remove usage of deprecated biopython IUPAC Alphabet (#26)

* remove usage of deprecated biopython IUPAC Alphabet * bump viral-core 2.1.8 -> 2.1.10 * wrap Seq() with SeqRecord() * strict conda channel priority
broadinstitute · Nov 18, 2020 · 08bd746 · 08bd746
1 parent 8c8b563
commit 08bd746
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Showing 3 changed files with 4 additions and 6 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-FROM quay.io/broadinstitute/viral-core:2.1.8
+FROM quay.io/broadinstitute/viral-core:2.1.10
 
 LABEL maintainer "viral-ngs@broadinstitute.org"
 
@@ -7,7 +7,7 @@ ENV VIRAL_CLASSIFY_PATH=$INSTALL_PATH/viral-classify \
 
 COPY requirements-conda.txt requirements-conda-env2.txt $VIRAL_CLASSIFY_PATH/
 RUN $VIRAL_NGS_PATH/docker/install-conda-dependencies.sh $VIRAL_CLASSIFY_PATH/requirements-conda.txt 
-RUN CONDA_PREFIX="$MINICONDA_PATH/envs/env2"; conda create -q -y -n env2; $VIRAL_NGS_PATH/docker/install-conda-dependencies.sh $VIRAL_CLASSIFY_PATH/requirements-conda-env2.txt
+RUN CONDA_PREFIX="$MINICONDA_PATH/envs/env2"; conda config --set channel_priority strict; conda create -q -y -n env2; $VIRAL_NGS_PATH/docker/install-conda-dependencies.sh $VIRAL_CLASSIFY_PATH/requirements-conda-env2.txt
 
 # Copy all source code into the base repo
 # (this probably changes all the time, so all downstream build

diff --git a/docs/conf.py b/docs/conf.py
@@ -23,8 +23,7 @@
 
 # -- Mock out the heavyweight pip packages, esp those that require C ----
 import mock
-MOCK_MODULES = ['scipy', 'pysam', 'Bio', 'Bio.AlignIO', 'Bio.Alphabet',
-                'Bio.Alphabet.IUPAC', 'Bio.SeqIO', 'Bio.Data.IUPACData',
+MOCK_MODULES = ['scipy', 'pysam', 'Bio', 'Bio.AlignIO', 'Bio.SeqIO', 'Bio.Data.IUPACData',
                 'Bio.Seq', 'Bio.SeqRecord', 'pybedtools', 'pybedtools.BedTool',
                 'arrow', 'zstd', 'bz2']
 for mod_name in MOCK_MODULES:

diff --git a/test/unit/test_kmer_utils.py b/test/unit/test_kmer_utils.py
@@ -13,7 +13,6 @@
 import Bio.SeqIO
 from Bio.Seq import Seq
 from Bio.SeqRecord import SeqRecord
-from Bio.Alphabet import IUPAC
 import pytest
 
 import kmer_utils
@@ -101,7 +100,7 @@ class KmcPy(object):
     def _revcomp(self, kmer):
         """Return the reverse complement of a kmer, given as a string"""
         assert isinstance(kmer, str)
-        return str(Seq(kmer, IUPAC.unambiguous_dna).reverse_complement())
+        return str(SeqRecord(Seq(kmer), annotations={"molecule_type": "DNA"}).seq.reverse_complement())
 
     def _canonicalize(self, kmer):
         """Return the canonical version of a kmer"""