Mercurial > repos > john-mccallum > pcr_markers
comparison 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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| 5:b321e0517be3 | 6:f201e8c6e004 |
|---|---|
| 157 for primerset in result: | 157 for primerset in result: |
| 158 amp_start=int(primerset['PRIMER_LEFT'].split(',')[0]) | 158 amp_start=int(primerset['PRIMER_LEFT'].split(',')[0]) |
| 159 amp_end=int(primerset['PRIMER_RIGHT'].split(',')[0]) | 159 amp_end=int(primerset['PRIMER_RIGHT'].split(',')[0]) |
| 160 ref_melt_Tm=0 | 160 ref_melt_Tm=0 |
| 161 var_melt_Tm=0 | 161 var_melt_Tm=0 |
| 162 diff_melt=0 | |
| 162 if my_args.run_uMelt: | 163 if my_args.run_uMelt: |
| 163 try: | 164 try: |
| 164 ref_melt_Tm=umelts.getTm(umelts.getmelt(amp_seq.tostring()[amp_start:amp_end+1])) | 165 ref_melt_Tm=umelts.getTm(umelts.getmelt(amp_seq.tostring()[amp_start:amp_end+1])) |
| 165 var_melt_Tm=umelts.getTm(umelts.getmelt(mutamp_seq.tostring()[amp_start:amp_end+1])) | 166 var_melt_Tm=umelts.getTm(umelts.getmelt(mutamp_seq.tostring()[amp_start:amp_end+1])) |
| 167 diff_melt=abs(ref_melt_Tm - var_melt_Tm) | |
| 166 except: | 168 except: |
| 167 ref_melt_Tm=0 ##preferably something more informative? | 169 ref_melt_Tm="NA" ##preferably something more informative? |
| 168 var_melt_Tm=0 ##exception handling to be added | 170 var_melt_Tm="NA" ##exception handling to be added |
| 171 diff_melt="NA" | |
| 169 reference_seq=target_feat.qualifiers['Reference_seq'][0] | 172 reference_seq=target_feat.qualifiers['Reference_seq'][0] |
| 170 if target_feat.qualifiers.has_key('Variant_seq'): | 173 if target_feat.qualifiers.has_key('Variant_seq'): |
| 171 variant_seq=target_feat.qualifiers['Variant_seq'][0] | 174 variant_seq=target_feat.qualifiers['Variant_seq'][0] |
| 172 else: | 175 else: |
| 173 variant_seq="NA" | 176 variant_seq="NA" |
| 174 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] | 177 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] |
| 175 | 178 |
| 176 my_args.gff_file.close() | 179 my_args.gff_file.close() |
| 177 my_args.in_file.close() | 180 my_args.in_file.close() |
| 178 | 181 |