removed bio.applications

Author: trvinh

fdog/libs/blast.py

@@ -17,7 +17,6 @@
 
 import os
 import sys
-from Bio.Blast.Applications import NcbiblastpCommandline
 import xml.etree.ElementTree as ET
 import subprocess
 
@@ -29,21 +28,21 @@ def do_blastsearch(
     """ Perform blastp search for a query fasta file
     Return an XML string contains blast result
     """
-    filter = 'no'
-    if lowComplexityFilter == True:
-        filter = 'yes'
+    filter_value = "yes" if lowComplexityFilter else "no"
     try:
-        blastp_cline = NcbiblastpCommandline(
-            query = query, db = blast_db, evalue = evalBlast, seg = filter,
-            max_target_seqs = 10, outfmt = 5)
-        stdout, stderr = blastp_cline()
-        return(stdout)
-    except:
-        sys.exit(
-            'ERROR: Error running blastp search for %s against %s\n%s'
-            % (query, blast_db, NcbiblastpCommandline(
-                query = query, db = blast_db, evalue = evalBlast, seg = filter,
-                max_target_seqs = 10, outfmt = 5)))
+        cmd = [
+            "blastp",
+            "-query", query,
+            "-db", blast_db,
+            "-evalue", str(evalBlast),
+            "-seg", filter_value,
+            "-max_target_seqs", "10",
+            "-outfmt", "5"
+        ]
+        result = subprocess.run(cmd, capture_output=True, text=True, check=True)
+        return result.stdout
+    except subprocess.CalledProcessError as e:
+        sys.exit(f"ERROR: Error running BLASTP search for {query} against {blast_db}\n{e.stderr}")
 
 
 def parse_blast_xml(blast_output):

fdog/libs/preparation.py

@@ -17,9 +17,9 @@
 
 import sys
 import os
+import subprocess
 from pathlib import Path
 from Bio import SeqIO
-from Bio.Blast.Applications import NcbiblastpCommandline
 from ete3 import NCBITaxa
 
 import fdog.libs.zzz as general_fn
@@ -107,17 +107,15 @@ def check_input(args):
 
 def check_blast_version(corepath, refspec):
     """ Check if blast DBs in corepath is compatible with blastp version """
-    fdog_path = os.path.realpath(__file__).replace('/libs/preparation.py','')
-    query = fdog_path + '/data/infile.fa'
-    blast_db = '%s/%s/%s' % (corepath, refspec, refspec)
+    fdog_path = os.path.realpath(__file__).replace('/libs/preparation.py', '')
+    query = os.path.join(fdog_path, 'data', 'infile.fa')
+    blast_db = os.path.join(corepath, refspec, refspec)
     try:
-        blastp_cline = NcbiblastpCommandline(
-            query = query, db = blast_db)
-        stdout, stderr = blastp_cline()
-    except:
-        sys.exit(
-            'ERROR: Error running blast (probably conflict with BLAST DBs versions)\n%s'
-            % (NcbiblastpCommandline(query = query, db = blast_db)))
+        cmd = ["blastp", "-query", query, "-db", blast_db]
+        result = subprocess.run(cmd, capture_output=True, text=True, check=True)
+    except subprocess.CalledProcessError as e:
+        sys.exit(f"ERROR: Error running BLAST (probably conflict with BLAST DB versions)\n{e.stderr}")
+
 
 def check_ranks_core_taxa(corepath, refspec, minDist, maxDist):
     """ Check if refspec (or all core taxa) have a valid minDist and maxDist tax ID