Merge pull request #14 from sigven/dev

1.5.0 release

README.md

@@ -15,34 +15,29 @@ The germline variant annotator (*gvanno*) is a software package intended for ana
 *gvanno* accepts query files encoded in the VCF format, and can analyze both SNVs and short InDels. The workflow relies heavily upon [Ensembl’s Variant Effect Predictor (VEP)](http://www.ensembl.org/info/docs/tools/vep/index.html), and [vcfanno](https://github.com/brentp/vcfanno). It produces an annotated VCF file and a file of tab-separated values (.tsv), the latter listing all annotations pr. variant record. Note that if your input VCF contains data (genotypes) from multiple samples (i.e. a multisample VCF), the output TSV file will contain one line/record __per sample variant__.
 
 ### News
+* September 24th 2022 - **1.5.0 release**
+  * Data updates: ClinVar, GENCODE GWAS catalog, CancerMine, Open Targets Platform
+  * Software updates: VEP 107
+  * Excluded UniProt KB from annotation tracks
 * December 21st 2021 - **1.4.4 release**
      * Data updates: ClinVar, GWAS catalog, CancerMine, UniProt KB, Open Targets Platform
 	* Software updates: VEP (v105)
 * August 25th 2021 - **1.4.3 release**
 	* Data updates: ClinVar, GWAS catalog, CancerMine, UniProt, Open Targets Platform
-* May 24th 2021 - **1.4.2 release**
-  * Software update (VEP 104)
-  * Data updates: ClinVar, GWAS catalog, CancerMine, Pfam, dbNSFP, UniProt
-  * Two new options added:
-	  * `--vep_regulatory` - annotates variants for overlap with regulatory regions (details below)
-	  * `--docker-uid` - set Docker user id
-  * New variant annotations for enhanced non-coding interpretation:
-	  * _REGULATORY_ANNOTATION_ : A comma-separated list of regulatory annotations from VEP's `--regulatory` option, i.e. __TF_binding_site__, overlap with __enhancer/promoter/open_chromatin__, __CTCF_binding_site__ etc. Included when the `--vep_regulatory` option is turned on in gvanno.
-	  * _NCER_PERCENTILE_: A genome-wide percentile rank score from the ncER algorithm (**n**on-**c**oding **E**ssential **R**egulation), [Wells et al., Nat Comm. (2019)](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6868241/).
-
-### Annotation resources (v1.4.4)
-
-* [VEP](http://www.ensembl.org/info/docs/tools/vep/index.html) - Variant Effect Predictor v105 (GENCODE v39/v19 as the gene reference dataset)
+
+### Annotation resources (v1.5.0)
+
+* [VEP](http://www.ensembl.org/info/docs/tools/vep/index.html) - Variant Effect Predictor v107 (GENCODE v41/v19 as the gene reference dataset)
 * [dBNSFP](https://sites.google.com/site/jpopgen/dbNSFP) - Database of non-synonymous functional predictions (v4.2, March 2021)
 * [gnomAD](http://gnomad.broadinstitute.org/) - Germline variant frequencies exome-wide (release 2.1, October 2018) - from VEP
 * [dbSNP](http://www.ncbi.nlm.nih.gov/SNP/) - Database of short genetic variants (build 154) - from VEP
 * [1000 Genomes Project - phase3](ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/) - Germline variant frequencies genome-wide (May 2013) - from VEP
-* [ClinVar](http://www.ncbi.nlm.nih.gov/clinvar/) - Database of variants related to human health/disease phenotypes (December 2021)
-* [CancerMine](http://bionlp.bcgsc.ca/cancermine/) - literature-mined database of drivers, oncogenes and tumor suppressors in cancer (version 41, December 2021)
-* [Open Targets Platform](https://targetvalidation.org) - Target-disease and target-drug associations (2021_11, Nocember 2021)
-* [UniProt/SwissProt KnowledgeBase](http://www.uniprot.org) - Resource on protein sequence and functional information (2021_04, November 2021)
+* [ClinVar](http://www.ncbi.nlm.nih.gov/clinvar/) - Database of variants related to human health/disease phenotypes (September 2022)
+* [CancerMine](http://bionlp.bcgsc.ca/cancermine/) - literature-mined database of drivers, oncogenes and tumor suppressors in cancer (version 47, July 2022)
+* [Open Targets Platform](https://targetvalidation.org) - Target-disease and target-drug associations (2022_06, June 2022)
 * [Pfam](http://pfam.xfam.org) - Database of protein families and domains (v35.0, November 2021)
-* [NHGRI-EBI GWAS Catalog](https://www.ebi.ac.uk/gwas/home) - Catalog of published genome-wide association studies (December 7th 2021)
+* [Mutation hotspots](cancerhotspots.org) - Database of mutation hotspots in cancer
+* [NHGRI-EBI GWAS Catalog](https://www.ebi.ac.uk/gwas/home) - Catalog of published genome-wide association studies (August 26th 2022)
 
