ó ƒå˜[c@`s¨ddlmZmZmZmZddlZddlZddlZddlZddl Z ddl Z ddl Z ddl Z ej eƒZddd„ƒYZdS(i(tabsolute_importtdivisiontprint_functiontunicode_literalsNtTrinity_fasta_parsercB`s)eZdZd„Zd„Zd„ZRS(u¡ Parses a Trinity.fasta file and stores the transcript name, sequence, and node path info. Instance member: trinity_gene_to_isoform_seqs : (defaultdict(list)) stores key,val of transcript_name,path_struct where path_struct has structure: { 'transcript_name' : accession, 'path' : path_str, 'seq' : sequence } cC`sÇtjtƒ|_t|ƒ£}d}d}xn|D]f}|jƒ}|ddkr|dkr|dkr|j||ƒn|}d}q4||7}q4W|dkr½|j||ƒnWdQXdS(Nuiu>(t collectionst defaultdicttlistttrinity_gene_to_isoform_seqstopentrstriptadd_trinity_seq_entry(tselfttrinity_fasta_filenametfhtheadertsequencetline((s„/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Trinity_fasta_parser.pyt__init__"s    c C`sğtjd|ƒ}|s0tdj|ƒƒ‚n|jdƒ}tjd|ƒ}|sotdj|ƒƒ‚n|jdƒ}tjdd|ƒ}||kr·tdj|ƒƒ‚n|j|}i|d 6|d 6|d 6}|j|ƒd S( uU entry looks like so: >TRINITY_DN16_c0_g1_i2 len=266 path=[1:0-48 27:49-49 28:50-50 27:51-51 28:52-52 27:53-53 28:54-54 27:55-55 28:56-56 27:57-57 28:58-58 27:59-59 28:60-60 27:61-61 29:62-265] [-1, 1, 27, 28, 27, 28, 27, 28, 27, 28, 27, 28, 27, 28, 27, 29, -2] CTGTTGTGTGGGGGGTGCGCTTGTTTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC TCAAGTTGATTCCTCCATGTTGCTTTACAGAGACCTGCCAACTACCCAGGAATGTAAAAG CATTCATAGTATTTGTCTAGTAGAGATGCTGTATGAAAAATGCCAAAACCAAAAAGAGAA AGAAGGAAAGAGAGATAGATAGATGACATAGATGACGGATGGATGGGTGGGTGGGTGGAT GGATGGATGGATGGATGGAGGGGGGC u^>(\S+)u-Error, cannot parse accession from header: {}iupath=\[([^\]]+)\]u5Error, cannot parse path info from header of line: {}u_i\d+$uu<Error, couldn't remove isoform ID from Trinity accession: {}utranscript_nameupathuseqN(tretsearcht RuntimeErrortformattgrouptsubRtappend( R RRtmt accessiontpath_strtgene_idt isoform_listt iso_struct((s„/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Trinity_fasta_parser.pyR ;s     cC`s|jS(N(R(R ((s„/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Trinity_fasta_parser.pyt get_trinity_gene_to_isoform_info`s(t__name__t __module__t__doc__RR R (((s„/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Trinity_fasta_parser.pyRs  %((t __future__RRRRtostsysRtloggingtargparseRtnumpyttimet getLoggerR!tloggerR(((s„/oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Trinity_fasta_parser.pyts"$