本文整理汇总了Python中CGATPipelines.PipelineLncRNA.flagExonStatus方法的典型用法代码示例。如果您正苦于以下问题：Python PipelineLncRNA.flagExonStatus方法的具体用法？Python PipelineLncRNA.flagExonStatus怎么用？Python PipelineLncRNA.flagExonStatus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.PipelineLncRNA的用法示例。
在下文中一共展示了PipelineLncRNA.flagExonStatus方法的3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: flagExonStatus
# 需要导入模块: from CGATPipelines import PipelineLncRNA [as 别名]
# 或者: from CGATPipelines.PipelineLncRNA import flagExonStatus [as 别名]
def flagExonStatus(infile, outfile):
'''
Adds two attributes to the gtf entry:
exon_status_locus - specifies whether the gene model is multi- or single exon
exon_status - specifies whether the transcript is mult- or single exon
'''
PipelineLncRNA.flagExonStatus(infile, outfile)示例2: buildRefcodingGeneSetStats
# 需要导入模块: from CGATPipelines import PipelineLncRNA [as 别名]
# 或者: from CGATPipelines.PipelineLncRNA import flagExonStatus [as 别名]
def buildRefcodingGeneSetStats(infile, outfile):
'''
counts:
no. of transcripts
no. genes
average number of exons per transcript
average number of exons per gene
no. multi-exon transcripts
no. single exon transcripts
no. multi-exon genes
no. single exon genes
in the coding and lncRNA genesets
'''
# calculate exon status for refcoding genes.
tmpf = P.getTempFilename(".") + ".gz"
PipelineLncRNA.flagExonStatus(infile, tmpf)
outf = open(outfile, "w")
outf.write("\t".join(["no_transcripts",
"no_genes",
"no_exons_per_transcript",
"no_exons_per_gene",
"no_single_exon_transcripts",
"no_multi_exon_transcripts",
"no_single_exon_genes",
"no_multi_exon_genes"]) + "\n")
outf.write("\t".join(map(str, [PipelineLncRNA.CounterTranscripts(tmpf).count(),
PipelineLncRNA.CounterGenes(tmpf).count(),
PipelineLncRNA.CounterExonsPerTranscript(tmpf).count(),
PipelineLncRNA.CounterExonsPerGene(tmpf).count(),
PipelineLncRNA.CounterSingleExonTranscripts(tmpf).count(),
PipelineLncRNA.CounterMultiExonTranscripts(tmpf).count(),
PipelineLncRNA.CounterSingleExonGenes(tmpf).count(),
PipelineLncRNA.CounterMultiExonGenes(tmpf).count()])))
os.unlink(tmpf)
os.unlink(tmpf + ".log")
os.unlink(P.snip(tmpf, ".gz"))示例3: flagExonStatus
# 需要导入模块: from CGATPipelines import PipelineLncRNA [as 别名]
# 或者: from CGATPipelines.PipelineLncRNA import flagExonStatus [as 别名]
def flagExonStatus(infile, outfile):
"""
Adds an attribute to the gtf entry dependent on whether the lncRNA
is multi or single exon
"""
PipelineLncRNA.flagExonStatus(infile, outfile)