σ ƒε˜[c@`sΐddlmZmZmZmZddlZddlZddlZddlZddl Z ddl Z ddl Z ddl Z ddl Z ddlZejeƒZddd„ƒYZdS(i(tabsolute_importtdivisiontprint_functiontunicode_literalsNtNode_alignmentcB`sώeZdZdZd„Zd„Zd„Zd„Zd„Z e d„ƒZ e d„ƒZ e d„ƒZ e d „ƒZd „Zd „Zd „Zd „Zd„Zd„Zd„Zd„Zd„Zd„Zd„Zd„Zd„Zed„ZRS(uλ Object has two members: transcript_names = [ transA, transB, transC, ... ] aligned_nodes = [ [transA_node_1, transA_node_2, ... ], [transB_node_1, transB_node_2, ... ], [ None, transC_node_1, ... ], ] Note, can have None at node positions to include gaps. cC`s||_||_||_dS(N(tgene_idttranscript_namest aligned_nodes(tselfRttranscript_name_listtnode_obj_matrix((s~/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Node_alignment.pyt__init__)s  cC`s|jS(N(R(R((s~/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Node_alignment.pyt get_gene_id.scC`s ||_dS(N(R(RR((s~/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Node_alignment.pyt set_gene_id1scC`s|jS(N(R(R((s~/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Node_alignment.pytget_transcript_names4scC`s|jS(N(R(R((s~/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Node_alignment.pytget_aligned_nodes8scC`sUtƒ}x!|jƒD]}|j|ƒqW|jƒ}t||g|gƒ}|S(uΘ Factory method: constructs a Node_alignment object from a Node_path object mostly just reshaping the info for use with the multiple alignment methods. (tlisttget_pathtappendtget_transcript_nameR(tpath_objt node_listtnode_objttranscript_nameR((s~/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Node_alignment.pytget_single_seq_node_alignment<s  cC`sRtj|ƒ}tj|ƒ}tj|ƒ}tj|ƒ}tj||ƒ}|S(uT given to Node_alignment objects, counts the number of shared nodes (Rt get_node_settget_node_loc_idstsett intersection(talign_Atalign_Bt node_set_at node_set_bt common_nodes((s~/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Node_alignment.pytcompute_number_common_nodesPs cC`s7tƒ}x'|D]}|jƒ}|j|ƒqW|S(ub private static method gets the list of loc_id among all nodes in the set (Rt get_loc_idtadd(tnode_sett loc_ids_settnodetloc_id((s~/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Node_alignment.pyRas    cC`s†t|ƒ}|jƒ}tƒ}x^td|ƒD]M}xDtd|ƒD]3}|j||}|dk rG|j|ƒqGqGWq1W|S(uW extracts a list of unique Node objects from the Node_alignment object iN(tlentwidthRtrangeRtNoneR$(t align_objt num_transtalignment_widthR%t align_numt align_posR((s~/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Node_alignment.pyRps    cC`sZtƒ}xJtdt|ƒƒD]3}|j||}|dk r|j|ƒqqW|S(u\ At a given column of the Node_alignment, extracts the list of unique nodes iN(RR+R)RR,R$(Rtcol_post node_objstiR((s~/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Node_alignment.pytget_node_set_at_column_pos„s  cC`st|j|ƒƒ}|dS(Ni(RR5(RR2R((s~/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Node_alignment.pytget_representative_column_node•scC`sKtƒ}x;tdt|ƒƒD]$}|j||}|j|ƒqW|S(Ni(RR+R)RR(RR2R3R4R((s~/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Node_alignment.pytget_node_LIST_at_column_posœs  cC`sV|j|ƒ}tƒ}x7|D]/}|dkrA|jtƒq|jtƒqW|S(N(R7RR,RtFalsetTrue(RR2Rtoccupancy_listR'((s~/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Node_alignment.pyt get_node_occupancy_at_column_pos₯s   