Refactor to collect re-use count

seqreport/SeqCollection.py

@@ -146,15 +146,15 @@ def calculate_values(self):
  next(reader) # ignore header
  for row in reader:
  all_rows += row[1:] # first column is construct name
- self.savings_list = []
+ self.savings_dict = {}
  self.total_savings = 0
  for record in self.sequences:
  count_in_plan = all_rows.count(record.id)
  if count_in_plan > 1: # we count re-use savings only
  self.total_savings += len(record.seq) * (
  count_in_plan - 1
  ) # ignore first synthesis
- self.savings_list += [record.id]
+ self.savings_dict[record.id] = count_in_plan
  # else we don't have any savings from the sequence.
  if count_in_plan < 1: # also find the ones not in the assembly plan
  self.not_in_plan += [record.id]
@@ -165,10 +165,12 @@ def calculate_values(self):
  self.total_cost_savings
  ) # (in)accuracy is fine for our purposes
  # For the PDF report:
- self.savings_list_text = " ; ".join(self.savings_list)
  self.not_in_plan_text = " ; ".join(self.not_in_plan)
+ self.savings_dict_text = " ; ".join(
+ [f"{key} (×{value})" for key, value in self.savings_dict.items()]
+ )
  else:
- self.savings_list_text = ""
+ self.savings_dict_text = ""
  self.not_in_plan_text = ""
 
 

seqreport/report_assets/seq_report.pug

@@ -69,9 +69,9 @@ else
 
 if seqcollection.assembly_plan
 
- if seqcollection.savings_list_text
+ if seqcollection.savings_dict_text
  p.
- Re-used sequences in the provided assembly plan: {{ seqcollection.savings_list_text }}.
+ Sequences used more than once in the provided assembly plan: {{ seqcollection.savings_dict_text }}.
  p.
  Total savings: <b>{{ seqcollection.total_savings }}</b> bp or <b>{{ seqcollection.currency_symbol }}{{ seqcollection.total_cost_savings }}</b>.
  else
@@ -94,10 +94,10 @@ div(style="margin-top:1cm; margin-bottom:1cm;")
 p
  strong Seq Report
 p.
- The report was generated by <a href="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/Edinburgh-Genome-Foundry/Seq_Report/">Seq Report</a>,
- a software published by the Edinburgh Genome Foundry (EGF).
- Seq Report is part of the <a href="https://edinburgh-genome-foundry.github.io/">EGF Codons</a>
- engineering biology software suite for DNA design, manufacturing and validation.
+ The sequence re-use section shows the basepair-<i>savings</i>, and also ignores
+ per-sequence cost. For example, savings for seq1 (×3) with length L is calculated as
+ 2 × L × {{ seqcollection.currency_symbol }}/base.
+
 
 p.
  Parameters:
@@ -106,6 +106,11 @@ p.
  <li>Cost per sequence = <b>{{ seqcollection.currency_symbol }}{{ seqcollection.cost_per_seq }}</b> </li>
  </ul>
 
+p.
+ The report was generated by <a href="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/Edinburgh-Genome-Foundry/Seq_Report/">Seq Report</a>,
+ a software published by the Edinburgh Genome Foundry (EGF).
+ Seq Report is part of the <a href="https://edinburgh-genome-foundry.github.io/">EGF Codons</a>
+ engineering biology software suite for DNA design, manufacturing and validation.
 
 
 style.