ó ƒå˜[c@`s´ddlmZmZmZmZddlZddlZddlZddlZddl Z ddl Z ddl Z ddl Z ddl Z ejeƒZddd„ƒYZdS(i(tabsolute_importtdivisiontprint_functiontunicode_literalsNtTGraphcB`steZd„Zd„Zd„Zd„Zd„Zd„Zd„Zd„Z d„Z d „Z d „Z d „Z RS( cC`stƒ|_||_dS(N(tdictt node_cachetgene_id(tselfR((sv/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/TGraph.pyt__init__s cC`sítjdj||ƒƒt|ƒdkr:tdƒ‚n||jkrÀ|j|}|j|ƒ|j|kr¹dj|jƒ|ƒdj|j|ƒ}tj |ƒt|ƒ‚qé|Sn)t j ||||ƒ}||j|<|SdS(uÐ Instantiates Node objects, and stores them in a graph. *** use this method for instantiating all Node objects *** use clear_node_cache() to clear the graph u{} {}iu6Error, non-zero length node_seq required for parameteru:ERROR: have conflicting node sequences for {} node_id: {} u {} vs. {}N( tloggertdebugtformattlent RuntimeErrorRtadd_transcriptstseqt get_gene_idtcriticaltTNode(Rt transcript_idt loc_node_idtnode_seqtnode_objterrmsg((sv/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/TGraph.pytget_nodes     cC`st|jjƒƒS(N(tlistRtvalues(R((sv/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/TGraph.pyt get_all_nodesAscC`s|jjƒdS(u" clears the graph N(Rtclear(R((sv/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/TGraph.pytclear_node_cacheDscC`s%x|jƒD]}|jƒq WdS(u@ clear the touch settings for each of the nodes N(Rt clear_touch(Rtnode((sv/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/TGraph.pytclear_touch_settingsJscC`s@x9|D]1}x(|D] }|j|ƒ|j|ƒqWqWdS(N(t add_next_nodet add_prev_node(Rtfrom_nodes_listt to_nodes_listt from_nodetto_node((sv/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/TGraph.pyt add_edgesTs   cC`s@x9|D]1}x(|D] }|j|ƒ|j|ƒqWqWdS(N(tremove_next_nodetremove_prev_node(RR$R%R&R'((sv/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/TGraph.pyt prune_edges[s   cC`sktjdj|ƒƒ|j|jƒ|gƒ|j|g|jƒƒt|_|jj |j ƒƒdS(Nupruning node: {}( R R R R+tget_prev_nodestget_next_nodestTruetdeadRtpopt get_loc_id(RR ((sv/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/TGraph.pyt prune_nodecs  cC`s"||jkr|j|SdSdS(up does not instantiate, only retrieves. If loc_node_id is not in the graph, returns None N(RtNone(Rtnode_id((sv/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/TGraph.pyt retrieve_nodeks cC`s|jS(N(R(R((sv/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/TGraph.pyRwsc C`sGtjdj|ƒƒt|dƒ}|jdƒx÷|jD]ì}|j|}|jƒ}|jƒ}|jƒ}t |ƒ}d} t | dƒ} || krÄ|d| !d||| |!}n|jdj|j ƒ|||j ƒ|ƒƒx3|D]+} |jd j|j ƒ| j ƒƒƒqùWq<W|jd ƒ|j ƒdS( Nudrawing graph: {}uwu digraph G { i2iiu...u{} [label="{}:Len{}:T{}:{}"] u{}->{} u} (R R R topentwriteRtget_seqtget_gene_node_idR-R tinttget_idtget_topological_ordertclose( RtfilenametofhR4R Rt gene_node_idt next_nodest node_seq_lent max_len_showtmax_len_show_halft next_node((sv/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/TGraph.pyt draw_graph{s&       # - cC`s5d}x(|jƒD]}||jƒd7}qW|S(Nuu (RttoString(RttxtR ((sv/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/TGraph.pyt__repr__™s(t__name__t __module__R RRRR!R(R+R2R5RRFRI(((sv/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/TGraph.pyRs  %       ((t __future__RRRRtostsystretloggingtargparset collectionstnumpyttimeRt getLoggerRJR R(((sv/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/TGraph.pyts"$