<commit_before># To change this license header, choose License Headers in Project Properties.
# To change this template file, choose Tools | Templates
# and open the template in the editor.

# HGNC
hgnc.url=ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/tsv/
hgnc.remoteFile=hgnc_complete_set.txt
hgnc.version=
hgnc.extractedName=hgnc_complete_set.txt
hgnc.extractScheme=copy
hgnc.parsedName=

# HPO
# change to purl.obolibrary.org/obo/hp.obo ?
hpo.url=http://purl.obolibrary.org/obo/
hpo.remoteFile=hp.obo
hpo.version=
hpo.extractedName=hpo.obo
hpo.extractScheme=copy
hpo.parsedName=hpo.pg

# FANTOM
fantom.url=http://enhancer.binf.ku.dk/presets/
fantom.remoteFile=hg19_permissive_enhancer_usage.csv.gz
fantom.version=
fantom.extractedName=hg19_permissive_enhancer_usage.csv
fantom.extractScheme=gz
fantom.parsedName=fantom.pg

# Ensembl enhancers
ensembl_enhancers.url=http://grch37.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%20%3C!DOCTYPE%20Query%3E%20%3CQuery%20%20virtualSchemaName%20=%20%22default%22%20formatter%20=%20%22TSV%22%20header%20=%20%220%22%20uniqueRows%20=%20%221%22%20count%20=%20%22%22%20datasetConfigVersion%20=%20%220.6%22%20%3E%20%20%3CDataset%20name%20=%20%22hsapiens_regulatory_feature%22%20interface%20=%20%22default%22%20%3E%3CFilter%20name%20=%20%22regulatory_feature_type_name%22%20value%20=%20%22Enhancer%22/%3E%3CAttribute%20name%20=%20%22chromosome_name%22%20/%3E%3CAttribute%20name%20=%20%22chromosome_start%22%20/%3E%3CAttribute%20name%20=%20%22chromosome_end%22%20/%3E%3CAttribute%20name%20=%20%22feature_type_name%22%20/%3E%3C/Dataset%3E%3C/
   #string2entrez.url=http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%20%3C!DOCTYPE%20Query%3E%20%3CQuery%20%20virtualSchemaName%20=%20%22default%22%20formatter%20=%20%22TSV%22%20header%20=%20%220%22%20uniqueRows%20=%20%220%22%20count%20=%20%22%22%20datasetConfigVersion%20=%20%220.6%22%20%3E%20%20%3CDataset%20name%20=%20%22hsapiens_gene_ensembl%22%20interface%20=%20%22default%22%20%3E%20%3CAttribute%20name%20=%20%22ensembl_peptide_id%22%20/%3E%20%3CAttribute%20name%20=%20%22entrezgene%22%20/%3E%20%3CAttribute%20name%20=%20%22hgnc_symbol%22%20/%3E%20%3C/Dataset%3E%20%3C/

ensembl_enhancers.remoteFile=Query%3E
ensembl_enhancers.version=
ensembl_enhancers.extractedName=ensembl_enhancers.tsv
ensembl_enhancers.extractScheme=copy
ensembl_enhancers.parsedName=ensembl_enhancers.pg

#NSFP - for pathogenicity scores
# For last release directly downloaded from gdrive link - was a lot faster
#this is a 16GB file so might take a while
# onedrive download seems a lot faster - configured to use this
nsfp.url=ftp://dbnsfp:dbnsfp@dbnsfp.softgenetics.com/
nsfp.remoteFile=dbNSFPv3.4a.zip
nsfp.version=3.4a
nsfp.extractedName=dbNSFPv3.4a.zip
nsfp.extractScheme=copy
nsfp.parsedName=variant.pg

#dbSNP - 1000 genomes Frequency data
dbSnp.url=ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh37p13/VCF/
dbSnp.remoteFile=00-All.vcf.gz
dbSnp.version=00
dbSnp.extractedName=dbSNP_00-All.vcf
#can also do a gz
dbSnp.extractScheme=copy
dbSnp.parsedName=frequency.pg

#ExAC Frequency data
exac.url=ftp://ftp.broadinstitute.org/pub/ExAC_release/current/
exac.remoteFile=ExAC.r0.3.1.sites.vep.vcf.gz
exac.version=0.3
exac.extractedName=ExAC.r0.3.1.sites.vep.vcf.gz
exac.extractScheme=copy
exac.parsedName=frequency.pg

#ESP Frequency data
esp.url=http://evs.gs.washington.edu/evs_bulk_data/
esp.remoteFile=ESP6500SI-V2-SSA137.GRCh38-liftover.snps_indels.vcf.tar.gz
esp.version=
esp.extractedName=ESP_snps_indels
esp.extractScheme=tgz
esp.parsedName=frequency.pg

#name of ucsc.ser file created from Jannovar for defining known exon locations
#this needs to be manually provided in the extracted data directory<commit_msg>Added comment to exomiser-db resource.properties explaining why ESP filename is really OK.<commit_after># To change this license header, choose License Headers in Project Properties.
# To change this template file, choose Tools | Templates
# and open the template in the editor.

