Add FASTA name

seqreport/SeqCollection.py

@@ -1,4 +1,5 @@
 import csv
+import os
 
 from Bio import SeqIO
 
@@ -35,10 +36,13 @@ class SeqCollection:
 
  **name_length**
  > Check which sequence IDs are longer than this cutoff. Genbank has a character
- limit.
+ limit (`int`).
 
  **assembly_plan**
- > An optional assembly plan for calculating savings by re-using DNA parts.
+ > Optional assembly plan CSV path for calculating savings by re-using DNA parts.
+
+ **fasta_name**
+ > Optional name of the fasta file for easy identification (`str`).
  """
 
  def __init__(
@@ -52,7 +56,8 @@ def __init__(
  min_length=100, # a good cutoff for min DNA synthesis length
  max_length=3000, # a good cutoff for max DNA synthesis length
  name_length=15, # max seq record name length. Genbank character limit.
- assembly_plan=""
+ assembly_plan="",
+ fasta_name="",
  ):
  self.sequences = records
  self.cost_per_base = cost_per_base
@@ -64,6 +69,7 @@ def __init__(
  self.max_length = max_length
  self.name_length = name_length
  self.assembly_plan = assembly_plan
+ self.fasta_name = fasta_name
  self.calculate_values()
 
  def calculate_values(self):
@@ -77,6 +83,7 @@ def calculate_values(self):
  n_bp += len(part.seq)
  self.n_bp = n_bp
  self.cost = self.n_seq * self.cost_per_seq + self.n_bp * self.cost_per_base
+ self.cost = round(self.cost) # (in)accuracy is fine for our purposes
 
  # Lengths section
  self.too_short = []
@@ -146,6 +153,7 @@ def calculate_values(self):
  self.total_savings += len(record.seq) * (count_in_plan - 1) # ignore first synthesis
  self.savings_list += [record.id]
  self.total_cost_savings = self.total_savings * self.cost_per_base # ignore cost / seq
+ self.total_cost_savings = round(self.total_cost_savings) # (in)accuracy is fine for our purposes
  # For the PDF report:
  self.savings_list_text = " ; ".join(self.savings_list)
  else:
@@ -170,7 +178,8 @@ def seqcollection_from_csv(csv_file, records=None, param_dict={}):
  The CSV file parameters override the default class parameters, and this function's
  parameters override the CSV file parameters. Either a FASTA file (in the CSV or in
  `param_dict`) or a list of `SeqRecords` must be specified.
- For the parameter descriptions, see the docstring of `SeqCollection`.
+ For the parameter descriptions, see parameters in the docstring of `SeqCollection`,
+ except records and fasta_name.
  """
  with open(csv_file, "r") as f:
  reader = csv.reader(f, skipinitialspace=True)
@@ -192,5 +201,9 @@ def seqcollection_from_csv(csv_file, records=None, param_dict={}):
  seq_coll = SeqCollection(records=records)
  for key, value in parameters.items():
  setattr(seq_coll, key, value)
+
+ # To ensure that the correct filename is used:
+ setattr(seq_coll, "fasta_name", os.path.basename(parameters["fasta"]))
  seq_coll.calculate_values()
+
  return seq_coll

seqreport/report_assets/seq_report.pug

@@ -10,6 +10,10 @@ hr
 p.
  This document reports basic sequence statistics.
 
+if seqcollection.fasta_name
+ p.
+ FASTA: <b>{{ seqcollection.fasta_name }}</b>
+
 if seqcollection.projectname
  p.
  Projectname: <b>{{ seqcollection.projectname }}</b>
@@ -68,6 +72,7 @@ if seqcollection.assembly_plan
  if seqcollection.savings_list_text
  p.
  Re-used sequences in the provided assembly plan: {{ seqcollection.savings_list_text }}.
+ p.
  Total savings: <b>{{ seqcollection.total_savings }}</b> bp or <b>{{ seqcollection.currency_symbol }} {{ seqcollection.total_cost_savings }}</b>.
  else
  p.

tests/test_SeqCollection.py

@@ -35,5 +35,6 @@ def test_read_fasta():
 
 def test_seqcollection_from_csv():
  csv_path = os.path.join(data_dir, "values.csv")
- seqreport.seqcollection_from_csv(csv_file=csv_path)
+ seq_coll = seqreport.seqcollection_from_csv(csv_file=csv_path)
+ assert seq_coll.fasta_name == "test.fa" # see in CSV file
  # (not tested passing records or param_dict above)