Mercurial > repos > john-mccallum > pcr_markers
diff design_primers.py @ 6:f201e8c6e004 draft default tip
Uploaded
| author | ben-warren |
|---|---|
| date | Mon, 07 Jul 2014 19:28:17 -0400 |
| parents | b321e0517be3 |
| children |
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--- a/design_primers.py Thu May 22 20:30:19 2014 -0400 +++ b/design_primers.py Mon Jul 07 19:28:17 2014 -0400 @@ -159,19 +159,22 @@ amp_end=int(primerset['PRIMER_RIGHT'].split(',')[0]) ref_melt_Tm=0 var_melt_Tm=0 + diff_melt=0 if my_args.run_uMelt: try: ref_melt_Tm=umelts.getTm(umelts.getmelt(amp_seq.tostring()[amp_start:amp_end+1])) var_melt_Tm=umelts.getTm(umelts.getmelt(mutamp_seq.tostring()[amp_start:amp_end+1])) + diff_melt=abs(ref_melt_Tm - var_melt_Tm) except: - ref_melt_Tm=0 ##preferably something more informative? - var_melt_Tm=0 ##exception handling to be added + ref_melt_Tm="NA" ##preferably something more informative? + var_melt_Tm="NA" ##exception handling to be added + diff_melt="NA" reference_seq=target_feat.qualifiers['Reference_seq'][0] if target_feat.qualifiers.has_key('Variant_seq'): variant_seq=target_feat.qualifiers['Variant_seq'][0] else: variant_seq="NA" - print mytarget.id, featLocation + 1 ,reference_seq, variant_seq,amp_end-amp_start,primerset['PRIMER_LEFT_SEQUENCE'],primerset['PRIMER_RIGHT_SEQUENCE'], ref_melt_Tm,var_melt_Tm,abs(ref_melt_Tm-var_melt_Tm)#, amp_seq.tostring()[amp_start:amp_end+1], mutamp_seq.tostring()[amp_start:amp_end+1] + print mytarget.id, featLocation + 1 ,reference_seq, variant_seq,amp_end-amp_start,primerset['PRIMER_LEFT_SEQUENCE'],primerset['PRIMER_RIGHT_SEQUENCE'], ref_melt_Tm,var_melt_Tm,diff_melt#, amp_seq.tostring()[amp_start:amp_end+1], mutamp_seq.tostring()[amp_start:amp_end+1] my_args.gff_file.close() my_args.in_file.close()