 
 ### Getting started
@@ -76,17 +71,17 @@ An installation of Python (version >=_3.6_) is required to run *gvanno*. Check t
 
 #### STEP 2: Download *gvanno* and data bundle
 
-1. [Download the latest version](https://github.com/sigven/gvanno/releases/tag/v1.4.4) (gvanno run script, v1.4.4)
+1. [Download the latest version](https://github.com/sigven/gvanno/releases/tag/v1.5.0) (gvanno run script, v1.5.0)
 2. Download (preferably using `wget`) and unpack the latest assembly-specific data bundle in the gvanno directory
-   * [grch37 data bundle](http://insilico.hpc.uio.no/pcgr/gvanno/gvanno.databundle.grch37.20211221.tgz) (approx 18Gb)
-   * [grch38 data bundle](http://insilico.hpc.uio.no/pcgr/gvanno/gvanno.databundle.grch38.20211221.tgz) (approx 20Gb)
+   * [grch37 data bundle](http://insilico.hpc.uio.no/pcgr/gvanno/gvanno.databundle.grch37.20220921.tgz) (approx 20Gb)
+   * [grch38 data bundle](http://insilico.hpc.uio.no/pcgr/gvanno/gvanno.databundle.grch38.20220921.tgz) (approx 28Gb)
    * Example commands:
-	* `wget http://insilico.hpc.uio.no/pcgr/gvanno/gvanno.databundle.grch37.20211221.tgz`
+	* `wget http://insilico.hpc.uio.no/pcgr/gvanno/gvanno.databundle.grch37.20220921.tgz`
 	* `gzip -dc gvanno.databundle.grch37.YYYYMMDD.tgz | tar xvf -`
 
-    A _data/_ folder within the _gvanno-1.4.4_ software folder should now have been produced
-3. Pull the [gvanno Docker image (1.4.4)](https://hub.docker.com/r/sigven/gvanno/) from DockerHub (approx 2.2Gb):
-   * `docker pull sigven/gvanno:1.4.4` (gvanno annotation engine)
+    A _data/_ folder within the _gvanno-1.5.0_ software folder should now have been produced
+3. Pull the [gvanno Docker image (1.5.0)](https://hub.docker.com/r/sigven/gvanno/) from DockerHub (approx 2.2Gb):
+   * `docker pull sigven/gvanno:1.5.0` (gvanno annotation engine)
 
 #### STEP 3: Input preprocessing
 
@@ -115,7 +110,7 @@ Run the workflow with **gvanno.py**, which takes the following arguments and opt
 	--query_vcf QUERY_VCF
 				    VCF input file with germline query variants (SNVs/InDels).
 	--gvanno_dir GVANNO_DIR
-				    Directory that contains the gvanno data bundle, e.g. ~/gvanno-1.4.4
+				    Directory that contains the gvanno data bundle, e.g. ~/gvanno-1.5.0
 	--output_dir OUTPUT_DIR
 				    Output directory
 	--genome_assembly {grch37,grch38}
@@ -152,10 +147,10 @@ Run the workflow with **gvanno.py**, which takes the following arguments and opt
 
 The _examples_ folder contains an example VCF file. Analysis of the example VCF can be performed by the following command:
 