# HGNC
hgnc.url=ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/tsv/
hgnc.remoteFile=hgnc_complete_set.txt
hgnc.version=
hgnc.extractedName=hgnc_complete_set.txt
hgnc.extractScheme=copy
hgnc.parsedName=

# HPO
# change to purl.obolibrary.org/obo/hp.obo ?
hpo.url=http://purl.obolibrary.org/obo/
hpo.remoteFile=hp.obo
hpo.version=
hpo.extractedName=hpo.obo
hpo.extractScheme=copy
hpo.parsedName=hpo.pg

# FANTOM
fantom.url=http://enhancer.binf.ku.dk/presets/
fantom.remoteFile=hg19_permissive_enhancer_usage.csv.gz
fantom.version=
fantom.extractedName=hg19_permissive_enhancer_usage.csv
fantom.extractScheme=gz
fantom.parsedName=fantom.pg

# Ensembl enhancers
ensembl_enhancers.url=http://grch37.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%20%3C!DOCTYPE%20Query%3E%20%3CQuery%20%20virtualSchemaName%20=%20%22default%22%20formatter%20=%20%22TSV%22%20header%20=%20%220%22%20uniqueRows%20=%20%221%22%20count%20=%20%22%22%20datasetConfigVersion%20=%20%220.6%22%20%3E%20%20%3CDataset%20name%20=%20%22hsapiens_regulatory_feature%22%20interface%20=%20%22default%22%20%3E%3CFilter%20name%20=%20%22regulatory_feature_type_name%22%20value%20=%20%22Enhancer%22/%3E%3CAttribute%20name%20=%20%22chromosome_name%22%20/%3E%3CAttribute%20name%20=%20%22chromosome_start%22%20/%3E%3CAttribute%20name%20=%20%22chromosome_end%22%20/%3E%3CAttribute%20name%20=%20%22feature_type_name%22%20/%3E%3C/Dataset%3E%3C/
   #string2entrez.url=http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%20%3C!DOCTYPE%20Query%3E%20%3CQuery%20%20virtualSchemaName%20=%20%22default%22%20formatter%20=%20%22TSV%22%20header%20=%20%220%22%20uniqueRows%20=%20%220%22%20count%20=%20%22%22%20datasetConfigVersion%20=%20%220.6%22%20%3E%20%20%3CDataset%20name%20=%20%22hsapiens_gene_ensembl%22%20interface%20=%20%22default%22%20%3E%20%3CAttribute%20name%20=%20%22ensembl_peptide_id%22%20/%3E%20%3CAttribute%20name%20=%20%22entrezgene%22%20/%3E%20%3CAttribute%20name%20=%20%22hgnc_symbol%22%20/%3E%20%3C/Dataset%3E%20%3C/

ensembl_enhancers.remoteFile=Query%3E
ensembl_enhancers.version=
ensembl_enhancers.extractedName=ensembl_enhancers.tsv
ensembl_enhancers.extractScheme=copy
ensembl_enhancers.parsedName=ensembl_enhancers.pg

#NSFP - for pathogenicity scores
# For last release directly downloaded from gdrive link - was a lot faster
#this is a 16GB file so might take a while
# onedrive download seems a lot faster - configured to use this
nsfp.url=ftp://dbnsfp:dbnsfp@dbnsfp.softgenetics.com/
nsfp.remoteFile=dbNSFPv3.4a.zip
nsfp.version=3.4a
nsfp.extractedName=dbNSFPv3.4a.zip
nsfp.extractScheme=copy
nsfp.parsedName=variant.pg

#dbSNP - 1000 genomes Frequency data
dbSnp.url=ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh37p13/VCF/
dbSnp.remoteFile=00-All.vcf.gz
dbSnp.version=00
dbSnp.extractedName=dbSNP_00-All.vcf
#can also do a gz
dbSnp.extractScheme=copy
dbSnp.parsedName=frequency.pg

#ExAC Frequency data
exac.url=ftp://ftp.broadinstitute.org/pub/ExAC_release/current/
exac.remoteFile=ExAC.r0.3.1.sites.vep.vcf.gz
exac.version=0.3
exac.extractedName=ExAC.r0.3.1.sites.vep.vcf.gz
exac.extractScheme=copy
exac.parsedName=frequency.pg

#ESP Frequency data
#The bulk files of the ESP 6500 exome data below are still primarily in GRCh37 (or HG19)
#the GRCh38 lifted-over positions are added in an extra column in the text file, or in an extra attribute in the INFO
#field in the VCF file.
esp.url=http://evs.gs.washington.edu/evs_bulk_data/
esp.remoteFile=ESP6500SI-V2-SSA137.GRCh38-liftover.snps_indels.vcf.tar.gz
esp.version=
esp.extractedName=ESP_snps_indels
esp.extractScheme=tgz
esp.parsedName=frequency.pg

#name of ucsc.ser file created from Jannovar for defining known exon locations
#this needs to be manually provided in the extracted data directory
{'fraction_non_alphanumeric': 0.13349330639050266, 'fraction_numerical': 0.11164435463500884, 'mean_word_length': 8.645554202192448, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 2, 'xml': 4}, 'pii_count': 2, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 4, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '2007026', 'n_tokens_mistral': 3763, 'n_tokens_neox': 3275, 'n_words': 372}