o RŀgO@s<dZddlZddlmZddlmZddlmZddlmZddlmZdd l m Z d Z e d Z e d Ze d Ze dZe dZe dZe dZddZd/ddZd0ddZddZddZddZdd Zd!d"Zd#d$Zd%d&Zd'd(ZGd)d*d*eZGd+d,d,eZ e!d-krdd.l"m#Z#e#dSdS)1z;Bio.SearchIO parser for Exonerate plain text output format.N)chain)_BaseExonerateIndexer)_BaseExonerateParser)_parse_hit_or_query_line) _STRAND_MAP) _RE_VULGAR)ExonerateTextParserExonerateTextIndexerz\s*\d+\s+: (.*) :\s+\d+z@[atgc ]{2}?(?:(?:[<>]+ \w+ Intron \d+ [<>]+)|(?:\.+))[atgc ]{2}?z%(?:(\d+) bp // (\d+) bp)|(?:(\d+) bp)z--<\s+\d+\s+>--z--<\s+(\d+)\s+>--z\{(\w{1,2})\}$z^\{(\w{1,2})\}cCsNd\}}t||D]\}}|dkr||7}||7}q ||7}||7}q ||fS)z=Flips the codon characters from one seq to another (PRIVATE).)r  )zip) codon_seq target_seqabchar1char2r[/var/www/html/myenv/lib/python3.10/site-packages/Bio/SearchIO/ExonerateIO/exonerate_text.py _flip_codons)s  rFc Cshd}g}|s t}nt}||d}t||D]}|||d|7}|t|}|||fq|S)zWReturn a list of start, end coordinates for each given block in the sequence (PRIVATE).rqueryN)_RE_EXON_RE_NERresplitfindlenappend) parsed_seqrow_dicthas_nerstartcoordssplitterseqblockendrrr_get_block_coords8s  r(cCs|dkr&dd|D}tt|dd}tt|ddd|dddStt|dd}tt|ddd|dddS)zReturn list of pairs covering intervening ranges (PRIVATE). 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