-	python ~/gvanno-1.4.4/gvanno.py
-	--query_vcf ~/gvanno-1.4.4/examples/example.grch37.vcf.gz
-	--gvanno_dir ~/gvanno-1.4.4
-	--output_dir ~/gvanno-1.4.4
+	python ~/gvanno-1.5.0/gvanno.py
+	--query_vcf ~/gvanno-1.5.0/examples/example.grch37.vcf.gz
+	--gvanno_dir ~/gvanno-1.5.0
+	--output_dir ~/gvanno-1.5.0
 	--sample_id example
 	--genome_assembly grch37
 	--container docker

data-raw/RELEASE_NOTES

@@ -1,14 +1,13 @@
-##GVANNO_SOFTWARE_VERSION = 1.4.4
-##GVANNO_DB_VERSION = 20211221
+##GVANNO_SOFTWARE_VERSION = 1.5.0
+##GVANNO_DB_VERSION = 20220913
 pfam = v35.0 (November 2021)
 ncER = v1.0 (March 2019)
-uniprot = release 2021_04
-corum = release 3.0 (20180903)
+uniprot = release 2022_03
 onekg = phase 3 (20130502)
-dbsnp = build 154/153
+dbsnp = build 154
 dbnsfp = v4.2 (April 2021)
 gnomad = r2.1 (October 2018)
-gwas = December 2021 (20211207)
-clinvar = December 2021 (20211130)
-opentargets = 2021_11
-gencode = 39/19
+gwas = August 2022 (20220826)
+clinvar = September 2022 (20220831)
+opentargets = 2022_06
+gencode = 41/19

gvanno.py

@@ -11,10 +11,10 @@
 import platform
 from argparse import RawTextHelpFormatter
 
-GVANNO_VERSION = '1.4.4'
-DB_VERSION = 'GVANNO_DB_VERSION = 20211221'
-VEP_VERSION = '105'
-GENCODE_VERSION = 'v39'
+GVANNO_VERSION = '1.5.0'
+DB_VERSION = 'GVANNO_DB_VERSION = 20220921'
+VEP_VERSION = '107'
+GENCODE_VERSION = 'v41'
 VEP_ASSEMBLY = "GRCh38"
 DOCKER_IMAGE_VERSION = 'sigven/gvanno:' + str(GVANNO_VERSION)
 
@@ -294,6 +294,9 @@ def run_gvanno(arg_dict, host_directories):
       container_command_run2 = container_command_run2 + " -W /workdir/output " + 'src/gvanno.sif' + " sh -c \""
       docker_command_run_end = '\"'
 
+   #logger.info(container_command_run1)
+   #logger.info(container_command_run2)
+
    ## GVANNO|start - Log key information about sample, options and assembly
    logger = getlogger("gvanno-start")
    logger.info("--- Germline variant annotation (gvanno) workflow ----")
@@ -306,6 +309,7 @@ def run_gvanno(arg_dict, host_directories):
    logger.info("STEP 0: Validate input data")
    vcf_validate_command = str(container_command_run1) + "gvanno_validate_input.py " + str(data_dir) + " " + str(input_vcf_docker) + " " + \
       str(vcf_validation) + " "  + str(arg_dict['genome_assembly']) + docker_command_run_end
+   #logger.info(vcf_validate_command)
 
