ó QŽfXc@sXddlZddlZddlZdd„Zdd„Zd„Zddd„ZdS(iÿÿÿÿNic Cs|jdƒ|jd|ƒ|jd|ƒ|jd|ƒtjj|ƒrbtj|ƒntj|ƒtjj|dƒ}tjj|dƒ}tjj|dƒ} |jd|ƒ|jd |ƒtj |d d t |ƒd d |||g || |ƒ|jd| ƒ| S(NsAligning paired-end librarys Left reads: s Right reads: sOutput directory: s output.logt err_outputs alignment.sams;Starting alignment of reads using bwa. See detailed log in s-Starting read alignment. See detailed log in tmems-ts-Ss-MsDone. See result in ( tinfotostpathtexiststshutiltrmtreetmakedirstjointsupporttuniversal_sys_calltstr( tcommandtindext reads_file1t reads_file2twork_dirtlogtthreadstlog_filet err_log_filetresult((sf/home/psgendb/BIRCHDEV/pkg/SPAdes-3.13.0/linux-x86_64/share/spades/spades_pipeline/common/alignment.pytalign_bwa_pe_lib s  7tisc Csâtjj|ƒr"tj|ƒntj|ƒ|jdƒtjj|dƒ}tjj|dƒ}tjj|dƒ}|jdj|dd|d||gƒƒtj |dd|d||g|||ƒ|jdƒ|S( NsConstructing bwa indexRs output.logRt s-as-psIndex constructed.( RRRRRRRR R R (R Rt referenceRt algorithmRRR((sf/home/psgendb/BIRCHDEV/pkg/SPAdes-3.13.0/linux-x86_64/share/spades/spades_pipeline/common/alignment.pyt index_bwas  ++ c Cs|jdƒg}d}x^|D]V\}} tjj|t|ƒƒ} |jt|||| | ||ƒƒ|d7}q W|jd|ƒ|S(Ns===== Starting read alignmentis-===== Read alignment finished. See result in (RRRR R tappendR( R RtreadsRRRRtlib_numt left_readst right_readstlib_dir((sf/home/psgendb/BIRCHDEV/pkg/SPAdes-3.13.0/linux-x86_64/share/spades/spades_pipeline/common/alignment.pytalign_bwa_pe_libs+s c Cs¿|dkrtjdƒ}ntjj|ƒr@tj|ƒntj|ƒtjj |dƒ}t ||||ƒ}g|D]"}|dd|ddf^q~} t ||| |||ƒS(NtRs left readsis right reads( tNonetloggingt getLoggerRRRRRRR RR#( R RtdatasetRRRt index_dirRtlibR((sf/home/psgendb/BIRCHDEV/pkg/SPAdes-3.13.0/linux-x86_64/share/spades/spades_pipeline/common/alignment.pyt align_bwa9s  /(R RRRRR#R%R+(((sf/home/psgendb/BIRCHDEV/pkg/SPAdes-3.13.0/linux-x86_64/share/spades/spades_pipeline/common/alignment.pyts