本文整理汇总了Python中CGATPipelines.PipelineMappingQC.buildPicardCoverageStats方法的典型用法代码示例。如果您正苦于以下问题：Python PipelineMappingQC.buildPicardCoverageStats方法的具体用法？Python PipelineMappingQC.buildPicardCoverageStats怎么用？Python PipelineMappingQC.buildPicardCoverageStats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.buildPicardCoverageStats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: buildCoverageStats
# 需要导入模块: from CGATPipelines import PipelineMappingQC [as 别名]
# 或者: from CGATPipelines.PipelineMappingQC import buildPicardCoverageStats [as 别名]
def buildCoverageStats(infile, outfile):
'''Generate coverage statistics for regions of interest from a
bed file using Picard'''
# TS check whether this is always required or specific to current baits file
# baits file requires modification to make picard accept it
# this is performed before CalculateHsMetrics
to_cluster = USECLUSTER
baits = PARAMS["roi_baits"]
modified_baits = infile + "_temp_baits_final.bed"
regions = PARAMS["roi_regions"]
statement = '''samtools view -H %(infile)s > %(infile)s_temp_header.txt;
awk 'NR>2' %(baits)s |
awk -F '\\t' 'BEGIN { OFS="\\t" } {print $1,$2,$3,"+",$4;}'
> %(infile)s_temp_baits.bed;
cat %(infile)s_temp_header.txt %(infile)s_temp_baits.bed
> %(modified_baits)s; checkpoint ;
rm -rf %(infile)s_temp_baits.bed %(infile)s_temp_header.txt
'''
P.run()
PipelineMappingQC.buildPicardCoverageStats(
infile, outfile, modified_baits, modified_baits)
IOTools.zapFile(modified_baits)