    check_subprocess(vcf_validate_command)
    logger.info('Finished')
@@ -378,10 +382,10 @@ def run_gvanno(arg_dict, host_directories):
       ## GVANNO|vcfanno - annotate VCF against a number of variant annotation resources
       print()
       logger = getlogger('gvanno-vcfanno')
-      logger.info("STEP 2: Clinical/functional variant annotations with gvanno-vcfanno (ClinVar, ncER, dbNSFP, GWAS catalog, UniProtKB, cancerhotspots.org)")
+      logger.info("STEP 2: Clinical/functional variant annotations with gvanno-vcfanno (ClinVar, ncER, dbNSFP, GWAS catalog, cancerhotspots.org)")
       logger.info('vcfanno configuration - number of processes (-p): ' + str(arg_dict['vcfanno_n_processes']))
       gvanno_vcfanno_command = str(container_command_run2) + "gvanno_vcfanno.py --num_processes "  + str(arg_dict['vcfanno_n_processes']) + \
-         " --dbnsfp --clinvar --ncer --uniprot --gvanno_xref --gwas --cancer_hotspots " + str(vep_vcf) + ".gz " + str(vep_vcfanno_vcf) + \
+         " --dbnsfp --clinvar --ncer --gvanno_xref --gwas --cancer_hotspots " + str(vep_vcf) + ".gz " + str(vep_vcfanno_vcf) + \
          " " + os.path.join(data_dir, "data", str(arg_dict['genome_assembly'])) + docker_command_run_end
       check_subprocess(gvanno_vcfanno_command)
       logger.info("Finished")
@@ -412,7 +416,7 @@ def run_gvanno(arg_dict, host_directories):
       print()
       ## GVANNO|vcf2tsv - convert VCF to TSV with https://github.com/sigven/vcf2tsv
       logger = getlogger("gvanno-vcf2tsv")
-      logger.info("STEP 4: Converting VCF to TSV with https://github.com/sigven/vcf2tsv")
+      logger.info("STEP 4: Converting VCF to TSV with https://github.com/sigven/vcf2tsvpy")
       gvanno_vcf2tsv_command_pass = str(container_command_run2) + "vcf2tsv.py " + str(output_pass_vcf) + " --compress " + str(output_pass_tsv) + docker_command_run_end
       gvanno_vcf2tsv_command_all = str(container_command_run2) + "vcf2tsv.py " + str(output_vcf) + " --compress --keep_rejected " + str(output_tsv) + docker_command_run_end
       logger.info("Conversion of VCF variant data to records of tab-separated values - PASS variants only")

src/Dockerfile

@@ -22,7 +22,7 @@ RUN apt-get update && apt-get -y install \
 ENV OPT /opt/vep
 ENV OPT_SRC $OPT/src
 ENV HTSLIB_DIR $OPT_SRC/htslib
-ENV BRANCH release/105
+ENV BRANCH release/107
 
 # Working directory
 WORKDIR $OPT_SRC
@@ -166,7 +166,7 @@ ENV PERL5LIB $PERL5LIB_TMP
 WORKDIR /
 ADD loftee_1.0.3.tgz $OPT/src/ensembl-vep/modules
 ADD UTRannotator.tgz $OPT/src/ensembl-vep/modules
-RUN wget -q "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/105/NearestExonJB.pm" -O $OPT/src/ensembl-vep/modules/NearestExonJB.pm
+RUN wget -q "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/107/NearestExonJB.pm" -O $OPT/src/ensembl-vep/modules/NearestExonJB.pm
 
 
 # Final steps
@@ -250,7 +250,9 @@ RUN rm miniconda.sh
 
 # update conda & install vt
 RUN /conda/bin/conda update conda
+#RUN /conda/bin/conda update python
 RUN /conda/bin/conda install -c bioconda vt
+#RUN /conda/bin/conda install -c bioconda vcf2tsvpy
 
 ## Clean Up
 RUN apt-get clean autoclean
@@ -271,7 +273,7 @@ RUN rm -rf $HOME/src/ensembl-vep/t/
 RUN rm -f $HOME/src/v335_base.tar.gz
 RUN rm -f $HOME/src/release-1-6-924.zip
 RUN rm -rf /samtools-1.10.tar.bz2
-RUN rm -f /conda/bin/python
+#RUN rm -f /conda/bin/python
 
 ADD gvanno.tgz /
 ENV PATH=$PATH:/conda/bin:/gvanno

src/buildDocker.sh

@@ -4,5 +4,5 @@ cp /Users/sigven/research/software/vcf2tsv/vcf2tsv.py gvanno/
 tar czvfh gvanno.tgz gvanno/
 echo "Build the Docker Image"
 TAG=`date "+%Y%m%d"`
-docker build --no-cache -t sigven/gvanno:$TAG --rm=true .
+docker build -t sigven/gvanno:$TAG --rm=true .
 

src/gvanno/gvanno_summarise.py

@@ -33,8 +33,8 @@ def extend_vcf_annotations(query_vcf, gvanno_db_directory, lof_prediction = 0, r
    """
 
