a ŽÞdéã@s\ddlZddlZe dd¡ZdZdZedeZdd„Zd d „Z d d „Z d d„Z dd„Z dS)éNZTGCAMRWSYKVHDBtgcamrwsykvhdbZACGTKYWSRMBDHVacgtkywsrmbdhv)ÚAÚCÚGÚT)zG>AzC>TzA>GzT>CzA>CzA>TzC>GzC>AzT>GzT>AzG>CzG>TzA>-zT>-zC>-zG>-z->Az->Tz->Cz->GÚS)ZTotalc Csp|jr dnd} t|ƒdkr,| d||f¡| d||d|||j| |f¡t|ƒdkrl| d||f¡dS)Nú-ú+rz>%s %s z>%s:%d-%d %s >%s_%s %s é)Ú is_reverseÚlenÚwriteZqname) ÚreadÚrefÚseqZrefseqÚstartÚendÚbeforeZafterZfoutÚstd©rú,lib/python3.9/site-packages/mapdamage/seq.pyÚ write_fastas  " rcCs| t¡ddd…S)z$ return reverse complemented string Néÿÿÿÿ)Ú translateÚTABLE)rrrrÚrevcompsrcCs@|jr dnd}t|ƒt|ƒ}|js<|||d|||<|S)zf record global length distribution don't record paired reads as they are normally not used for aDNA rrr )r ÚmaxÚminZ is_paired)r Z coordinateZtabrÚlengthrrrÚ record_lgs rc Csdd„}i}t|dƒ¦}|D]}| d¡}t|ƒdkr\|dt|ƒ||ƒWdƒdSzt|dƒ||d <Wqtyª|d |d||ƒYWdƒdS0qWdƒn1sÂ0Y|stj d |f¡tj d ¡tj d ¡dS|S)zG from a fasta index file, fai, return dictionary of references:lengths cSs8tj d|¡tj d|¡tj dt|ƒ¡dS)Nz Error: %s z Filename: %s z Line: %s )ÚsysÚstderrr Úrepr)ÚmsgÚfilenameÚlinerrrÚ print_err-sz#read_fasta_index..print_errÚrú ézJLine in fasta index contains wrong number of fields, found %i, expected 5:Nr rz=Column 2 in FASTA index did not contain a number, found '%s':z0Error: Index for %r does contain any sequences. z3 Please ensure that FASTA file is valid, and z, re-index file using 'samtool faidx'. )ÚopenÚsplitr ÚintÚ ValueErrorrr r )r#r%ZfaiZhandler$rrrrÚread_fasta_index+s.   ÿÿ 6  r-cCs8||kr dStj d¡t|ƒt|ƒ@}|ssÿ