From bf724ffac688e051a1d8fccb8d7baf375e04bd1e Mon Sep 17 00:00:00 2001
From: Remi PLANEL <rplanel@pasteur.fr>
Date: Thu, 7 Mar 2024 16:30:30 +0100
Subject: [PATCH] fix bug display proteins when mutiple nt contigs as input
---
backend/analysis/models.py | 34 ++++++++++++++++++++++++++++------
1 file changed, 28 insertions(+), 6 deletions(-)
diff --git a/backend/analysis/models.py b/backend/analysis/models.py
index 3d42eb6..b72fc81 100644
--- a/backend/analysis/models.py
+++ b/backend/analysis/models.py
@@ -261,11 +261,10 @@ class Analysis(Invocation):
queryset = Protein.objects.filter(analysis=self)
if self.status == DONE and queryset.count() == 0:
file_path = self.load_dataset("proteins", "proteins")
- proteins = self.read_fasta_file(file_path)
+ proteins = self.read_fasta_file(file_path, isFromNt=True)
if len(proteins) <= 1:
file_path = self.load_dataset("sequences", "proteins")
proteins = self.read_fasta_file(file_path)
- # print(proteins)
json_prots = [ProteinEntry(**prot).dict() for prot in proteins]
prots = Protein(analysis=self, proteins=json_prots)
@@ -283,24 +282,47 @@ class Analysis(Invocation):
self.stderr = job.wrapped["tool_stderr"]
self.save()
- def read_fasta_file(self, file_path):
+ def read_fasta_file(self, file_path, isFromNt=False):
+
+ # if is from Nt, need to sum prot length.
+ # In order to get proteins that belongs to same contig
+ # just remove (_\d+) to the id
+
sequences = []
if file_path is not None:
with open(file_path) as handle:
-
+ current_contig = None
+ offset = 0
+ last_prot_end = 0
for record in SeqIO.parse(handle, "fasta"):
+
prot = {"id": record.id, "length": len(record), "strand": None}
+
+ if isFromNt:
+ contig = "-".join(prot["id"].split("_")[0:-1])
+ if current_contig is None or contig != current_contig:
+ current_contig = contig
+ if current_contig is not None:
+ offset = offset + last_prot_end
+ print(offset)
+
description_list = record.description.split(" # ")
if len(description_list) == 5:
start = description_list[1]
end = description_list[2]
strand = description_list[3]
+
if strand == "1" or strand == "-1":
prot["strand"] = int(strand)
- prot["start"] = int(start)
- prot["end"] = int(end)
else:
strand = None
+ if isFromNt:
+ prot["start"] = offset + int(start)
+ prot["end"] = offset + int(end)
+ last_prot_end = prot["end"]
+ else:
+ prot["start"] = int(start)
+ prot["end"] = int(end)
sequences.append(prot)
return sequences
--
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