    ## read VEP and PCGR tags to be appended to VCF file
-   vcf_infotags_meta = annoutils.read_infotag_file(os.path.join(gvanno_db_directory,'gvanno_infotags.tsv'))
-   gvanno_xref_map = annoutils.read_genexref_namemap(os.path.join(gvanno_db_directory,'gvanno_xref', 'gvanno_xref.namemap.tsv'))
+   vcf_infotags_meta = annoutils.read_infotag_file(logger, os.path.join(gvanno_db_directory,'gvanno_infotags.tsv'))
+   gvanno_xref_map = annoutils.read_genexref_namemap(logger, os.path.join(gvanno_db_directory,'gvanno_xref', 'gvanno_xref_namemap.tsv'))
    out_vcf = re.sub(r'\.vcf(\.gz){0,}$','.annotated.vcf',query_vcf)
 
    meta_vep_dbnsfp_info = annoutils.vep_dbnsfp_meta_vcf(query_vcf, vcf_infotags_meta)

src/gvanno/gvanno_validate_input.py

@@ -34,7 +34,7 @@ def check_existing_vcf_info_tags(input_vcf, gvanno_directory, genome_assembly, l
    If any coinciding tags, an error will be returned
    """
 
-   gvanno_infotags_desc = annoutils.read_infotag_file(os.path.join(gvanno_directory,'data',genome_assembly,'gvanno_infotags.tsv'))
+   gvanno_infotags_desc = annoutils.read_infotag_file(logger, os.path.join(gvanno_directory,'data',genome_assembly,'gvanno_infotags.tsv'))
 
    vcf = VCF(input_vcf)
    logger.info('Checking if existing INFO tags of query VCF file coincide with gvanno INFO tags')

src/gvanno/gvanno_vcfanno.py

@@ -20,7 +20,7 @@ def __main__():
    parser.add_argument("--ncer",action = "store_true", help="Annotate VCF with ranking of variant deleteriousness in non-coding regions (ncER)")
    parser.add_argument("--clinvar",action = "store_true", help="Annotate VCF with annotations from ClinVar")
    parser.add_argument("--dbnsfp",action = "store_true", help="Annotate VCF with annotations from database of non-synonymous functional predictions")
-   parser.add_argument("--uniprot",action = "store_true", help="Annotate VCF with protein functional features from the UniProt Knowledgebase")
+   #parser.add_argument("--uniprot",action = "store_true", help="Annotate VCF with protein functional features from the UniProt Knowledgebase")
    parser.add_argument("--gvanno_xref",action = "store_true", help="Annotate VCF with transcript annotations from gvanno (protein complexes, disease associations, etc)")
    parser.add_argument("--gwas",action = "store_true", help="Annotate VCF with against known loci associated with cancer, as identified from genome-wide association studies (GWAS)")
    parser.add_argument("--cancer_hotspots",action = "store_true", help="Annotate VCF with mutation hotspots from cancerhotspots.org")
@@ -31,7 +31,7 @@ def __main__():
    vcfheader_file = args.out_vcf + '.tmp.' + str(random.randrange(0,10000000)) + '.header.txt'
    vcfanno_conf_fname = args.out_vcf + '.tmp.conf.toml'
    print_vcf_header(args.query_vcf, vcfheader_file, chromline_only = False)
-   run_vcfanno(args.num_processes, args.query_vcf, vcfanno_conf_fname, query_info_tags, vcfheader_file, args.gvanno_db_dir, args.out_vcf, args.ncer, args.clinvar, args.dbnsfp, args.uniprot, args.gvanno_xref,args.gwas, args.cancer_hotspots)
+   run_vcfanno(args.num_processes, args.query_vcf, vcfanno_conf_fname, query_info_tags, vcfheader_file, args.gvanno_db_dir, args.out_vcf, args.ncer, args.clinvar, args.dbnsfp, args.gvanno_xref,args.gwas, args.cancer_hotspots)
 
 
 def prepare_vcfanno_configuration(vcfanno_data_directory, vcfanno_conf_fname, vcfheader_file, logger, datasource_info_tags, query_info_tags, datasource):
@@ -41,15 +41,14 @@ def prepare_vcfanno_configuration(vcfanno_data_directory, vcfanno_conf_fname, vc
    append_to_conf_file(datasource, datasource_info_tags, vcfanno_data_directory, vcfanno_conf_fname)
    append_to_vcf_header(vcfanno_data_directory, datasource, vcfheader_file)
 
