From c16c61d53f111719d37cf1fe75b822729025f1ee Mon Sep 17 00:00:00 2001 From: gbouras13 Date: Wed, 20 Nov 2024 19:14:06 +1030 Subject: [PATCH] fix mmseqs colnames format --- .github/workflows/ci.yaml | 2 +- README.md | 2 +- src/dnaapler/utils/cds_methods.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 700778d..500ef38 100644 --- a/.github/workflows/ci.yaml +++ b/.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 diff --git a/README.md b/README.md index 9fe1fb5..589b319 100644 --- a/README.md +++ b/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 diff --git a/src/dnaapler/utils/cds_methods.py b/src/dnaapler/utils/cds_methods.py index c0ed374..21b55cb 100644 --- a/src/dnaapler/utils/cds_methods.py +++ b/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)