本文整理汇总了Python中CGATPipelines.PipelineMappingQC.buildPicardAlignmentStats方法的典型用法代码示例。如果您正苦于以下问题：Python PipelineMappingQC.buildPicardAlignmentStats方法的具体用法？Python PipelineMappingQC.buildPicardAlignmentStats怎么用？Python PipelineMappingQC.buildPicardAlignmentStats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CGATPipelines.PipelineMappingQC的用法示例。
在下文中一共展示了PipelineMappingQC.buildPicardAlignmentStats方法的4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: buildPicardStats
# 需要导入模块: from CGATPipelines import PipelineMappingQC [as 别名]
# 或者: from CGATPipelines.PipelineMappingQC import buildPicardAlignmentStats [as 别名]
def buildPicardStats(infile, outfile):
'''build alignment stats using picard.
Note that picards counts reads but they are in fact alignments.
'''
if PARAMS["pool_reads"]:
reffile = os.path.join(
os.path.dirname(infile), "agg-agg-agg.filtered.contigs.fa")
else:
reffile = P.snip(infile, ".bam") + ".fa"
PipelineMappingQC.buildPicardAlignmentStats(infile,
outfile,
reffile)示例2: runPicardOnRealigned
# 需要导入模块: from CGATPipelines import PipelineMappingQC [as 别名]
# 或者: from CGATPipelines.PipelineMappingQC import buildPicardAlignmentStats [as 别名]
def runPicardOnRealigned(infile, outfile):
to_cluster = USECLUSTER
job_options = getGATKOptions()
# TS no multithreading so why 6 threads?
# job_threads = 6
tmpdir_gatk = P.getTempDir('/ifs/scratch')
# threads = PARAMS["gatk_threads"]
outfile_tumor = outfile.replace("Control", PARAMS["mutect_tumour"])
infile_tumor = infile.replace("Control", PARAMS["mutect_tumour"])
track = P.snip(os.path.basename(infile), ".bam")
track_tumor = track.replace("Control", PARAMS["mutect_tumour"])
genome = "%s/%s.fa" % (PARAMS["bwa_index_dir"],
PARAMS["genome"])
PipelineMappingQC.buildPicardAlignmentStats(infile, outfile, genome)
PipelineMappingQC.buildPicardAlignmentStats(infile_tumor,
outfile_tumor, genome)
# check above functions then remove statement
statement = '''
cat %(infile)s
| python %%(scriptsdir)s/bam2bam.py -v 0 --method=set-sequence
| CollectMultipleMetrics
INPUT=/dev/stdin
REFERENCE_SEQUENCE=%%(bwa_index_dir)s/%%(genome)s.fa
ASSUME_SORTED=true
OUTPUT=%(outfile)s
VALIDATION_STRINGENCY=SILENT
>& %(outfile)s;
cat %(infile_tumor)s
| python %%(scriptsdir)s/bam2bam.py -v 0
--method=set-sequence --output-sam
| CollectMultipleMetrics
INPUT=/dev/stdin
REFERENCE_SEQUENCE=%%(bwa_index_dir)s/%%(genome)s.fa
ASSUME_SORTED=true
OUTPUT=%(outfile_tumor)s
VALIDATION_STRINGENCY=SILENT
>& %(outfile_tumor)s;''' % locals()示例3: runPicardOnRealigned
# 需要导入模块: from CGATPipelines import PipelineMappingQC [as 别名]
# 或者: from CGATPipelines.PipelineMappingQC import buildPicardAlignmentStats [as 别名]
def runPicardOnRealigned(infile, outfile):
to_cluster = USECLUSTER
job_memory = PARAMS["gatk_memory"]
tmpdir_gatk = P.getTempDir()
outfile_tumor = outfile.replace(
PARAMS["sample_control"], PARAMS["sample_tumour"])
infile_tumor = infile.replace(
PARAMS["sample_control"], PARAMS["sample_tumour"])
track = P.snip(os.path.basename(infile), ".bam")
track_tumor = track.replace(
PARAMS["sample_control"], PARAMS["sample_tumour"])
genome = "%s/%s.fa" % (PARAMS["bwa_index_dir"],
PARAMS["genome"])
PipelineMappingQC.buildPicardAlignmentStats(infile, outfile, genome)
PipelineMappingQC.buildPicardAlignmentStats(infile_tumor,
outfile_tumor, genome)示例4: buildPicardAlignmentStats
# 需要导入模块: from CGATPipelines import PipelineMappingQC [as 别名]
# 或者: from CGATPipelines.PipelineMappingQC import buildPicardAlignmentStats [as 别名]
def buildPicardAlignmentStats(infile, outfile):
'''Gather BAM file alignment statistics using Picard '''
PipelineMappingQC.buildPicardAlignmentStats(infile, outfile,
os.path.join(PARAMS["bwa_index_dir"],
PARAMS["genome"] + ".fa"))