<commit_before>; INI file with default data sources for Jannovar.
;
; This file is packed into the Jannovar JAR file.
;
; Each data source is described in one section. By convention, the section
; and data source name is given as "${organism}/${source}". Jannovar will
; serialize the file to "de.charite.compbio:jannovar-cli.replace('/', '_').replace("\", "_").
;
; Users can provide their own INI files using the --data-source parameter
; to Jannovar, even orriding the defaults from this file. 
;
; Each section contains a "type" entry that will make Jannovar use the
; appropriate DataSource and JannovarDataFactory type for downloading and
; parsing.
;
; Name / Contig ID Mapping
; ========================
;
; Independent of the type, the "chromInfo" and "chrToAccessions" entry are
; expected and give URLs to the "chromInfo.txt.gz" at UCSC describing the
; contig/chromosome lengths and "chrToAccessions" at RefSeq with the
; official contig names and RefSeq/GenBank identifiers.
;
; Transcript Files
; ================
;
; Keys for the types:
;
; * ucsc: knownGene, knownGeneMrna, kgXref, knownToLocusLink
; * ensembl: gtf, cdna, ncrna
; * refseq: gff, dna 
;
; Aliasing
; ========
;
; The mitochondrial chromosome has the key "MT" in RefSeq but "M" in UCSC.
; Thus, we allow to create manual aliasing that is executed after loading the
; chrToAccessions file from RefSeq and before loading the chromInfo file from
; UCSC. Each line has the "alias" key. The value "MT,M,chrM" means that the
; contig names "M" and "chrM" are aliased to the contig name "MT" that is
; already known from the chrToAccessions file.
;
; Note that all alias lines are processed in linear order. If the name in the
; first entry of the list is not known yet then it is created with the next
; free number. This is useful for adding a adding the missing MT chromosome
; entry for hg18, for example.

; ---------------------------------------------------------------------------
; hg18/GRCh36
; ---------------------------------------------------------------------------

; HG18 from UCSC
[hg18/ucsc]
type=ucsc
alias=MT,M,chrM
chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/chromInfo.txt.gz
chrToAccessions=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/Assembled_chromosomes/chr_NC_gi
chrToAccessions.format=chr_NC_gi
chrToAccessions.matchLast=HuRef
knownCanonical=http://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/knownCanonical.txt.gz
knownGene=http://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/knownGene.txt.gz
knownGeneMrna=http://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/knownGeneMrna.txt.gz
kgXref=http://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/kgXref.txt.gz
knownToLocusLink=http://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/knownToLocusLink.txt.gz

; HG19 from Ensembl
[hg18/ensembl]
type=ensembl
alias=MT,M,chrM
chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/chromInfo.txt.gz
chrToAccessions=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/Assembled_chromosomes/chr_NC_gi
chrToAccessions.format=chr_NC_gi
chrToAccessions.matchLast=HuRef
gtf=ftp://ftp.ensembl.org/pub/release-54/gtf/homo_sapiens/Homo_sapiens.NCBI36.54.gtf.gz
cdna=ftp://ftp.ensembl.org/pub/release-54/fasta/homo_sapiens/cdna/Homo_sapiens.NCBI36.54.cdna.all.fa.gz

; HG18 from RefSeq
[hg18/refseq]
type=refseq
alias=MT,M,chrM
chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/chromInfo.txt.gz
chrToAccessions=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/Assembled_chromosomes/chr_NC_gi
chrToAccessions.format=chr_NC_gi
chrToAccessions.matchLast=HuRef
gff=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/GFF/ref_NCBI36_top_level.gff3.gz
rna=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/RNA/rna.fa.gz

; HG18 from RefSeq (only curated data sets)
[hg18/refseq_curated]
type=refseq
alias=MT,M,chrM
onlyCurated=true
chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/chromInfo.txt.gz
chrToAccessions=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/Assembled_chromosomes/chr_NC_gi
chrToAccessions.format=chr_NC_gi
chrToAccessions.matchLast=HuRef
gff=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/GFF/ref_NCBI36_top_level.gff3.gz
rna=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/RNA/rna.fa.gz

; ---------------------------------------------------------------------------
; hg19/GRCh37
; ---------------------------------------------------------------------------

; HG19 from UCSC
[hg19/ucsc]
type=ucsc
alias=MT,M,chrM
chromInfo = http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz
chrToAccessions = https://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/Assembled_chromosomes/chr_accessions_GRCh37.p13
chrToAccessions.format = chr_accessions
knownCanonical=http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/knownCanonical.txt.gz
knownGene=http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz
knownGeneMrna=http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/knownGeneMrna.txt.gz
kgXref=http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/kgXref.txt.gz
knownToLocusLink=http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/knownToLocusLink.txt.gz