cC`s8x1tdt|ƒƒD]}|j|j|ƒqWdS(Ni(R+R)RR(RRR4((s~/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Node_alignment.pytappend_node_to_each_entry³scC`s_xXtdt|ƒƒD]A}||tkrC|j|j|ƒq|j|jdƒqWdS(Ni(R+R)R9RRR,(RRtoccupancy_patternR4((s~/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Node_alignment.pyt*append_node_according_to_occupancy_patternΈscC`sct|ƒ}t|ƒ|kr-tdƒ‚nx/td|ƒD]}|j|j||ƒq=WdS(Nu.Error, column size differs from num_alignmentsi(R)t RuntimeErrorR+RR(Rtcolumn_node_listtnum_alignmentsR4((s~/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Node_alignment.pyt add_columnΓs  cC`s t|jƒS(uD number of transcripts represented in the alignment (R)R(R((s~/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Node_alignment.pyt__len__ΜscC`st|jdƒS(u< width of the alignment (number of columns) i(R)R(R((s~/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Node_alignment.pyR*Σsc C`s=t|jƒ}dj|dj|jƒƒ}|jƒ}d}xΊtd||ƒD]¦}x“td|ƒD]‚}|j|}|j|}|dj|ƒ7}xBt|||ƒD]-} | |krΕPn|dj|| ƒ7}q―W|d7}qhW|d7}qRWx:td|ƒD])}|j|ƒ} || jƒd7}q W|S(Nu/ # Alignment obj contains: {} transcripts: {} u,i iu{}u {}u ( R)RtformattjoinR*R+RR6ttoString( Rtnum_transcriptstret_textt align_widthtNODES_PER_LINER4tjRtaligned_nodes_entrytxt repr_node((s~/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Node_alignment.pyt__repr__Ϊs&    c C`s«t|ƒ}|jƒ}tƒ}x$td|ƒD]}|jgƒq1Wt|jƒ|jƒ|ƒ}g}|jdƒ}xHtd|ƒD]7}|j|ƒ}||krΌ|j|ƒn|}q‹W|j|ƒt j dj |ƒƒtƒ} x²td|dƒD]}||kr~d} t| ƒdkrEt j j| ƒ} n | d} |j|dƒ} |j| | ƒtƒ} n||kr| j|j|ƒƒqqW|S(u: merge unbranched nodes into single nodes iiuBlock_breakpoints: {}N(R)R*RR+RRR RR;tloggertdebugRDR,tTNodet merge_nodesR>R6( RRGR*R R4tsqueezed_alignmenttblock_breakpointstprev_col_node_settnode_column_sett blocked_nodest node_to_addtblocked_node_occupancy((s~/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Node_alignment.pytsqueezes8           cC`sΓ|jƒ}d}tƒ}tƒ}tƒ}tƒ}x9|D]1}d||{} len={} path=[{}] {} (RtdictRR+R*R6tget_seqR)R?tstrR#R;R9RERDRtvalues(Rt gene_nameRtgene_seqttranscript_to_gtf_linesttranscript_to_malignttranscript_to_Trinity_fa_seqttranscript_to_Trinity_fa_pathRR4Rtnode_seqtnode_idtnode_occupancyt pos_starttpos_endRKt cdna_seq_lentrel_node_startt rel_node_endRMtgene_gtfttrinity_fasta_textttranscript_seqt path_listtpath_list_text((s~/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Node_alignment.pytto_gene_fasta_and_gtf4sZ             #   cC`sFx?td|jƒƒD](}|j|ƒ}|jt|ƒƒqWdS(Ni(R+R*R6t set_loc_idR^(RR4RN((s~/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Node_alignment.pyt$reassign_node_loc_ids_by_align_orderscC`sz|jƒ}|jƒ}tj|ƒ}tƒ}x›td|ƒD]Š}|j|ƒ}tjdj|j ƒƒƒ|j ƒ} |j ƒ} |r’dt |ƒ} n|j | | |jƒƒ} |j| ƒq@Wxt|D]l} d} x]td|ƒD]L}| |dkrρ| dkr0|j| g||gƒn||} qρqρWqΥWtjdƒx!|D]}tj|j ƒƒqYW|S(Niu repr node: {}uloc_uNew graph node listing:(RR*tTGraphRR+R6RPRQRDRFtget_transcriptsR#R^tget_nodeR]RR,t add_edges(RR`treset_node_idsRR*trefined_tgrapht new_node_listR4RNt transcriptsR(tnew_nodetiso_node_alignmenttprevR'((s~/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Node_alignment.pytto_splice_graph‰s0         N(t__name__t __module__t__doc__R,tGAPR R R RRt staticmethodRR"RRR5R6R7R;R<R>RBRCR*ROR[RsRuR8R(((s~/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Node_alignment.pyRs2            & 4 M ((t __future__RRRRtostsystretloggingtargparset collectionstnumpyttimeRRRvt getLoggerR‚RPR(((s~/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Node_alignment.pyts"$