From bdf94c777ba64b35c5087f3d0647be9eee6a68bf Mon Sep 17 00:00:00 2001
From: Samuel Lampa <samuel.lampa@scilifelab.se>
Date: Tue, 13 Aug 2024 18:45:16 +0200
Subject: [PATCH] Keep only 100% identity matches

---
 microSALT/utils/scraper.py | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/microSALT/utils/scraper.py b/microSALT/utils/scraper.py
index 00782a8..fade756 100644
--- a/microSALT/utils/scraper.py
+++ b/microSALT/utils/scraper.py
@@ -409,12 +409,18 @@ def scrape_blast(self, type="", file_list=[]):
                     pass
             ind += 1
 
+        hypo_filtered = []
+
+        for h in hypo:
+            if float(h["identity"]) == 100.0 and float(h["evalue"]) == 0.0:
+                hypo_filtered.append(h)
+
         self.logger.info(
             "{} {} hits were added after removing overlaps and duplicate hits".format(
-                len(hypo), type
+                len(hypo_filtered), type
             )
         )
-        for hit in hypo:
+        for hit in hypo_filtered:
             self.logger.debug(
                 "Kept {}:{} with span {} and id {}".format(
                     hit.get("loci"),
@@ -438,7 +444,7 @@ def scrape_blast(self, type="", file_list=[]):
                         self.name, str(e)
                     )
                 )
-        return hypo
+        return hypo_filtered
 
     def load_resistances(self):
         """Legacy function, loads common resistance names for genes from notes file"""