diff --git a/.travis.yml b/.travis.yml index 819d01d..0ad2d76 100644 --- a/.travis.yml +++ b/.travis.yml @@ -11,7 +11,6 @@ git: # https://github.com/travis-ci/travis-ci/issues/4575 depth: 10 cache: - pip: true # cache pip files; directory used for Ensembl downloads of GTF and FASTA files # along with the indexed db of intervals and ID mappings and pickles # of sequence dictionaries; vaxrank directory containing FM index of reference kmers @@ -20,6 +19,7 @@ cache: - $HOME/.cache/pyensembl/GRCh38/ensembl87/ - $HOME/.cache/pyensembl/GRCm38/ensembl87/ - $HOME/.cache/vaxrank + - $HOME/.cache/pip before_install: - | if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then diff --git a/vaxrank/__init__.py b/vaxrank/__init__.py index 894cebc..fe7c60e 100644 --- a/vaxrank/__init__.py +++ b/vaxrank/__init__.py @@ -1 +1 @@ -__version__ = "0.7.8" +__version__ = "0.7.9" diff --git a/vaxrank/report.py b/vaxrank/report.py index 56fefca..84203b4 100644 --- a/vaxrank/report.py +++ b/vaxrank/report.py @@ -116,14 +116,16 @@ def _patient_info(self): ]) return patient_info - def _variant_data(self, top_vaccine_peptide): + def _variant_data(self, variant, top_vaccine_peptide): """ Returns an OrderedDict with info used to populate variant info section. """ variant_data = OrderedDict() mutant_protein_fragment = top_vaccine_peptide.mutant_protein_fragment top_score = _sanitize(top_vaccine_peptide.combined_score) + igv_locus = "chr%s:%d" % (variant.contig, variant.start) variant_data = OrderedDict([ + ('IGV locus', igv_locus), ('Gene name', mutant_protein_fragment.gene_name), ('Top score', top_score), ('RNA reads supporting variant allele', mutant_protein_fragment.n_alt_reads), @@ -300,7 +302,7 @@ def compute_template_data(self): num += 1 top_peptide = vaccine_peptides[0] - variant_data = self._variant_data(top_peptide) + variant_data = self._variant_data(variant, top_peptide) predicted_effect = top_peptide.mutant_protein_fragment.predicted_effect() effect_data = self._effect_data(predicted_effect)