdir(directory):
fileName = directory + "/" + fileName
if os.path.isdir(fileName):
self.findFastqFiles(fileName, inFormat)
else:
if inFormat == "bam":
if fileName.endswith(".bam") or fileName.endswith(".bam.gz"):
newSamp = Sample.Sample(self.pool, os.path.basename(os.path.splitext(fileName)[0]))
self.samples.append(newSamp)
newSamp.bam = BamFile.BamFile(self.pool, newSamp, fileName, sortedBam = True, headerLine = True, duplicates = False, mdTag = True, index = True)
self.pool.addSample(newSamp)
elif inFormat == "fq":
if fileName.endswith(".fq") or fileName.endswith(".fq.gz"):
fastqFiles.append(fileName)
elif inFormat == "vcf":
if fileName.endswith(".vcf") or fileName.endswith(".vcf.gz"):
if len(os.listdir(directory)) == 1:
chrom = None
else:
chrom = self.getChromosomeFromVcf(fileName)
self.pool.vcf[chrom] = VcfFile.VcfFile(self.pool, fileName, bcf=False, filtered=True, phased=True, chrom=chrom)
elif fileName.endswith(".bcf") or fileName.endswith(".bcf.gz"):
chrom = Tools.getChromosomeOfFile(Program.config.getPath("refGenome"), fileName)
self.pool.vcf[chrom] = VcfFile.VcfFile(self.pool, fileName, bcf=True, filtered=True, phased=True, chrom=chrom)
if inFormat == "bam" or inFormat =="vcf":
return
if len(fastqFiles) > 0:
#create a library name from the file name
libName = os.path.basename(fastqFiles[0])
if libName.endswith("_1.fq") or libName.endswith("_2.fq"):
libName = libName[:-5]
if libName.endswith("_1.fq.gz") or libName.endswith("_2.fq.gz"):
libName = libName[:-8]
else:
libName = libName[:-3]
#create the sample
sample = Sample.Sample(self.pool, libName)
self.pool.addSample(sample)
#add the fastq files to the sample
if len(fastqFiles) == 1:
sample.setForwardFq(fastqFiles[0])
elif len(fastqFiles) == 2:
sample.setForwardFq(fastqFiles[0])
sample.setReversedFq(fastqFiles[1])
elif len(fastqFiles) > 2:
if fastqFiles[0].endswith("_1.fq"):
suffix = "_1.fq"
elif fastqFiles[0].endswith("_1.fq.gz"):
suffix = "_1.fq.gz"
else:
print("WARNING: files do not end with _1.fq or _1.fq.gz or _2.fq or _2.fq.gz, using all files in one directory as 1 sample with only forward reads")
suffix = fastqFiles[0][-3:]
#create a list of forward fastq files and one of reversed fastq files
forward = []
reversedFastq = []
for fastqFile in fastqFiles:
if fastqFile.endswith(suffix):
forward.append(fastqFile)
else:
reversedFastq.append(fastqFile)
#Convert files to fastqFile objects
for i in range(len(forward)):
forward[i] = FastqFile.FastqFile(self.pool, sample, forward[i])
for i in range(len(reversedFastq)):
reversedFastq[i] = FastqFile.FastqFile(self.pool, sample, reversedFastq[i], forward=False)
#add the fastq files to the sample
sample.forwardFq = forward
sample.reversedFq = reversedFastq