a ŽÞdÑã@sjddlZddlZddlZddlmZdd„Zdd„Zdd„Zd d „Zd d „Z d d„Z dd„Z ddd„Z dS)éN)Ú __version__c Csli}|D]^}i}||<dD]H}i}||<dD]2}i}||<tjjD]} t t|ƒd¡|| <qHq0qq|S)N©Ú5pÚ3p©ú+ú-r)Ú mapdamageÚseqÚHEADERÚdictÚfromkeysÚrange) ÚrefÚlengthÚtabÚcontigÚ tab_contigÚendÚtab_endÚstdÚtab_stdÚmut©rú/lib/python3.9/site-packages/mapdamage/tables.pyÚinitialize_muts    rcCst|tjj||dddS)Né)Úoffset)Ú_print_freq_tabler r r )rÚoptÚoutrrrÚ print_mutsr!c Cs²tt| dƒƒttd|dƒƒtt| dƒƒttd|dƒƒdœ}i}|D]^}i}||<dD]H}i}||<dD]2} i} || <tjjD]} t ||d¡| | <qŽqvqbqN|S)Nrr)rrrr)Úlistrr r ÚLETTERSr r ) rZaroundrÚkeysrrrrrrrZlettersrrrÚinitialize_comps  ÿ    r%cCstjjd}t||||ƒdS)N)ÚTotal)r r r#r)Úcomprr ÚcolumnsrrrÚ print_comp+s r)cCs i}dD]}t t¡||<q|S)Nr)Ú collectionsÚ defaultdictÚint)rrrrrÚ initialize_lg0sr-c CsŠ| dt¡| d|j|jf¡|jdkr>| d|j¡| d¡| d¡|D].}||D] }| d|||||f¡qbqVdS)Nú)# table produced by mapDamage version %s ú0# using mapped file %s and %s as reference file rz5# Quality filtering of bases with a Phred score < %d z# Std: strand of reads zStd Length Occurences z %s %d %d )ÚwriterÚfilenamerÚminqual)rrr rÚirrrÚprint_lg8s    r4c CsÔd}dD]²}tj |d|¡s2td|ƒdSttj ||¡ƒf}|D]2}| ¡ d¡}|ddkrJ|t|d ƒ7}qœqJtd |ƒWd ƒdSWd ƒq1s°0Yq|d krÐtd |ƒdS)z Returns true if the damage frequencies are too low to allow Bayesian estimation of DNA damages, i.e < 1% at first position. g)z5pCtoT_freq.txtz3pGtoA_freq.txtú/z[Error: Required table has not been created ('%s'), bayesian computation cannot be performedTú rÚ1rzUError: Could not find pos = 1 in table '%s', bayesian computation cannot be performedNg{®Gáz„?zeWarning: DNA damage levels are too low, the Bayesian computation should not be performed (%f < 0.01) F) ÚosÚpathÚexistsÚprintÚopenÚjoinÚstripÚsplitÚfloat)ZfolderÚtotalr1ZhandleÚlineZfreqrrrÚ'check_table_and_warn_if_dmg_freq_is_lowDs(ÿ ÿ2 rCc s(| dt¡| d|j|jf¡|jdkr>| d|j¡| d¡| dd |¡¡t| ¡ƒD]º\}}t| ¡ƒD]¤\}}t| ¡ƒD]Ž\} ‰iˆd<tˆ|dƒD]l‰t‡‡fd d „t j j Dƒƒˆdˆ<| d ||| ˆ|f¡|D]} | d ˆ| ˆ¡qö| d ¡q°qq|qhdS)Nr.r/rz2# Bases with a Phred score < %d were filtered out ze# Chr: reference from sam/bam header, End: from which termini of DNA sequences, Std: strand of reads zChr End Std Pos %s r6r&c3s|]}ˆ|ˆVqdS)Nr)Ú.0Zletter©ÚindexZsubtablerrÚ móz$_print_freq_table..z %s %s %s %dz %dÚ ) r0rr1rr2r=ÚsortedÚitemsÚsumr r r#) Útabler(rr rZ referenceZendsrZstrandsZstrandÚbaserrErr`s   $r)r) r8r*r Zmapdamage.versionrrr!r%r)r-r4rCrrrrrÚs