fix mmseqs colnames format

.github/workflows/ci.yaml

@@ -34,7 +34,7 @@ jobs:
       - name: Install project
         shell: bash -l {0}
         run: |
-          mamba install python=${{ matrix.python-version }}
+          conda install python=${{ matrix.python-version }}
           python -m pip install --upgrade pip
           pip install -e .
           pip install black

README.md

@@ -189,7 +189,7 @@ Options:
   -t, --threads INTEGER    Number of threads to use with BLAST  [default: 1]
   -p, --prefix TEXT        Prefix for output files  [default: dnaapler]
   -f, --force              Force overwrites the output directory
-  -e, --evalue TEXT        e value for MMseqs  [default: 1e-10]
+  -e, --evalue TEXT        e value for MMseqs2  [default: 1e-10]
   --ignore PATH            Text file listing contigs (one per row) that are to
                            be ignored
   -a, --autocomplete TEXT  Choose an option to autocomplete reorientation if

src/dnaapler/utils/cds_methods.py

@@ -229,7 +229,7 @@ def run_MMseqs2_based_method(
     MMseqs2_output_tmpdir = Path(f"{output}/tmp_MMseqs2_output")
     MMseqs2_output_file = Path(f"{output}/{prefix}_MMseqs2_output.txt")
     # matches the blast ones to make subbing MMseqs2 for BLAST as easy as possible
-    MMseqs2_columns = "query,qlen,target,tlen,alnlen,qstart,qstart,qend,tstart,tend,fident,nident,gapopen,mismatch,evalue,bits,qaln,taln"
+    MMseqs2_columns = "query,qlen,target,tlen,alnlen,qstart,qend,tstart,tend,fident,nident,gapopen,mismatch,evalue,bits,qaln,taln"
 
 
     db = os.path.join(DNAAPLER_DB, db_name)