本文整理汇总了Python中CGAT.Fastq.getOffset方法的典型用法代码示例。如果您正苦于以下问题：Python Fastq.getOffset方法的具体用法？Python Fastq.getOffset怎么用？Python Fastq.getOffset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CGAT.Fastq的用法示例。
在下文中一共展示了Fastq.getOffset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: build
# 需要导入模块: from CGAT import Fastq [as 别名]
# 或者: from CGAT.Fastq import getOffset [as 别名]
def build(self, infiles, outfiles, output_prefix):
prefix = self.prefix
offset = Fastq.getOffset("sanger", raises=False)
outdir = os.path.join(output_prefix + ".dir")
track = os.path.basename(output_prefix)
processing_options = self.processing_options
infile1, infile2 = infiles
outfile = outfiles[0]
cmd = '''flash %(infile1)s %(infile2)s
-p %(offset)s
%(processing_options)s
-o %(track)s
-d %(outdir)s
>& %(output_prefix)s-flash.log;
checkpoint;
gzip %(outdir)s/*;
checkpoint;
mv %(outdir)s/%(track)s.extendedFrags.fastq.gz %(outfile)s;
''' % locals()
return cmd示例2: setfastqAttr
# 需要导入模块: from CGAT import Fastq [as 别名]
# 或者: from CGAT.Fastq import getOffset [as 别名]
def setfastqAttr(self, infiles):
self.offset = Fastq.getOffset(self.f_format, raises=False)示例3: processReads
# 需要导入模块: from CGAT import Fastq [as 别名]
# 或者: from CGAT.Fastq import getOffset [as 别名]
#.........这里部分代码省略.........
%(threads)s
--compress
%(infile)s %(infile2)s >> %(outfile)s.log
'''
P.run()
if PARAMS["combine_reads_concatenate"]:
infiles = " ".join([track + x for x in [".notCombined_1.fastq.gz", ".notCombined_2.fastq.gz", ".extendedFrags.fastq.gz"]])
statement = '''zcat %(infiles)s | gzip > %(outfile)s; rm -rf %(infiles)s'''
else:
statement = '''mv %(track)s.extendedFrags.fastq.gz %(outfile)s'''
P.run()
return
if PARAMS["process_sample"] and infile2:
E.warn( "sampling can not be combined with other processing for paired ended reads")
statement = '''zcat %(infile)s
| python %(scriptsdir)s/fastq2fastq.py
--sample=%(sample_proportion)f
--pair=%(infile2)s
--outfile-pair=%(outfile2)s
--log=%(outfile)s_sample.log
| gzip
> %(outfile)s
'''
P.run()
return
# fastx does not like quality scores below 64 (Illumina 1.3 format)
# need to detect the scores and convert
format = Fastq.guessFormat( IOTools.openFile(infile ) , raises = False)
E.info( "%s: format guess: %s" % (infile, format))
offset = Fastq.getOffset( format, raises = False )
if PARAMS["process_remove_contaminants"]:
adaptors = listAdaptors(contaminant_file)
# %(contamination_trim_type)s
s = [ '''
cutadapt
%(adaptors)s
--overlap=%(contamination_min_overlap_length)i
--format=fastq
%(contamination_options)s
<( zcat < %(infile)s )
2>> %(outfile)s_contaminants.log
''' ]
do_sth = True
else:
s = ['zcat %(infile)s' ]
if PARAMS["process_artifacts"]:
s.append( 'fastx_artifacts_filter -Q %(offset)i -v %(artifacts_options)s 2>> %(outfile)s_artifacts.log' )
do_sth = True
if PARAMS["process_trim"]:
s.append( 'fastx_trimmer -Q %(offset)i -v %(trim_options)s 2>> %(outfile)s_trim.log' )
do_sth = True
# NICK - may replace fastx trimmer
if PARAMS["process_trim_quality"]:
s.append( 'fastq_quality_trimmer -Q %(offset)i -v %(trim_quality_options)s 2>> %(outfile)s_trim.log' )
do_sth = True
if PARAMS["process_filter"]:
s.append( 'fastq_quality_filter -Q %(offset)i -v %(filter_options)s 2>> %(outfile)s_filter.log')示例4: processReads
# 需要导入模块: from CGAT import Fastq [as 别名]
# 或者: from CGAT.Fastq import getOffset [as 别名]
def processReads( infiles, outfile ):
'''process reads.'''
infile, contaminant_file = infiles
do_sth = False
to_cluster = True
infile2 = checkPairs( infile )
if infile2:
track = P.snip( outfile, ".fastq.1.gz" )
outfile2 = P.snip( outfile, ".fastq.1.gz" ) + ".fastq.2.gz"
else:
track = P.snip( outfile, ".fastq.gz" )
if PARAMS["process_sample"] and infile2:
E.warn( "sampling can not be combined with other processing for paired ended reads")
statement = '''zcat %(infile)s
| python %(scriptsdir)s/fastq2fastq.py
--sample=%(sample_proportion)f
--pair=%(infile2)s
--outfile-pair=%(outfile2)s
--log=%(outfile)s_sample.log
| gzip
> %(outfile)s
'''
P.run()
return
# fastx does not like quality scores below 64 (Illumina 1.3 format)
# need to detect the scores and convert
format = Fastq.guessFormat( IOTools.openFile(infile ) , raises = False)
E.info( "%s: format guess: %s" % (infile, format))
offset = Fastq.getOffset( format, raises = False )
if PARAMS["process_remove_contaminants"]:
adaptors = listAdaptors(contaminant_file)
# %(contamination_trim_type)s
s = [ '''
cutadapt
%(adaptors)s
--overlap=%(contamination_min_overlap_length)i
--format=fastq
%(contamination_options)s
<( zcat < %(infile)s )
2>> %(outfile)s_contaminants.log
''' ]
do_sth = True
else:
s = ['zcat %(infile)s' ]
if PARAMS["process_artifacts"]:
s.append( 'fastx_artifacts_filter -Q %(offset)i -v %(artifacts_options)s 2>> %(outfile)s_artifacts.log' )
do_sth = True
if PARAMS["process_trim"]:
s.append( 'fastx_trimmer -Q %(offset)i -v %(trim_options)s 2>> %(outfile)s_trim.log' )
do_sth = True
# NICK - may replace fastx trimmer
if PARAMS["process_trim_quality"]:
s.append( 'fastq_quality_trimmer -Q %(offset)i -v %(trim_options)s 2>> %(outfile)s_trim.log' )
do_sth = True
if PARAMS["process_filter"]:
s.append( 'fastq_quality_filter -Q %(offset)i -v %(filter_options)s 2>> %(outfile)s_filter.log')
do_sth = True
if PARAMS["process_sample"]:
s.append( 'python %(scriptsdir)s/fastq2fastq.py --sample=%(sample_proportion)f --log=%(outfile)s_sample.log' )
if not do_sth:
E.warn( "no filtering specified for %s - nothing done" % infile )
return
s.append( "gzip" )
if not infile2:
statement = " | ".join( s ) + " > %(outfile)s"
P.run()
else:
tmpfile = P.getTempFilename(".")
tmpfile1 = tmpfile + ".fastq.1.gz"
tmpfile2 = tmpfile + ".fastq.2.gz"
E.warn( "processing first of pair")
# first read pair
statement = " | ".join( s ) + " > %(tmpfile1)s"
P.run()
# second read pair
E.warn( "processing second of pair")
infile = infile2
statement = " | ".join( s ) + " > %(tmpfile2)s"
P.run()
# reconcile
E.info("starting reconciliation" )
#.........这里部分代码省略.........