Ñò Ìa,Jc @sÁddkZddkZddkZddkZddkTddkTddklZeidƒZ eidƒZ d„Z d„Z d„Z d „Zd „Zed joeeiƒndS( iÿÿÿÿN(t*(t OptionParsers\+s\-c Csbt|ƒ}d}d}tt|dƒƒ}g}xÞ|D]Ö}tid|ƒp½|iƒ}|iƒ}ti|dƒo/t|dƒ|} |i | ƒ|d7}qt i|dƒoJt|dƒd|} | djo d} n|i | ƒ|d7}qq;q;W|i ƒ||} dt | ƒd t |ƒd t |ƒGH|i ƒ|S( s¥ *This takes into account the identical tags *Tags on different strands are positioned differently -> tag start (atoi(sline[1])) + fragment_size/2 <- tag start (atoi(sline[2])) - 1 - fragment_size/2, the extra -1 is because that bed format has open-half, the sline[2] is not included. The stored positions are not the midpoint rathan than the start The interface is no longer the same as that for getBedCoords(file) input: file: the file that has the raw tag data from one chromosome fragment_size: the fragment size after CHIP experiment. output: return: a sorted list of positions which might have redundent entries gittrackiigð?istotal tag count is: s = t+(topentinttroundtretmatchtstriptsplittplustatoitappendtminustsorttstrtclose( tfilet fragment_sizetinfiletpostive_tag_countstnegative_tag_countstshiftttaglisttlinetslinetpositionttotal_tag_counts((sK/woldlab/castor/data00/home/georgi/SICER_v1.01/SICER/lib/make_graph_file.pytget_bed_coords6s2        + c Cssh}t|dƒ}t|ƒdjo=|d||}d}xÅtdt|ƒƒD]®}||||} | |jo|d7}qV| |joi|||<||d} |dt|ƒdt| ƒdt|ƒd} |i| ƒ| }d}qVdGHqVW|||<||d} |dt|ƒdt| ƒdt|ƒd} |i| ƒn|iƒ|S(s  taglist: sorted list of positions that includes every tag on a chromosome window_size: the artificial bin size for binning the tags bed_vals: a dictionary keyed by the start of tag_containing windows, with value being the tag count in the window. In this function, the bins are set up using an absolute coordinate system. Namely [0, window_size-1),[window_size, 2*window_size-1),... The result writen into the file is guaranteed to be already sorted within a chromosome. twiis s sSomething is wrong!!!!!!!(RtlentrangeRtwriteR( Rtchromt window_sizeRtbed_valstoutfiletcurrent_window_startttag_count_in_current_windowtitstarttcurrent_window_endtoutline((sK/woldlab/castor/data00/home/georgi/SICER_v1.01/SICER/lib/make_graph_file.pytGenerate_windows_and_count_tagsfs0   4    4 cCst|iƒƒS(N(Rtkeys(R$((sK/woldlab/castor/data00/home/georgi/SICER_v1.01/SICER/lib/make_graph_file.pytTotal_number_of_windows–scCs(t||ƒ}t||||ƒ}dS(N(RR,(ttagfileR"R#RR%ttag_listR$((sK/woldlab/castor/data00/home/georgi/SICER_v1.01/SICER/lib/make_graph_file.pytmake_graph_filešsc Csitƒ}|iddddddddd d d d ƒ|id dddddddd dd dƒ|iddddddddd dd dƒ|iddddddddd dd dƒ|iddddddddd dd d ƒ|i|ƒ\}}t|ƒd jo|iƒtid!ƒnt|i|i ƒ}t ||i |i |i ƒ}dS("Ns-fs --tagfiletactiontstorettypetstringtdestR/thelps"file with tag coords in bed formattmetavarss-cs--chromR"schromosome name for graphss-ws --window_sizeRR#swindow size to make summaryss-is--fragment_sizeRs0average size of a fragment after CHIP experiments-os --outfileR%soutput file namei i(Rt add_optiont parse_argsRt print_helptsystexitRR/RR,R"R#R%(targvtparsertopttargsR0R$((sK/woldlab/castor/data00/home/georgi/SICER_v1.01/SICER/lib/make_graph_file.pytmainŸs.        t__main__(RtosR<tshutiltmathR5toptparseRtcompileR RRR,R.R1RBt__name__R>(((sK/woldlab/castor/data00/home/georgi/SICER_v1.01/SICER/lib/make_graph_file.pyts0   0 0