ó N{=Oc@s+ddlZd„Zd„Zd„ZdS(i’’’’Nc Csśg}g}d}d}xItt|ƒƒD]5} |t|| || || ƒkr+| }Pq+q+W|dkrƒd}|||fS|dkr0xž|dkr,t||||||ƒ} ||g7}|| g7}|d}|| }|t|ƒkr|dkrd}n|||fS||}q’Wn|dkrķx®|dkrét||||dƒ} |jd|| dƒ|jd| ƒ|d}|| }|dkrŠ|dkrĆd}n|||fS||||d}q?Wn|||fS(s“ This function returns the corresponding segstart and seg length (as in the list) parameters: pos: the position to be queried seglen: the length of the segment direction: 1 (forward), -1 (backward) exonstart,exonlen: the exon positions Return value: (segstart,seglength,status) status is used to indicate the possible errors 0: normal 1: the position is not in the exon range 2: the segment exceeds the boundary i’’’’iii(trangetlentmintinsert( tpostseglent directiont exonstarttexonlentsegstartt seglengtht posexonidtstatustnetlentoadd((sB/home/wli/Dropbox/work/NGSTools/rnaseqreadsimulator/src/getSegs.pytgetSegssH%                 cCs€tj||ƒ}|t|ƒkrEt|ƒd}|dd}n|dkrn|||||d}n|||}|S(s Convertion from coordinates in a transcript to coordinates in a reference. Need to provide exon start position and the cumulate exon length as input. ii’’’’i(tbisectt bisect_rightR(ttpostcumlenRtselsegR((sB/home/wli/Dropbox/work/NGSTools/rnaseqreadsimulator/src/getSegs.pyttpos2pos9s cCsP|d|d|df}g|D]}||d^q#}|dkrRd}n|dkrgd}n|j|dt|dƒdt|dƒd|dd|dt|dƒdt|dƒddtt|ƒƒddjg|D]}t|ƒd ^qõƒddjg|D]}t|ƒd ^q#ƒdd ƒd S( s Write one line in .bed file. Need to provide information of chromosome, id, direction, segment starts and segment lengths ii’’’’it+t-s s0 tt,s N(twritetstrRtjoin(tfidtlineidt chromosomeRt startrangetlenrangetbedrangeti((sB/home/wli/Dropbox/work/NGSTools/rnaseqreadsimulator/src/getSegs.pyt writeBedlineIs!    (RRRR$(((sB/home/wli/Dropbox/work/NGSTools/rnaseqreadsimulator/src/getSegs.pyts  4