B b@s4dZGdddZGdddZddZddZd S) aCode to parse output from the EMBOSS eprimer3 program. As elsewhere in Biopython there are two input functions, read and parse, for single record output and multi-record output. For primer3, a single record object is created for each target sequence and may contain multiple primers. i.e. If you ran eprimer3 with a single target sequence, use the read function. If you ran eprimer3 with multiple targets, use the parse function to iterate over the retsults. c@seZdZdZddZdS)RecordzRepresent information from a primer3 run finding primers. Members: - primers - list of Primer objects describing primer pairs for this target sequence. - comments - the comment line(s) for the record cCsd|_g|_dS)zInitialize the class.N)commentsprimers)selfr1lib/python3.7/site-packages/Bio/Emboss/Primer3.py__init__%szRecord.__init__N)__name__ __module__ __qualname____doc__rrrrrrs rc@s eZdZdZddZddZdS)PrimersaA primer set designed by Primer3. Members: - size - length of product, note you can use len(primer) as an alternative to primer.size - forward_seq - forward_start - forward_length - forward_tm - forward_gc - reverse_seq - reverse_start - reverse_length - reverse_tm - reverse_gc - internal_seq - internal_start - internal_length - internal_tm - internal_gc cCsdd|_d|_d|_d|_d|_d|_d|_d|_d|_d|_ d|_ d|_ d|_ d|_ d|_d|_dS)zInitialize the class.rgN)size forward_seq forward_startforward_length forward_tm forward_gc reverse_seq reverse_startreverse_length reverse_tm reverse_gc internal_seqinternal_startinternal_length internal_tm internal_gc)rrrrrGs zPrimers.__init__cCs|jS)z1Length of the primer product (i.e. product size).)r)rrrr__len__ZszPrimers.__len__N)r r r r rrrrrrr +sr ccsx|}|rPqWd}d}xz|ds8|drb|dk rF|Vt}|j|7_d}n|dr|dkr|j|7_n|sn|dddkrt}t|dd|_|j |n|ddd krP| }|r|jd kr t}|j |t|d |_ t|d |_ t |d |_t |d|_|d|_n$|dddkr| }|r||jd krt}|j |t|d |_t|d |_t |d |_t |d|_|d|_n|dddkrt| }|r|jd krt}|j |t|d |_t|d |_t |d |_t |d|_y|d|_Wntk rrd|_YnXy t|}Wq$tk rPYq$Xq$W|r|VdS)zAIterate over primer3 output as Bio.Emboss.Primer3.Record objects.Nz # EPRIMER3z # PRIMER3#z9# Start Len Tm GC% SequencezPRODUCT SIZE: zFORWARD PRIMERrzREVERSE PRIMERzINTERNAL OLIGOr)readlinestrip startswithrrr intrrappendsplitrrfloatrrrrrrrrrrrrr IndexErrornext StopIteration)handlelinerecordZprimerZwordsrrrparse_s|        r4cCsbt|}y t|}Wntk r2tddYnXyt|tdWntk r\YnX|S)zParse primer3 output into a Bio.Emboss.Primer3.Record object. This is for when there is one and only one target sequence. If designing primers for multiple sequences, use the parse function. zNo records found in handleNz$More than one record found in handle)r4r/r0 ValueError)r1iteratorr3rrrreads  r7N)r rr r4r7rrrrs4H