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comparison dapars.py @ 4:73b932244237 draft

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planemo upload for repository https://github.com/mvdbeek/dapars commit c2344ee1b8c6371007b7484b02d17fb056eb2427-dirty
author mvdbeek
date Wed, 28 Oct 2015 06:22:18 -0400
parents aca85eb3eb5b
children a5d8b08af089
comparison
equal deleted inserted replaced
3:aca85eb3eb5b 4:73b932244237
183 w.writerow(header) # field header 183 w.writerow(header) # field header
184 w.writerows( self.result_d.values()) 184 w.writerows( self.result_d.values())
185 185
186 def write_bed(self): 186 def write_bed(self):
187 w = csv.writer(self.bed_output, delimiter='\t') 187 w = csv.writer(self.bed_output, delimiter='\t')
188 bed = [(result.chr, result.breakpoint, result.breakpoint+1, result.gene+"_"+result.breakpoint_type, 0, result.strand) for result in self.result_d.itervalues()] 188 bed = [(result.chr, result.breakpoint, int(result.breakpoint)+1, result.gene+"_"+result.breakpoint_type, 0, result.strand) for result in self.result_d.itervalues()]
189 w.writerows(bed) 189 w.writerows(bed)
190 190
191 191
192 def calculate_all_utr(utr_coverage, utr, utr_d, result_tuple_fields, coverage_weights, num_samples, num_control, 192 def calculate_all_utr(utr_coverage, utr, utr_d, result_tuple_fields, coverage_weights, num_samples, num_control,
193 num_treatment, search_start, coverage_threshold): 193 num_treatment, search_start, coverage_threshold):
206 breakpoint_to_result(res_control, utr, utr_d, control_breakpoint, "control_breakpoint", control_abundance, is_reverse, num_samples, 206 breakpoint_to_result(res_control, utr, utr_d, control_breakpoint, "control_breakpoint", control_abundance, is_reverse, num_samples,
207 num_control, num_treatment) 207 num_control, num_treatment)
208 if treatment_breakpoint: 208 if treatment_breakpoint:
209 breakpoint_to_result(res_treatment, utr, utr_d, treatment_breakpoint, "treatment_breakpoint", treatment_abundance, is_reverse, 209 breakpoint_to_result(res_treatment, utr, utr_d, treatment_breakpoint, "treatment_breakpoint", treatment_abundance, is_reverse,
210 num_samples, num_control, num_treatment) 210 num_samples, num_control, num_treatment)
211 if res_control == dict(zip(result_tuple_fields, result_tuple_fields)):
212 res_control = False
213 if res_treatment == dict(zip(result_tuple_fields, result_tuple_fields)):
214 res_treatment == False
211 return res_control, res_treatment 215 return res_control, res_treatment
212 216
213 217
214 def breakpoint_to_result(res, utr, utr_d, breakpoint, breakpoint_type, 218 def breakpoint_to_result(res, utr, utr_d, breakpoint, breakpoint_type,
215 abundances, is_reverse, num_samples, num_control, num_treatment): 219 abundances, is_reverse, num_samples, num_control, num_treatment):