made a new PAMFinder class

GenBankParser.py

@@ -1,3 +1,4 @@
+import re
 from Bio import SeqIO
 import pyranges as pr
 import pandas as pd
@@ -15,13 +16,65 @@ def __init__(self, filename):
  def records(self):
  with open(self.filename, "r") as handle:
  return SeqIO.to_dict(SeqIO.parse(handle, "genbank"))
-
-
+
+
+class PAMFinder:
+ def __init__(self, records, pam, direction):
+ self.records = records
+ self.pam = pam
+ self.pam_length = len(pam)
+ self.pam_pattern = self.pam.replace("N", "[ATCG]")
+
+ self.direction = direction
+
+ def get_pam_seq(self, row):
+ # Fetch the sequence for the range
+ sequence = self.records[row.Chromosome].seq[row.Start : row.End]
+
+ # If the strand is "-", get the reverse complement of the sequence
+ if row.Strand == "-":
+ sequence = sequence.reverse_complement()
+
+ # Get the PAM sequence
+ if self.direction == "upstream":
+
+ if row.Strand == "+":
+ pam_sequence = self.records[row.Chromosome].seq[
+ row.Start - self.pam_length : row.Start
+ ]
+ else:
+ pam_sequence = self.records[row.Chromosome].seq[
+ row.End : row.End + self.pam_length
+ ]
+ elif self.direction == "downstream":
+ if row.Strand == "+":
+ pam_sequence = self.records[row.Chromosome].seq[
+ row.End : row.End + self.pam_length
+ ]
+ else:
+ pam_sequence = self.records[row.Chromosome].seq[
+ row.Start - self.pam_length : row.Start
+ ]
+ else:
+ raise ValueError("direction must be 'upstream' or 'downstream'")
+
+ # If the strand is "-", get the reverse complement of the PAM sequence
+ if row.Strand == "-":
+ pam_sequence = pam_sequence.reverse_complement()
+
+ return str(pam_sequence)
+
+ def pam_matches(self, sequence):
+ # check if the sequence matches the PAM pattern
+ return bool(re.search(self.pam_pattern, sequence))
+
+
 class GenBankParser(Logger):
  def __init__(self, filename):
  super().__init__()
  self.reader = GenBankReader(filename)
  self.records = self.reader.records
+ # self.pam_finder = PAMFinder(self.records)
  self.info(f"Found the following records:")
  self.json(self.organisms)
 
@@ -104,7 +157,7 @@ def make_fasta(self, filename):
  # Write the records to a FASTA file
  with open(filename, "w") as fasta_file:
  SeqIO.write(self.records.values(), fasta_file, "fasta")
- 
+
  def find_gene_name_for_locus(self, locus_tag):
  # Iterate through all records in the GenBank file
  for record_id, record in self.records.items():
@@ -119,39 +172,3 @@ def find_gene_name_for_locus(self, locus_tag):
  return feature.qualifiers.get("gene", [locus_tag])[0]
  # Return None or locus_tag if not found; depends on how you want to handle not found cases
  return None
-
- def get_pam_sequence(self, row, pam_length, direction):
- # Fetch the sequence for the range
- sequence = self.records[row.Chromosome].seq[row.Start : row.End]
-
- # If the strand is "-", get the reverse complement of the sequence
- if row.Strand == "-":
- sequence = sequence.reverse_complement()
-
- # Get the PAM sequence
- if direction == "upstream":
- if row.Strand == "+":
- pam_sequence = self.records[row.Chromosome].seq[
- row.Start - pam_length : row.Start
- ]
- else:
- pam_sequence = self.records[row.Chromosome].seq[
- row.End : row.End + pam_length
- ]
- elif direction == "downstream":
- if row.Strand == "+":
- pam_sequence = self.records[row.Chromosome].seq[
- row.End : row.End + pam_length
- ]
- else:
- pam_sequence = self.records[row.Chromosome].seq[
- row.Start - pam_length : row.Start
- ]
- else:
- raise ValueError("direction must be 'upstream' or 'downstream'")
-
- # If the strand is "-", get the reverse complement of the PAM sequence
- if row.Strand == "-":
- pam_sequence = pam_sequence.reverse_complement()
-
- return str(pam_sequence)