ó ƒĺ˜[c@`sĘddlmZmZmZmZddlZddlZddlZddlZddl Z ddl Z ddl Z ddl Z ddl m Z ddlZejeƒZde j fd„ƒYZdS(i(tabsolute_importtdivisiontprint_functiontunicode_literalsN(tTopological_sorttCompact_graph_partialcB`s>eZd„Zd„Zd„Zd„Zd„Zd„ZRS(cC`sdS(N((tself((s…/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Compact_graph_partial.pyt__init__sc C`sđt}d}xÝ|rë|d7}tjdj|ƒƒ|jƒt}tj|jƒƒ}t j r˜dj|ƒ}|j |ƒtjdj|ƒƒnxů|D]ń}|j ƒdkr˝qŸntjdj||j ƒƒƒ|jƒ}t|ƒdkr6|j|ƒr6|j||ƒr6|j|ƒr6t}q6n|jƒ}t|ƒdkrŸ|j|ƒrŸ|j||ƒrŸ|j|ƒrt}qqŸqŸW|rt j rŘdj|ƒ}|j |ƒtjdj|ƒƒn|j|ƒqqWdS(Niiu) ### Partial graph compaction, Round: {}u+ladeda.BEGIN.compacted_partial.round_{}.dotu-wrote dot: {}u8 /////////// R[{}] Exploring compaction from node: {} u)ladeda.END.compacted_partial.round_{}.dot(tTruetloggertdebugtformattclear_touch_settingstFalseRttopologically_sortt get_all_nodestTGLOBALStDEBUGt draw_graphtget_touched_valttoStringtget_prev_nodestlent untouchedt$all_have_lower_topological_orderingstcompact_upwardtget_next_nodest%all_have_higher_topological_orderingstcompact_downwardtcompact_unbranched( Rttgraphtcompacted_flagtroundt sorted_nodest dot_filenametnodet prev_nodest next_nodes((s…/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Compact_graph_partial.pyt compact_graphs<       3  3  cC`sŒtjdj|ƒƒt|ƒ}xctdt|ƒdƒD]H}x?t|dt|ƒƒD]$}|j||||ƒr\tSq\Wq<WtS(Nucompact_upward: Partial {}ii( R R R tlisttrangeRtcompact_upward_node_pairRR (RR$titj((s…/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Compact_graph_partial.pyRNs    cC`s1tjdj|jƒ|jƒƒƒ|j|ƒsC|j|ƒr`tjdj||ƒƒtSt|jƒƒt|jƒƒkr”||}}n|jƒ}|jƒ}t|ƒ}|ddd…}|ddd…}d}x9td|ƒD](} || || kr|d7}qôPqôW|dkrItjdj||ƒƒtS|j ƒ} |d|} |dt|ƒ|!} |dt|ƒ|!} tjdj||| ƒƒt|ƒt| ƒt| ƒksŐt ‚t|ƒt| ƒt| ƒksýt ‚tjdj|jƒƒƒtjd j|jƒƒƒ|j ƒj |j ƒƒ}d |j ƒd |j ƒ}| j||| ƒ}|j| ƒ|j| ƒ|jƒj |jƒƒ}| j|g|jƒƒ| j|g|jƒƒ| j|g|ƒ|jƒt| ƒdkrB| j|jƒ|gƒ| j|ƒn | j|g|gƒ|jƒt| ƒdkr| j|jƒ|gƒ| j|ƒn | j|g|gƒ|jƒtjd j|jƒƒƒtjd j|jƒƒƒtjdj|jƒƒƒtjdj|||ƒƒtS(Nu/compact_upward_node_pair: node_A: {} node_B: {}u6-not parallel paths. excluding compaction of {} and {}i˙˙˙˙iiu$no matching suffix between {} and {}u#Suffices: seqA:{} SeqB:{} Shared:{}unode_A before mods: {}unode_B before mods: {}uUpart:u,unode_A after mods: {}unode_B after mods: {}unode_C after mods: {}u7 *** partially UP-compacted nodes: {} and {} + {} ***(R R R Rt is_ancestralR Rtget_seqR(t get_graphtAssertionErrortget_transcriptstuniont get_loc_idtget_nodetset_seqRt prune_edgest add_edgesttouchRt prune_nodeR(Rtnode_Atnode_BtseqAtseqBt shorter_lentseqA_revtseqB_revt num_matchesR*Rt shared_seqt uniqA_seqt uniqB_seqtcombined_transcriptstcombined_loc_idtnode_Ctall_next_nodes((s…/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Compact_graph_partial.pyR)[sj%$      ((     cC`sŒtjdj|ƒƒt|ƒ}xctdt|ƒdƒD]H}x?t|dt|ƒƒD]$}|j||||ƒr\tSq\Wq<WtS(Nucompact_downward: Partial {}ii( R R R R'R(Rtcompact_downward_node_pairRR (RR%R*R+((s…/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Compact_graph_partial.pyRĹs    cC`s tjdj|jƒ|jƒƒƒ|j|ƒsC|j|ƒr`tjdj||ƒƒtSt|jƒƒt|jƒƒkr”||}}n|jƒ}|jƒ}t|ƒ}d}x9td|ƒD](}||||krő|d7}qÎPqÎW|dkr#tjdj||ƒƒtS|j ƒ}|d|!} ||} ||} tjdj||| ƒƒtjdj|jƒƒƒtjdj|jƒƒƒ|j ƒj |j ƒƒ} d |j ƒd |j ƒ} |j | | | ƒ}|j| ƒ|j| ƒ|jƒj |jƒƒ}|j|jƒ|gƒ|j|jƒ|gƒ|j||gƒ|jƒt| ƒdkrą|j|g|jƒƒ|j|ƒn |j|g|gƒ|jƒt| ƒdkr |j|g|jƒƒ|j|ƒn |j|g|gƒ|jƒtjd j|jƒƒƒtjd j|jƒƒƒtjd j|jƒƒƒtjdj|||ƒƒtS(Nu1compact_downward_node_pair: node_A: {} node_B: {}u6-not parallel paths. excluding compaction of {} and {}iiu+-no matching prefix match between {} and {}u#Prefixes: seqA:{} SeqB:{} Shared:{}unode_A before mods: {}unode_B before mods: {}uDpart:u,unode_A after mods: {}unode_B after mods: {}unode_C after mods: {}u4 *** partially compacted nodes: {} and {} + {} ***(R R R Rt is_descendantR RR-R(R.R0R1R2R3R4RR5R6R7RR8R(RR9R:R;R<R=R@R*RRARBRCRDRERFtall_prev_nodes((s…/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Compact_graph_partial.pyRHŃsb%$              (t__name__t __module__RR&RR)RRH(((s…/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Compact_graph_partial.pyRs   2 j (t __future__RRRRtostsystretloggingtTGraphtTNodetNode_alignmenttCompact_graph_wholeRRt getLoggerRKR R(((s…/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Compact_graph_partial.pyts"$