further changes to adapt to new fDOG version

fdog/data/conda_requirements.yml

@@ -4,3 +4,5 @@ fasta3=36.3.8i
 clustalw
 mafft
 muscle=5.1
+augustus
+metaeuk

fdog/fDOGassembly.py

@@ -361,7 +361,9 @@ def checkCoOrthologs(candidate_name, best_hit, ref, fdog_ref_species, candidates
     name_file = candidate_name + ".co"
     output_file = tmp_path + name_file + '.fasta'
     aln_file = tmp_path + name_file + '.aln'
-    genome_dir_path = dataPath + '/genome_dir/%s/%s.fa'%(fdog_ref_species, fdog_ref_species)
+    genome_dir_path = dataPath + '/searchTaxa_dir/%s/%s.fa'%(fdog_ref_species, fdog_ref_species)
+    if not os.path.exists(genome_dir_path):
+        genome_dir_path = dataPath + '/genome_dir/%s/%s.fa'%(fdog_ref_species, fdog_ref_species)
     #print(searchTool)
 
     out = open(output_file, "w")
@@ -424,7 +426,9 @@ def backward_search(candidatesOutFile, fasta_path, strict, fdog_ref_species, eva
     #print(fasta_path)
     orthologs = []
     #print(seedDic)
-    blast_dir_path = dataPath + "/blast_dir/"
+    blast_dir_path = dataPath + "/coreTaxa_dir/"
+    if not os.path.exists(blast_dir_path):
+        blast_dir_path = dataPath + "/blast_dir"
     if strict != True:
         seed = [fdog_ref_species]
         try:
@@ -866,7 +870,7 @@ def main():
     #################### handle user input #####################################
 
     start = time.time()
-    version = '0.1.3'
+    version = '0.1.4'
     ################### initialize parser ######################################
     parser = argparse.ArgumentParser(description='You are running fdog.assembly version ' + str(version) + '.')
     parser.add_argument('--version', action='version', version=str(version))

fdog/setupfDog.py

@@ -248,7 +248,7 @@ def main():
     ## FAS
     if not woFAS:
         install_fas(woFAS)
-    ## hmmer, blast+, clustalw, mafft, muscle
+    ## hmmer, blast+, clustalw, mafft, muscle, augustus, metaeuk
     missing_tools = check_dependencies(fdogPath)
     if len(missing_tools) > 0:
         if check_conda_env() == True:

setup.py

@@ -58,7 +58,7 @@
                             "fdog.mergeOutput = fdog.mergeOutput:main",
                             "fdog.uninstall = fdog.removefDog:main",
                             "fdog.assembly = fdog.fDOGassembly:main",
-                            "fdog.mergeAssembly = fdog.mergeAssemblyOutput:main"],
+                            "fdog.addCoreGroup = fdog.makeCoreGroupFromFasta:main"],
     },
     license="GPL-3.0",
     classifiers=[