本文整理汇总了Python中CGATPipelines.PipelineLncRNA.filterMAF方法的典型用法代码示例。如果您正苦于以下问题：Python PipelineLncRNA.filterMAF方法的具体用法？Python PipelineLncRNA.filterMAF怎么用？Python PipelineLncRNA.filterMAF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.filterMAF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: createMAFAlignment
# 需要导入模块: from CGATPipelines import PipelineLncRNA [as 别名]
# 或者: from CGATPipelines.PipelineLncRNA import filterMAF [as 别名]
def createMAFAlignment(infiles, outfile):
"""
Takes all .axt files in the input directory, filters them to remove
files based on supplied regular expressions, converts to a single maf file
using axtToMaf, filters maf alignments under a specified length.
"""
outfile = P.snip(outfile, ".gz")
axt_dir = PARAMS["phyloCSF_location_axt"]
to_ignore = re.compile(PARAMS["phyloCSF_ignore"])
axt_files = []
for axt_file in os.listdir(axt_dir):
if axt_file.endswith("net.axt.gz") and not to_ignore.search(axt_file):
axt_files.append(os.path.join(axt_dir, axt_file))
axt_files = (" ").join(sorted(axt_files))
E.info("axt files from which MAF alignment will be created: %s" %
axt_files)
target_genome = PARAMS["phyloCSF_target_genome"]
target_contigs = os.path.join(PARAMS["annotations_annotations_dir"],
PARAMS_ANNOTATIONS["interface_contigs"])
query_genome = PARAMS["phyloCSF_query_genome"]
query_contigs = os.path.join(PARAMS["phyloCSF_query_assembly"],
PARAMS_ANNOTATIONS["interface_contigs"])
tmpf1 = P.getTempFilename("./phyloCSF")
tmpf2 = P.getTempFilename("./phyloCSF")
to_cluster = False
# concatenate axt files, then remove headers
statement = ("zcat %(axt_files)s"
" > %(tmpf1)s;"
" axtToMaf "
" -tPrefix=%(target_genome)s."
" -qPrefix=%(query_genome)s."
" %(tmpf1)s"
" %(target_contigs)s"
" %(query_contigs)s"
" %(tmpf2)s")
P.run()
E.info("Temporary axt file created %s" % os.path.abspath(tmpf1))
E.info("Temporary maf file created %s" % os.path.abspath(tmpf2))
removed = P.snip(outfile, ".maf") + "_removed.maf"
to_cluster = False
filtered = PipelineLncRNA.filterMAF(tmpf2,
outfile,
removed,
PARAMS["phyloCSF_filter_alignments"])
E.info("%s blocks were ignored in MAF alignment"
" because length of target alignment was too short" % filtered[0])
E.info("%s blocks were output to filtered MAF alignment" % filtered[1])
os.unlink(tmpf1)
os.unlink(tmpf2)
to_cluster = False
statement = ("gzip %(outfile)s;"
" gzip %(removed)s")
P.run()