Merge pull request #233 from sigven/vep112

Bump VEP to 112
sigven · Jun 10, 2024 · 28262d1 · 28262d1
2 parents a5510e9 + afba305
commit 28262d1
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Showing 6 changed files with 2 additions and 25 deletions.
diff --git a/conda/env/yml/pcgr.yml b/conda/env/yml/pcgr.yml
@@ -10,7 +10,7 @@ dependencies:
   - bedtools
   - bcftools
   - cyvcf2
-  - ensembl-vep ==111.0
+  - ensembl-vep ==112.0
   - htslib
   - pandoc
   - bioconda::perl-bio-bigfile

diff --git a/conda/recipe/pcgr/build.sh b/conda/recipe/pcgr/build.sh
@@ -1,17 +1,4 @@
 #!/usr/bin/env bash
 set -x
 
-# Conda env vars: https://docs.conda.io/projects/conda-build/en/latest/user-guide/environment-variables.html
-
-#---- Loftee ----# 
-# This is used in CPSR for now.
-# To make sure same LoF version is used in dockerized and non-dockerized installation.
-# ensembl-vep conda package installs most recent version of LoF automatically, however
-# it doesn't work with the most recent perl 5.26 (see https://github.com/sigven/cpsr/issues/2).
-# Also Loftee for hg38 needs Perl-Bio-BigFile (doesn't come with ensemble-vep, but will come
-# with https://github.com/bioconda/bioconda-recipes/pull/18808 once merged).
-mkdir ${PREFIX}/share/loftee
-tar -xzf ${SRC_DIR}/src/loftee_1.0.3.tgz -C ${PREFIX}/share/loftee
-
-#---- PCGR Python Package Installation ----#
 $PYTHON -m pip install . --no-deps -v
diff --git a/pcgr/cpsr.py b/pcgr/cpsr.py
@@ -197,7 +197,7 @@ def run_cpsr(conf_options, input_data, output_data):
             outfile.write(yaml.dump(yaml_data))
         outfile.close()
 
-        ## CPSR|VEP - run Variant Effect Predictor on query VCF with LoF and NearestExonJB plugins
+        ## CPSR|VEP - run Variant Effect Predictor on query VCF with NearestExonJB plugins
         vep_command = get_vep_command(file_paths = input_data, 
                                       conf_options = yaml_data, 
                                       input_vcf = input_vcf_validated, 

diff --git a/pcgr/utils.py b/pcgr/utils.py
@@ -88,10 +88,6 @@ def pcgrr_conda_env_export(pcgrr_env):
     cmd = f"export CONDA_PREFIX={pcgrr_conda_env} && export PATH={pcgrr_conda_env}/bin:\"$PATH\""
     return cmd
 
-def get_loftee_dir():
-    pcgr_conda_env = conda_prefix_basename()
-    return script_path(pcgr_conda_env, "share/loftee")
-
 def get_pcgr_bin():
     """Return abs path to e.g. conda/env/pcgr/bin
     """

diff --git a/pcgr/vep.py b/pcgr/vep.py
@@ -57,12 +57,6 @@ def get_vep_command(file_paths, conf_options, input_vcf, output_vcf, debug = Fal
         vep_options += ' --gencode_basic'
         gencode_set_in_use = "GENCODE - basic transcript set (--gencode_basic)"
 
-    ## LOFTEE plugin - variant loss-of-function annotation        
-    #loftee_dir = utils.get_loftee_dir()
-    #assert os.path.isdir(loftee_dir), f'LoF VEP plugin is not found in {loftee_dir}. Please make sure you installed pcgr conda package and have corresponding conda environment active.'
-    #vep_options += f" --plugin LoF,loftee_path:{loftee_dir},human_ancestor_fa:{ancestor_assembly},use_gerp_end_trunc:0 --dir_plugins {loftee_dir}"
-
-
     # Compose full VEP command
     vep_main_command = f'{utils.get_perl_exports()} && vep --input_file {input_vcf} --output_file {output_vcf} {vep_options}'
     vep_bgzip_command = f'bgzip -f -c {output_vcf} > {output_vcf_gz}'

diff --git a/src/loftee_1.0.3.tgz b/src/loftee_1.0.3.tgz