本文整理汇总了Python中CGATPipelines.PipelineLncRNA.extractMAFGeneBlocks方法的典型用法代码示例。如果您正苦于以下问题：Python PipelineLncRNA.extractMAFGeneBlocks方法的具体用法？Python PipelineLncRNA.extractMAFGeneBlocks怎么用？Python PipelineLncRNA.extractMAFGeneBlocks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.extractMAFGeneBlocks方法的2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: extractLncRNAFastaAlignments
# 需要导入模块: from CGATPipelines import PipelineLncRNA [as 别名]
# 或者: from CGATPipelines.PipelineLncRNA import extractMAFGeneBlocks [as 别名]
def extractLncRNAFastaAlignments(infiles, outfile):
"""
Recieves a MAF file containing pairwise alignments and a gtf12 file
containing intervals. Outputs a single fasta file containing aligned
sequence for each interval.
"""
bed_file, maf_file = infiles
maf_tmp = P.getTempFilename("./phyloCSF")
to_cluster = False
statement = ("gunzip -c %(maf_file)s > %(maf_tmp)s")
P.run()
target_genome = PARAMS["genome"]
query_genome = PARAMS["phyloCSF_query_genome"]
genome_file = os.path.join(PARAMS["genomedir"], PARAMS["genome"])
gene_models = PipelineLncRNA.extractMAFGeneBlocks(bed_file,
maf_tmp,
genome_file,
outfile,
target_genome,
query_genome,
keep_gaps=False)
E.info("%i gene_models extracted" % gene_models)
os.unlink(maf_tmp)示例2: extractControllLncRNAFastaAlignments
# 需要导入模块: from CGATPipelines import PipelineLncRNA [as 别名]
# 或者: from CGATPipelines.PipelineLncRNA import extractMAFGeneBlocks [as 别名]
def extractControllLncRNAFastaAlignments(infiles, outfile):
bed_file, maf_file = infiles
maf_tmp = P.getTempFilename("/ifs/scratch")
to_cluster = False
statement = ("gunzip -c %(maf_file)s > %(maf_tmp)s")
P.run()
target_genome = PARAMS["genome"]
query_genome = PARAMS["phyloCSF_query_genome"]
genome_file = os.path.join(PARAMS["genomedir"], PARAMS["genome"])
gene_models = PipelineLncRNA.extractMAFGeneBlocks(bed_file,
maf_tmp,
genome_file,
outfile,
target_genome,
query_genome,
keep_gaps=False)
E.info("%i gene_models extracted" % gene_models)
os.unlink(maf_tmp)