ó ƒå˜[c@`s´ddlmZmZmZmZddlZddlZddlZddlZddl Z ddl Z ddl Z ddl Z ddl Z ejeƒZddd„ƒYZdS(i(tabsolute_importtdivisiontprint_functiontunicode_literalsNtTNodecB`sjeZdZeƒZdZdZd„Zd„Zd„Z d„Z d„Z d„Z d„Z d „Zd%d „Zd%d „Zd „Zd „Zd„Zd„Zd„Zd„Zd„Zd„Zd„Zd„Zd„Zd„Zd„Zd„Zd„Z d„Z!d„Z"d„Z#d„Z$d„Z%d „Z&d!„Z'd"„Z(e)d#„ƒZ*d$„Z+RS(&uR generic Trinity graph node object representing a node in the Trinity isoform reconstruction graph Node's are objects within a gene and can be shared among transcript isoforms. instance members include: tgraph : (TGraph obj) graph for the Trinity gene, which will hold the nodes. transcripts: list(str) names of the isoforms that contains this node. loc_node_id : (int) identifier of the node seq : (str) nucleotide sequence for this node in the transcript len : (int) length of the node sequence prev : (set) node objects connected as parental nodes in the graph next : (set) node objects connected as descendant nodes in the graph class members include: merged_nodeset_counter : (int) 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||_dS(N(R(Rt topo_order((su/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/TNode.pytset_topological_order¶scC`s|jS(N(R (R((su/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/TNode.pytget_transcripts¹scC`sZt|ƒtkr%|jj|ƒn1t|ƒtkrJ|jj|ƒn tdƒ‚dS(Nu+Error, parameter must be a string or a set (ttypeRR tupdatetstrR'R(Rttranscript_name_or_set((su/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/TNode.pyR ¼s cC`s t|jƒS(N(RR(R((su/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/TNode.pytget_prev_nodesÄscC`s t|jƒS(N(RR(R((su/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/TNode.pytget_next_nodesÇscC`s|jj|ƒdS(N(RR'(Rt 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into a single new node that has concatenated sequences of the input nodes uMerging nodes: {}uiuM{}iunode being merge: {}( tloggertdebugRQRtmerged_nodeset_counterR5RSR0t intersectionR/( tclst node_listtmerged_node_seqtmerged_loc_node_idR tnode_objR Rt merged_node((su/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/TNode.pyt merge_nodess   cC`s|jƒr|jƒrtSt|jƒƒdksLt|jƒƒdkrPtSt|jƒƒdkr¨t|jƒƒdkr¨t|jƒjƒjƒƒdkr¨tSt|jƒƒdkrt|jƒƒdkrt|jƒjƒjƒƒdkrtStS(uB returns true if node (x) is in this graphical context: X X \ or / C-- A--? ?-- A--B where X dangles. So, X has only one parent or child and not otherwise connected in the graph. ii(R:R;RRtpopR&(R((su/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/TNode.pytis_burr1s0$$N(,t__name__t __module__t__doc__tdictt node_cacheRVR RRRRRR"R#R$R%R(R-R/R0R1R2R4R5R R:R;R=R@RBRDRERFRGRKRLRMRNRORPRSt classmethodR^R`(((su/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/TNode.pyRsN  "                                ((t __future__RRRRtostsystretloggingtargparset collectionstnumpyttimetTGrapht getLoggerRaRTR(((su/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/TNode.pyts"$