; HG19 from Ensembl
[hg19/ensembl]
type = ensembl
alias = MT,M,chrM
chromInfo = http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz
chrToAccessions = https://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/Assembled_chromosomes/chr_accessions_GRCh37.p13
chrToAccessions.format = chr_accessions
gtf = ftp://ftp.ensembl.org/pub/grch37/current/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf.gz
cdna = ftp://ftp.ensembl.org/pub/grch37/current/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh37.cdna.all.fa.gz
table_gene_main = ftp://ftp.ensembl.org/pub/grch37/release-95/mysql/ensembl_mart_95/hsapiens_gene_ensembl__gene__main.txt.gz.bz2
table_hgnc = ftp://ftp.ensembl.org/pub/grch37/release-95/mysql/ensembl_mart_95/hsapiens_gene_ensembl__ox_hgnc__dm.txt.gz.bz2
table_entrezgene = ftp://ftp.ensembl.org/pub/grch37/release-95/mysql/ensembl_mart_95/hsapiens_gene_ensembl__ox_entrezgene__dm.txt.gz.bz2

; HG19 from RefSeq
[hg19/refseq]
type = refseq
alias = MT,M,chrM
allowNonCodingNm = true
chromInfo = http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz
chrToAccessions = https://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/Assembled_chromosomes/chr_accessions_GRCh37.p13
chrToAccessions.format = chr_accessions
gff = https://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/GFF/ref_GRCh37.p13_top_level.gff3.gz
rna = https://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/RNA/rna.fa.gz
faMT = https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?save=file&db=nuccore&report=fasta&id=251831106

; HG19 from RefSeq (only curated data sets)
[hg19/refseq_curated]
type = refseq
alias = MT,M,chrM
onlyCurated = true
allowNonCodingNm = true
chromInfo = http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz
chrToAccessions = https://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/Assembled_chromosomes/chr_accessions_GRCh37.p13
chrToAccessions.format = chr_accessions
gff = https://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/GFF/ref_GRCh37.p13_top_level.gff3.gz
rna = https://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/RNA/rna.fa.gz
faMT = https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?save=file&db=nuccore&report=fasta&id=251831106

; HG19 from RefSeq interim alignment (see https://www.ncbi.nlm.nih.gov/books/NBK430989/#_news_02-14-2017-interim-annotation-update-human_)
[hg19/refseq_interim]
type = refseq
alias = MT,M,chrM
allowNonCodingNm = true
chromInfo = http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz
chrToAccessions = https://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/Assembled_chromosomes/chr_accessions_GRCh37.p13<commit_msg>Update Jannovar default_sources.ini to use RefSeq archive<commit_after>; INI file with default data sources for Jannovar.
;
; This file is packed into the Jannovar JAR file.
;
; Each data source is described in one section. By convention, the section
; and data source name is given as "${organism}/${source}". Jannovar will
; serialize the file to "de.charite.compbio:jannovar-cli.replace('/', '_').replace("\", "_").
;
; Users can provide their own INI files using the --data-source parameter
; to Jannovar, even orriding the defaults from this file. 
;
; Each section contains a "type" entry that will make Jannovar use the
; appropriate DataSource and JannovarDataFactory type for downloading and
; parsing.
;
; Name / Contig ID Mapping
; ========================
;
; Independent of the type, the "chromInfo" and "chrToAccessions" entry are
; expected and give URLs to the "chromInfo.txt.gz" at UCSC describing the
; contig/chromosome lengths and "chrToAccessions" at RefSeq with the
; official contig names and RefSeq/GenBank identifiers.
;
; Transcript Files
; ================
;
; Keys for the types:
;
; * ucsc: knownGene, knownGeneMrna, kgXref, knownToLocusLink
; * ensembl: gtf, cdna, ncrna
; * refseq: gff, dna 
;
; Aliasing
; ========
;
; The mitochondrial chromosome has the key "MT" in RefSeq but "M" in UCSC.
; Thus, we allow to create manual aliasing that is executed after loading the
; chrToAccessions file from RefSeq and before loading the chromInfo file from
; UCSC. Each line has the "alias" key. The value "MT,M,chrM" means that the
; contig names "M" and "chrM" are aliased to the contig name "MT" that is
; already known from the chrToAccessions file.
;
; Note that all alias lines are processed in linear order. If the name in the
; first entry of the list is not known yet then it is created with the next
; free number. This is useful for adding a adding the missing MT chromosome
; entry for hg18, for example.

; ---------------------------------------------------------------------------
; hg18/GRCh36
; ---------------------------------------------------------------------------

; HG18 from UCSC
[hg18/ucsc]
type=ucsc
alias=MT,M,chrM
chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/chromInfo.txt.gz
chrToAccessions=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/Assembled_chromosomes/chr_NC_gi
chrToAccessions.format=chr_NC_gi
chrToAccessions.matchLast=HuRef
knownCanonical=http://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/knownCanonical.txt.gz
knownGene=http://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/knownGene.txt.gz
knownGeneMrna=http://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/knownGeneMrna.txt.gz
kgXref=http://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/kgXref.txt.gz
knownToLocusLink=http://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/knownToLocusLink.txt.gz

