added check for invalid min-/maxDist; works with fasta36.3.8g

Author: trvinh

.github/workflows/github_build.yml

@@ -41,13 +41,19 @@ jobs:
         pwd
         pip install .
         path=$(fdog.setup -d ./ --getSourcepath); for i in $(less $path/data/dependencies.txt); do sudo apt-get install -y -qq $i; done
+        echo "TEST fdog.setup"
         fdog.setup -d /home/runner/work/fDOG/fDOG/dt --woFAS
+        echo "TEST fdog.checkData"
         fdog.checkData -s /home/runner/work/fDOG/fDOG/dt/searchTaxa_dir -c /home/runner/work/fDOG/fDOG/dt/coreTaxa_dir -a /home/runner/work/fDOG/fDOG/dt/annotation_dir --reblast
+        echo "TEST fdog.showTaxa"
         fdog.showTaxa
+        echo "TEST fdog.run"
         fdog.run --seqFile infile.fa --jobName test --refspec HUMAN@9606@3 --fasOff
         mkdir seeds
         path=$(fdog.setup -d ./ --getSourcepath); a="1 2 3"; for i in ${a[@]}; do cp $path/data/infile.fa seeds/$i.fa; done
+        echo "TEST fdog.run with only 2 search taxa"
         fdogs.run --seqFolder seeds --jobName test_multi --refspec HUMAN@9606@3 --fasOff --searchTaxa PARTE@5888@3,THAPS@35128@3
+        echo "TEST fdog.addTaxon"
         head /home/runner/work/fDOG/fDOG/dt/searchTaxa_dir/HUMAN@9606@3/HUMAN@[email protected] > hm.fa
         fdog.addTaxon -f hm.fa -i 9606 -o ./ -c -a
         ls

fdog/libs/alignment.py

@@ -140,6 +140,10 @@ def calc_aln_score(fa1, fa2, aln_strategy = 'local', debugCore = False):
     Return dictionary {gene_id:aln_score}
     """
     fdog_path = os.path.realpath(__file__).replace('/libs/alignment.py','')
+    if os.path.exists('fasta36_1.fa'):
+        os.remove('fasta36_1.fa')
+    if os.path.exists('fasta36_2.fa'):
+        os.remove('fasta36_2.fa')
     os.symlink(fa1, 'fasta36_1.fa')
     os.symlink(fa2, 'fasta36_2.fa')
     # fasta36_options = '%s %s -s BP62 -m 9 -d 0 -z -1 -E 100' % (fa1, fa2)

setup.py

@@ -26,7 +26,7 @@
 
 setup(
     name="fdog",
-    version="0.1.18",
+    version="0.1.19",
     python_requires='>=3.7.0',
     description="Feature-aware Directed OrtholoG search tool",
     long_description=long_description,