fastANI version capture

ArthurVM · Apr 12, 2023 · c7be492 · c7be492
1 parent 126a360
commit c7be492
Show file tree

Hide file tree

Showing 5 changed files with 11 additions and 9 deletions.
diff --git a/src/Afanc/get_dataset/download_assemblies.py → src/Afanc/get_dataset/downloadAssemblies.py b/src/Afanc/get_dataset/download_assemblies.py → src/Afanc/get_dataset/downloadAssemblies.py
diff --git a/src/Afanc/screen/getGenomes.py b/src/Afanc/screen/getGenomes.py
@@ -162,15 +162,12 @@ def getLocalGenomes(out_json, args):
                 taxID = str(subdict["taxon_id"])
                 assemblyID = subdict["name"]
 
-                print(taxID, assemblyID)
-
             else:
                 taxID = str(subdict["taxon_id"])
                 assemblyID = subdict["name"]
 
             species_ID = assemblyID.replace(" ", "_")
 
-            print(assembly_dict)
             ## copy assembly to the bt2 working directory for bt2 db construction
             if taxID in assembly_dict:
                 assembly_path = assembly_dict[taxID][0]

diff --git a/src/Afanc/screen/runFuncs.py b/src/Afanc/screen/runFuncs.py
@@ -203,7 +203,7 @@ def makeFinalReport(args, variant_profile, reports):
     import json
     from os import listdir
 
-    from Afanc.utilities.get_versions import get_versions_screen
+    from Afanc.utilities.getVersions import get_versions_screen
 
     subprocessID = "REPORT"
     vprint(

diff --git a/src/Afanc/utilities/get_versions.py → src/Afanc/utilities/getVersions.py b/src/Afanc/utilities/get_versions.py → src/Afanc/utilities/getVersions.py
@@ -53,4 +53,7 @@ def get_versions_screen():
     bt2_stdout, bt2_stderr = command(f"bowtie2 --version", "GET-VERSIONS").run_comm_quiet(1)
     version_dict["Bowtie2"] = bt2_stdout.decode().split("\n")[0].split("version ")[1]
 
+    fastANI_stdout, fastANI_stderr = command(f"fastANI -v", "GET-VERSIONS").run_comm_quiet(1)
+    version_dict["fastANI"] = fastANI_stderr.decode().split("\n")[0].split("version ")[1]
+
     return version_dict
diff --git a/test/afanc_test.py b/test/afanc_test.py
@@ -58,7 +58,7 @@ def run_test(args):
             sys.exit(1)
 
         runline = f"afanc screen -o {prefix} -v {args.variants} {args.db} {fq1} {fq2} -c > {prefix}.log"
-        # print(runline)
+        print(runline)
 
         if not os.path.exists(prefix):
             subprocess.call(runline, shell=True)
@@ -142,22 +142,24 @@ def get_cluster_hits(hits, truth_val):
     names_box = [name for (name, perc) in cluster_box]
 
     if len(cluster_box) == 1:
+        tophit = cluster_box[0][0].split(" (")[0]
         ## return a PASS if there is only 1 hit and it is the truth value
-        if cluster_box[0][0] == truth_val:
+        if tophit == truth_val:
             return "PASS", cluster_box[0][0]
         ## return a T3 INNACURACY if there is only 1 hit and the species matches the species of the truth value
-        elif " ".join(cluster_box[0][0].split(" ")[:2]) == " ".join(truth_val.split(" ")[:2]):
+        elif " ".join(tophit.split(" ")[:2]) == " ".join(truth_val.split(" ")[:2]):
             return "TYPE-3 INNACURACY", cluster_box[0][0]
         ## return a FAIL if there is only 1 hit and it does not match the truth value or its broader species
         else:
             return "FAIL", cluster_box[0][0]
 
     elif len(cluster_box) > 1:
+        tophit = cluster_box[0][0].split(" (")[0]
         ## return a T1 INNACURACY if there are multiple hits but the top one matches the truth value
-        if cluster_box[0][0] == truth_val:
+        if tophit == truth_val:
             return "TYPE-1 INNACURACY", ",".join(names_box)
         ## return a T4 INNACURACY if there are multiple hits but the species of the top one matches the species of truth value
-        elif " ".join(cluster_box[0][0].split(" ")[:2]) == " ".join(truth_val.split(" ")[:2]):
+        elif " ".join(tophit.split(" ")[:2]) == " ".join(truth_val.split(" ")[:2]):
             return "TYPE-4 INNACURACY", ",".join(names_box)
         ## return a T2 INNACURACY if there are multiple hits and one of the non-top hits matches the truth value
         elif truth_val in names_box: