ó QŽfXc@ssddlZddlZddlZddlZddlZddlZdZdZd„Zd„Z d„Z dS(iÿÿÿÿNt TACGCTTGCATt ATGCAAGCGTAc Csšg}x|D]…}|j|ƒr xm|j|ƒD]Y}xP|j|ƒD]?} x6|j| ƒD]%} |j| ƒr^|j| ƒq^q^WqHWq2Wq q W|S(N(tFiltertBreaktappend( tcontigstcoverage_breakert length_filtert n_breakertpattern_breakertpattern_filtertresulttcontigt subcontigt subsubcontigtsubsubsubcontig((sw/home/psgendb/BIRCHDEV/pkg/SPAdes-3.13.0/linux-x86_64/share/spades/spades_pipeline/truspades/moleculo_postprocessing.pytSplitAndFilters #cCsIt|d|dƒ}x!|D]}tj|||ƒqW|jƒdS(Nt.tw(topentSeqIOtwritetclose(t output_filetformatR toutputR ((sw/home/psgendb/BIRCHDEV/pkg/SPAdes-3.13.0/linux-x86_64/share/spades/spades_pipeline/truspades/moleculo_postprocessing.pyt OutputResultss c Cs>|jdƒ|jd|ƒ|jdƒttjt|dƒdƒƒ}tjg|D]}tj|ƒ^qYƒ}tj ||ƒt j ||t t ƒ}t jdƒ}tj||ddƒ} tjt t d ƒ} tjd ƒ} t|| || | |ƒ} t|d| ƒt|d | ƒ|jd |d ƒdS(Ns5===== Starting postprocessing based on read alignmentsProcessing scaffolds from s3Using read alignments to break and filter scaffoldstrUtfastaiÜidi2i–itfastqs7===== Postprocessing finished. Results can be found in s.fastq(tinfotlistRtparseRt sam_parsertSamChaintSamfiletgenerate_qualitytGenerateQualitytmoleculo_filter_contigstPatternContigFiltertpatternt rc_patterntContigLengthFiltertbreak_by_coveraget ContigBreakertPatternBreakertNBreakerRR( t contigs_fileRt sam_filestlogRtsam_filetsamR RRR RR ((sw/home/psgendb/BIRCHDEV/pkg/SPAdes-3.13.0/linux-x86_64/share/spades/spades_pipeline/truspades/moleculo_postprocessing.pytmoleculo_postprocessing$s  !+( R&R+RtsysR$R!R(R)RRR4(((sw/home/psgendb/BIRCHDEV/pkg/SPAdes-3.13.0/linux-x86_64/share/spades/spades_pipeline/truspades/moleculo_postprocessing.pyts