Xf ^dZGddZGddZGddZdZdS) z;Code to interact with the primersearch program from EMBOSS.c$eZdZdZdZdZdZdS) InputRecordzRepresent the input file into the primersearch program. This makes it easy to add primer information and write it out to the simple primer file format. cg|_dSInitialize the class.N primer_infoselfs 7lib/python3.11/site-packages/Bio/Emboss/PrimerSearch.py__init__zInputRecord.__init__scBd}|jD]\}}}||d|d|dz }|S)z4Summarize the primersearch input record as a string.  r)r outputnameprimer1primer2s r __str__zInputRecord.__str__sJ&*&6 6 6 "D'7 5555'555 5FF r c@|j|||fdS)z%Add primer information to the record.N)rappend)r primer_namefirst_primer_seqsecond_primer_seqs r add_primer_setzInputRecord.add_primer_sets( .>@Q RSSSSSr N)__name__ __module__ __qualname____doc__r rrr r rr sP TTTTTr rceZdZdZdZdS) OutputRecordzRepresent the information from a primersearch job. amplifiers is a dictionary where the keys are the primer names and the values are a list of PrimerSearchAmplifier objects. ci|_dSr) amplifiersr s r r zOutputRecord.__init__)s r Nrrrr r r!r r r#r#"s- r r#ceZdZdZdZdS) Amplifierz/Represent a single amplification from a primer.c"d|_d|_dS)rrN)hit_infolengthr s r r zAmplifier.__init__1s  r Nr&r!r r r(r(.s)99r r(ct}|D]}|s|dr%|d}g|j|<R|dr/t }|j|||dr|dd|_|dr0|d}t||_  |xj|z c_|jD]0}|j|D] }|j |_!1|S)z=Get output from primersearch into a PrimerSearchOutputRecord.z Primer nameAmplimerz Sequence: rz Amplimer length: ) r#strip startswithsplitr%r(rreplacer+intr,rstrip)handlerecordliner amplifierr,s r readr;7sj ^^F''zz|| '  __] + + '::<<#D&(F d # # __Z ( ( '! I  d # * *9 5 5 5 5 __^ , , '!%nb!A!AI   __2 3 3 'ZZ\\"%F"6{{I     $ &   !==*40 = =I!*!3!:!:!r<sBATTTTTTTT.        r