-def run_vcfanno(num_processes, query_vcf, vcfanno_conf_fname, query_info_tags, vcfheader_file, gvanno_db_directory, output_vcf, ncer, clinvar, dbnsfp, uniprot, gvanno_xref,gwas, cancer_hotspots):
+def run_vcfanno(num_processes, query_vcf, vcfanno_conf_fname, query_info_tags, vcfheader_file, gvanno_db_directory, output_vcf, ncer, clinvar, dbnsfp,  gvanno_xref,gwas, cancer_hotspots):
    """
    Function that annotates a VCF file with vcfanno against a user-defined set of germline and somatic VCF files
    """
    clinvar_info_tags = ["CLINVAR_MSID","CLINVAR_PMID","CLINVAR_CLNSIG","CLINVAR_VARIANT_ORIGIN","CLINVAR_CONFLICTED","CLINVAR_UMLS_CUI","CLINVAR_HGVSP",
                         "CLINVAR_UMLS_CUI_SOMATIC","CLINVAR_CLNSIG_SOMATIC","CLINVAR_PMID_SOMATIC","CLINVAR_ALLELE_ID","CLINVAR_MOLECULAR_EFFECT",
-                        "CLINVAR_REVIEW_STATUS_STARS"]
+                        "CLINVAR_REVIEW_STATUS_STARS","CLINVAR_CLASSIFICATION"]
    dbnsfp_info_tags = ["DBNSFP"]
-   uniprot_info_tags = ["UNIPROT_FEATURE"]
    gvanno_xref_info_tags = ["GVANNO_XREF"]
    gwas_info_tags = ["GWAS_HIT"]
    ncer_info_tags = ["NCER_PERCENTILE"]
@@ -61,8 +60,6 @@ def run_vcfanno(num_processes, query_vcf, vcfanno_conf_fname, query_info_tags, v
       prepare_vcfanno_configuration(gvanno_db_directory, vcfanno_conf_fname, vcfheader_file, logger, clinvar_info_tags, query_info_tags, "clinvar")
    if dbnsfp is True:
       prepare_vcfanno_configuration(gvanno_db_directory, vcfanno_conf_fname, vcfheader_file, logger, dbnsfp_info_tags, query_info_tags, "dbnsfp")
-   if uniprot is True:
-      prepare_vcfanno_configuration(gvanno_db_directory, vcfanno_conf_fname, vcfheader_file, logger, uniprot_info_tags, query_info_tags, "uniprot")
    if gvanno_xref is True:
       prepare_vcfanno_configuration(gvanno_db_directory, vcfanno_conf_fname, vcfheader_file, logger, gvanno_xref_info_tags, query_info_tags, "gvanno_xref")
    if gwas is True:
@@ -97,7 +94,7 @@ def append_to_conf_file(datasource, datasource_info_tags, gvanno_db_directory, v
    The datasource defines the set of tags that will be appended during annotation
    """
    fh = open(vcfanno_conf_fname,'a')
-   if datasource != 'uniprot' and datasource != 'gvanno_xref' and datasource != 'ncer':
+   if datasource != 'gvanno_xref' and datasource != 'ncer':
       fh.write('[[annotation]]\n')
       fh.write('file="' + str(gvanno_db_directory) + '/' + str(datasource) + '/' + str(datasource) + '.vcf.gz"\n')
       fields_string = 'fields = ["' + '","'.join(datasource_info_tags) + '"]'
@@ -106,8 +103,8 @@ def append_to_conf_file(datasource, datasource_info_tags, gvanno_db_directory, v
       fh.write(fields_string + '\n')
       fh.write(ops_string + '\n\n')
    else:
-      if datasource == 'uniprot' or datasource == 'gvanno_xref' or datasource == 'ncer':
-         if datasource == 'uniprot' or datasource == 'gvanno_xref':
+      if datasource == 'gvanno_xref' or datasource == 'ncer':
+         if datasource == 'gvanno_xref':
             fh.write('[[annotation]]\n')
             fh.write('file="' + str(gvanno_db_directory) + '/' + str(datasource) + '/' + str(datasource) + '.bed.gz"\n')
             fh.write('columns=[4]\n')