Ñò Xs*Jc@sEddkZddkZddkZddkZddkTddkTddklZddkZddk Z ddk Z ddk Z ddk Z ddk Z eiƒZdZdZeidƒZeidƒZd„Zd „Zd „Zd „Zd „Zd „Zd„Zd„Zd„Zdd„Zd„Zd„Z dS(iÿÿÿÿN(t*(t OptionParsers /bin/greps/bin/cats\+s\-cCsog}g}xV|D]N}ti|iƒo|i|ƒqti|iƒo|i|ƒqqW||fS(sq input: a list of bed6 object Return: two lists of bed6 objects, one for plus strand, one for minus strand. (tplustmatchtstrandtappendtminus(tbed_listt plus_bed_listtminus_bed_listtb((sM/woldlab/castor/data00/home/georgi/SICER_v1.01/SICER/lib/bed_preprocessing.pytbreakUpStrands(scCsOti|ƒdjpt‚dgd}t|ƒdjot|ƒ}|di}d}xžtdt|ƒƒD]‡}||}|i|jo]t|ƒd|jo#|dg|t|ƒd7}n||cd7<|i}d}qr|d7}qrWt|ƒd|jo#|dg|t|ƒd7}n||cd7cutoff, only cutoff number of copies of the read are retained. Output: write bed objects with the extra redundant copies filtered out. Return: the number of reads remained iitw( R R RRtopenRRtwritetclose( Rtcutofftoutfiletcounter2toutRRRt current_tagRR((sM/woldlab/castor/data00/home/georgi/SICER_v1.01/SICER/lib/bed_preprocessing.pyt filter_reads§s6            c Cs8d}t|ƒdjot|dƒ}t|ƒ}|di}d}|d}xªtdt|ƒƒD]“} || } | i|joA||jot||ƒ|d7}n| i}d}| }qg||jot||ƒ|d7}n|d7}qgW||jot||ƒ|d7}n|iƒn|S(sf A read has n copies in the sorted_bed_list. If n<=cutoff, all the copies are retained. If n>cutoff, only cutoff number of copies of the read are retained. Output: write bed objects with the extra redundant copies filtered out. This function uses out = open(outfile, 'a') instead of out = open(outfile, 'w') Return: the number of reads remained itai(RR#RRR$R%( RR&R'R(R)RRRR*RR((sM/woldlab/castor/data00/home/georgi/SICER_v1.01/SICER/lib/bed_preprocessing.pytfilter_reads_addÍs4             cCsm|idt|iƒdt|iƒd|idtt|iƒƒd|id}|i|ƒdS(sV write one line into outfile. The file openning and closing is handled by outside. s s N( tchromtstrRtendtnametinttscoreRR$(RR)toutline((sM/woldlab/castor/data00/home/georgi/SICER_v1.01/SICER/lib/bed_preprocessing.pyR$òs\cCs"x|D]}t||ƒqWdS(s[ write a bed6_list into outfile. The file openning and closing is handled from outside. N(R$(t bed6_listR)R((sM/woldlab/castor/data00/home/georgi/SICER_v1.01/SICER/lib/bed_preprocessing.pyt write_listúscCs•g}t|ƒt|ƒjo;|}xitt|ƒƒD]}||c||7s40            ' ) & %