; HG19 from Ensembl
[hg18/ensembl]
type=ensembl
alias=MT,M,chrM
chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/chromInfo.txt.gz
chrToAccessions=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/Assembled_chromosomes/chr_NC_gi
chrToAccessions.format=chr_NC_gi
chrToAccessions.matchLast=HuRef
gtf=ftp://ftp.ensembl.org/pub/release-54/gtf/homo_sapiens/Homo_sapiens.NCBI36.54.gtf.gz
cdna=ftp://ftp.ensembl.org/pub/release-54/fasta/homo_sapiens/cdna/Homo_sapiens.NCBI36.54.cdna.all.fa.gz

; HG18 from RefSeq
[hg18/refseq]
type=refseq
alias=MT,M,chrM
chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/chromInfo.txt.gz
chrToAccessions=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/Assembled_chromosomes/chr_NC_gi
chrToAccessions.format=chr_NC_gi
chrToAccessions.matchLast=HuRef
gff=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/GFF/ref_NCBI36_top_level.gff3.gz
rna=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/RNA/rna.fa.gz

; HG18 from RefSeq (only curated data sets)
[hg18/refseq_curated]
type=refseq
alias=MT,M,chrM
onlyCurated=true
chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/chromInfo.txt.gz
chrToAccessions=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/Assembled_chromosomes/chr_NC_gi
chrToAccessions.format=chr_NC_gi
chrToAccessions.matchLast=HuRef
gff=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/GFF/ref_NCBI36_top_level.gff3.gz
rna=ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/RNA/rna.fa.gz

; ---------------------------------------------------------------------------
; hg19/GRCh37
; ---------------------------------------------------------------------------

; HG19 from UCSC
[hg19/ucsc]
type=ucsc
alias=MT,M,chrM
chromInfo = http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz
chrToAccessions = https://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Homo_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/Assembled_chromosomes/chr_accessions_GRCh37.p13
chrToAccessions.format = chr_accessions
knownCanonical=http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/knownCanonical.txt.gz
knownGene=http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz
knownGeneMrna=http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/knownGeneMrna.txt.gz
kgXref=http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/kgXref.txt.gz
knownToLocusLink=http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/knownToLocusLink.txt.gz

; HG19 from Ensembl
[hg19/ensembl]
type = ensembl
alias = MT,M,chrM
chromInfo = http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz
chrToAccessions = https://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Homo_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/Assembled_chromosomes/chr_accessions_GRCh37.p13
chrToAccessions.format = chr_accessions
gtf = ftp://ftp.ensembl.org/pub/grch37/current/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf.gz
cdna = ftp://ftp.ensembl.org/pub/grch37/current/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh37.cdna.all.fa.gz
table_gene_main = ftp://ftp.ensembl.org/pub/grch37/release-95/mysql/ensembl_mart_95/hsapiens_gene_ensembl__gene__main.txt.gz.bz2
table_hgnc = ftp://ftp.ensembl.org/pub/grch37/release-95/mysql/ensembl_mart_95/hsapiens_gene_ensembl__ox_hgnc__dm.txt.gz.bz2
table_entrezgene = ftp://ftp.ensembl.org/pub/grch37/release-95/mysql/ensembl_mart_95/hsapiens_gene_ensembl__ox_entrezgene__dm.txt.gz.bz2

; HG19 from RefSeq
[hg19/refseq]
type = refseq
alias = MT,M,chrM
allowNonCodingNm = true
chromInfo = http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz
chrToAccessions = https://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Homo_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/Assembled_chromosomes/chr_accessions_GRCh37.p13
chrToAccessions.format = chr_accessions
gff = https://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Homo_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/GFF/ref_GRCh37.p13_top_level.gff3.gz
rna = https://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Homo_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/RNA/rna.fa.gz
faMT = https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?save=file&db=nuccore&report=fasta&id=251831106

; HG19 from RefSeq (only curated data sets)
[hg19/refseq_curated]
type = refseq
alias = MT,M,chrM
onlyCurated = true
allowNonCodingNm = true
chromInfo = http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz
chrToAccessions = https://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Homo_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/Assembled_chromosomes/chr_accessions_GRCh37.p13
chrToAccessions.format = chr_accessions
gff = https://ftp.ncbi.nlm.nih.gov/archive/old_refseq/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/GFF/ref_GRCh37.p13_top_level.gff3.gz
rna = https://ftp.ncbi.nlm.nih.gov/archive/old_refseq/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/RNA/rna.fa.gz
faMT = https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?save=file&db=nuccore&report=fasta&id=251831106

; HG19 from RefSeq interim alignment (see https://www.ncbi.nlm.nih.gov/books/NBK430989/#_news_02-14-2017-interim-annotation-update-human_)
[hg19/refseq_interim]
type = refseq
alias = MT,M,chrM
allowNonCodingNm = true
chromInfo = http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz
chrToAccessions = https://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/Assembled_chromosomes/chr_accessions_GRCh37.p13
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{'dir': 'git-commits-cleaned', 'id': '2273695', 'n_tokens_mistral': 6983, 'n_tokens_neox': 6220, 'n_words': 867}