ó ƒå˜[c@`sddlmZmZmZmZddlZddlZddlZddlZddl Z ddl Z ddl Z ddl Z ddl Z ddlZddlZddlZddlmZddlZddlZejeƒZejejƒƒddd„ƒYZdS(i(tabsolute_importtdivisiontprint_functiontunicode_literalsN(tGraphCycleExceptiontGene_splice_modelercB`sƒeZdZd„Zd„Zd„Zd„Zd„Zd„Ze d„ƒZ e d„ƒZ e d „ƒZ e d d „ƒZ RS( uŒ Builds supertranscipts. object instance members: gene_id : str alignments : list of Node_alignment objects cC`sn||_tƒ|_tjdj|ƒƒx<|D]4}|jƒ}tjj|ƒ}|jj |ƒq2WdS(u? initialize alignments list with simple single 'alignment' objects with each path as an individual alignment with just its path nodes. params: gene_id : str node_path_obj_list : list of Node_path objects, each Node_path corresponding to an individual Trinity isoform uGene_splice_modeler inputs: {}N( tgene_idtlistt alignmentstloggertdebugtformattget_transcript_nametNode_alignmenttget_single_seq_node_alignmenttappend(tselfRtnode_path_obj_listt node_path_objttranscript_namet alignment_obj((sƒ/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Gene_splice_modeler.pyt__init__&s    cC`s|jS(N(R(R((sƒ/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Gene_splice_modeler.pyt get_gene_idAscC`sF|jƒs8y|jƒSWqBtk r4|jƒSXn |jƒSdS(u' method to construct the super transcript. Tries 2 approaches: a. If there isn't an obvious repetitive node structure and so the graph formas a DAG, we build a splice graph and perform topological sorting of the nodes. b. If there is some repetitive structure, we resort to performing a multiple alignment-based method to organize relationships among nodes in isoforms, and the multiple alignment produces the linear ordering for the supertranscript. N(talignment_contains_repeat_nodettopological_order_splice_modelRtmultiple_alignment_splice_model(R((sƒ/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Gene_splice_modeler.pytbuild_splice_modelEs   cC`syxr|jD]g}tƒ}xUtd|jƒƒD]>}|j|ƒ}|jƒ}||kr`tS|j|ƒq/Wq WtS(Ni( Rtsettrangetwidthtget_representative_column_nodet get_loc_idtTruetaddtFalse(Rt alignmenttloc_idstitnode_objtloc_id((sƒ/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Gene_splice_modeler.pyR`s   cC`sétjdƒ|jƒ}tj|ƒ}xg|jD]\}tjdt|ƒƒ|jƒd}|jƒd}tjdt|ƒƒxtdt |ƒƒD]î}||}|j ƒ}|j |||j ƒƒ} tjdt| ƒƒ|dkr5||d} |j || j ƒ| j ƒƒ} | j | ƒn|t |ƒdkrœ||d} |j || j ƒ| j ƒƒ} | j| ƒqœqœWq2Wtjdt|ƒƒtjj|jƒƒ}tjdt|ƒƒtƒ}x7tdt |ƒƒD] }||j ƒ}|||}t ƒ}x|D]}|j||ƒq$W|j|ƒqWtjd t|ƒƒtj|jƒ||ƒ}tjd t|ƒƒ|S(uò Computes a mismatch-free multiple alignment (just matches and gaps) between two Node_alignment objects returns single Node_alignment object containing the contents of aligned align_a and align_b as aligned. uMerging alignments {} and {}uEError, transcripts in alignments to merge are not disjoint: {} and {}iuDEL_BiubtuDEL_AuscoreuDIAGubt: ({},{}), bt_dir not defineduMerged alignment nodes list: umerged alignment node matrix: umerged alignment obj: N(R R R RR+t isdisjointRJRt DP_matrixtbuild_DP_matrixRRtget_match_scoreRtget_node_LIST_at_column_posR,RR5treverseR)R R(RPRQttranscript_names_align_Attranscript_names_align_Btwidth_atwidth_bt dp_matrixR%RZtscore_cell_matcht score_diagt score_del_at score_del_btmax_itmax_jtall_merged_alignment_nodes_listt score_structt nodes_align_at nodes_align_bt align_nodestbt_dirtxtmerged_transcript_name_listtnode_obj_matrixtrowt node_obj_listtmerged_alignment_obj((sƒ/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Gene_splice_modeler.pyRIÿs„    $                  cC`s`|j|ƒ}|j|ƒ}tjj|ƒ}tjj|ƒ}tj||ƒrXdSdSdS(u] just determines if indices in two transcripts have the same node identifier iiN(tget_node_set_at_column_posR tget_node_loc_idsRt intersection(RPtidx_aRQtidx_bt node_set_at node_set_b((sƒ/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Gene_splice_modeler.pyRa•sidc C`s»t|jƒƒ}t||dƒ}d}d}xi||krxB|D]:}|||t|||ƒ!} ||d| d7}qHW|d7}||7}q5W|jdj||ƒƒdS(uW writes the multiply aligned isoform sequences to an output filehandle iuu u u // {} {} N(RtkeysR,tmintwriteR ( t gene_namet malign_dicttofht align_widthttranscript_namestalignment_lengtht align_startt align_textRt align_region((sƒ/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Gene_splice_modeler.pyt write_malign§s  (t__name__t __module__t__doc__RRRRRRt staticmethodRERIRaRŽ(((sƒ/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Gene_splice_modeler.pyRs      > ;–((t __future__RRRRtostsystretloggingtargparset collectionsRGttimeR(tTNodet Node_pathR RR1R_t getLoggerRR t addHandlert NullHandlerR(((sƒ/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Gene_splice_modeler.pyts "$