Extract function to get fasta chunk name.

griffithlab · Dec 1, 2016 · 47a031d · 47a031d
1 parent 82e771b
commit 47a031d
Showing 1 changed file with 8 additions and 5 deletions.
diff --git a/pvacseq/lib/pipeline.py b/pvacseq/lib/pipeline.py
@@ -156,9 +156,12 @@ def generate_fasta(self):
 
     def split_fasta_file_path(self, split_start, split_end):
         basename    = os.path.join(self.tmp_dir, self.sample_name + "_" + str(self.peptide_sequence_length) + ".fa.split")
-        fasta_chunk = "%d-%d" % (split_start*2-1, split_end*2)
+        fasta_chunk = self.split_fasta_chunk(split_start, split_end)
         return "%s_%s" % (basename, fasta_chunk)
 
+    def split_fasta_chunk(self, split_start, split_end):
+        return "%d-%d" % (split_start*2-1, split_end*2)
+
     @abstractmethod
     def call_iedb_and_parse_outputs(self, chunks):
         pass
@@ -312,7 +315,7 @@ def __init__(self, **kwargs):
     def generate_fasta(self, chunks):
         status_message("Generating Variant Peptide FASTA and Key Files")
         for (split_start, split_end) in chunks:
-            fasta_chunk = "%d-%d" % (split_start*2-1, split_end*2)
+            fasta_chunk = self.split_fasta_chunk(split_start, split_end)
             split_tsv_file_path       = self.split_tsv_file_path(split_start, split_end)
             split_fasta_file_path     = self.split_fasta_file_path(split_start, split_end)
             if os.path.exists(split_fasta_file_path):
@@ -335,7 +338,7 @@ def generate_fasta(self, chunks):
     def call_iedb_and_parse_outputs(self, chunks):
         split_parsed_output_files = []
         for (split_start, split_end) in chunks:
-            fasta_chunk = "%d-%d" % (split_start*2-1, split_end*2)
+            fasta_chunk = self.split_fasta_chunk(split_start, split_end)
             for a in self.alleles:
                 for epl in self.epitope_lengths:
                     split_fasta_file_path = self.split_fasta_file_path(split_start, split_end)
@@ -404,7 +407,7 @@ def __init__(self, **kwargs):
     def generate_fasta(self, chunks):
         status_message("Generating Variant Peptide FASTA and Key Files")
         for (split_start, split_end) in chunks:
-            fasta_chunk = "%d-%d" % (split_start*2-1, split_end*2)
+            fasta_chunk = self.split_fasta_chunk(split_start, split_end)
             split_tsv_file_path       = self.split_tsv_file_path(split_start, split_end)
             split_fasta_file_path     = self.split_fasta_file_path(split_start, split_end)
             if os.path.exists(split_fasta_file_path):
@@ -427,7 +430,7 @@ def generate_fasta(self, chunks):
     def call_iedb_and_parse_outputs(self, chunks):
         split_parsed_output_files = []
         for (split_start, split_end) in chunks:
-            fasta_chunk = "%d-%d" % (split_start*2-1, split_end*2)
+            fasta_chunk = self.split_fasta_chunk(split_start, split_end)
             for a in self.alleles:
                 split_fasta_file_path = self.split_fasta_file_path(split_start, split_end)
                 split_iedb_output_files = []