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Funcotator Update for Datasource Release V1.8 #8512

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merged 13 commits into from
Oct 11, 2023
Merged

Funcotator Update for Datasource Release V1.8 #8512

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3e98bd7
updated hgnc download approach
jamesemery Jun 28, 2023
2c90ca5
switching to other work
jamesemery Jul 7, 2023
0c11683
updates to get the cosmic scripts workign
jamesemery Jul 20, 2023
2e3a6df
updated the gencode_x_ cripts
jamesemery Jul 25, 2023
7a972de
adding a debug string
jamesemery Jul 25, 2023
1a5e6c5
proposed fix for the allele checking code
jamesemery Jul 25, 2023
a552501
testing old matching code
jamesemery Jul 25, 2023
c4dc5e9
removed the old method i was using for tests
jamesemery Jul 26, 2023
bd1004a
adding gencode v43 constants to the MAF output constants
jamesemery Aug 17, 2023
f626f4d
Changes to datasource downloader script to support the new srouce out…
jamesemery Sep 1, 2023
7d6785d
fix date typo
jamesemery Sep 1, 2023
cf5670f
fix typo
jamesemery Sep 1, 2023
62abde0
fixed the broken test for PR review
jamesemery Sep 11, 2023
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4 changes: 2 additions & 2 deletions scripts/funcotator/data_sources/cosmic/createCosmicFusionGeneTsv.py
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Expand Up @@ -90,7 +90,7 @@ def renderFusionGeneDictEntry(geneKey, fusionGeneDict):
tsvReader = GenericTsvReader(inputFilename)
headers = tsvReader.getFieldNames()
print('Found headers (input): ' + str(headers))
if "Translocation Name" not in headers:
if "TRANSLOCATION_NAME" not in headers:
raise NotImplementedError("Could not find Translocation Name column in the input file.")

outputHeaders = ['gene', 'fusion_genes', 'fusion_id']
Expand All @@ -99,7 +99,7 @@ def renderFusionGeneDictEntry(geneKey, fusionGeneDict):
fusionGeneDict = OrderedDict()
last_i = 0
for i, line in enumerate(tsvReader):
fusion_gene_description = line['Translocation Name']
fusion_gene_description = line['TRANSLOCATION_NAME']

if len(fusion_gene_description.strip()) == 0:
# blank
Expand Down
6 changes: 6 additions & 0 deletions scripts/funcotator/data_sources/cosmic/createSqliteCosmicDb.sh
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Expand Up @@ -18,6 +18,7 @@ set -e

COSMIC_FILE=CosmicCompleteTargetedScreensMutantExport.tsv
OUT_DB_FILE="Cosmic.db"
OUT_TMP_FOLDER="~/tmp"
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Why did you decide to remove the temp dir?

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Other way around... i added a tmp folder and i needed to do so because i was running into space issues on-prem


################################################################################

Expand All @@ -29,6 +30,10 @@ if [[ $# -gt 1 ]] ; then
OUT_DB_FILE=$2
fi

if [[ $# -gt 2 ]] ; then
OUT_TMP_FOLDER=$3
fi

if [ ! -f ${COSMIC_FILE} ] ; then
echo "ERROR: Given COSMIC file does not exist: ${COSMIC_FILE}" 1>&2
exit 1
Expand All @@ -42,6 +47,7 @@ sqlite3 ${OUT_DB_FILE} <<EOF
.echo on
.mode tabs
.import ${COSMIC_FILE} RawCosmic
pragma temp_store_directory = ${OUT_TMP_FOLDER};
CREATE TABLE Cosmic AS SELECT * FROM RawCosmic WHERE ("Mutation AA" != "" OR "Mutation genome position" != "");
DROP TABLE RawCosmic;
UPDATE Cosmic SET "Mutation genome position" = "chr"||"Mutation genome position" WHERE "Mutation genome position" != "";
Expand Down
15 changes: 6 additions & 9 deletions scripts/funcotator/data_sources/cosmic/getCosmicDataSources.sh
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Expand Up @@ -11,7 +11,7 @@ SCRIPTNAME=$( echo $0 | sed 's#.*/##g' )

################################################################################

version="v84"
version="v98"

EMAIL=""
PASSWORD=""
Expand Down Expand Up @@ -135,15 +135,12 @@ mkdir -vp cosmic/hg19 cosmic/hg38 cosmic_fusion/hg19 cosmic_fusion/hg38 cosmic_t
# Get the data files:

echo "Getting files ... "
lftp --norc -u "${EMAIL}","${PASSWORD}" sftp://sftp-cancer.sanger.ac.uk <<EOF
AUTH_TOKEN=$(echo -n "$EMAIL:$PASSWORD" | base64)

get cosmic/grch37/cosmic/${version}/CosmicCompleteTargetedScreensMutantExport.tsv.gz -o cosmic/hg19/CosmicCompleteTargetedScreensMutantExport.tsv.gz
get cosmic/grch37/cosmic/${version}/CosmicFusionExport.tsv.gz -o cosmic_fusion/hg19/CosmicFusionExport.tsv.gz
get cosmic/grch38/cosmic/${version}/CosmicCompleteTargetedScreensMutantExport.tsv.gz -o cosmic/hg38/CosmicCompleteTargetedScreensMutantExport.tsv.gz
get cosmic/grch38/cosmic/${version}/CosmicFusionExport.tsv.gz -o cosmic_fusion/hg38/CosmicFusionExport.tsv.gz
bye

EOF
curl -sS "$(curl -H "Authorization: Basic $AUTH_TOKEN" https://cancer.sanger.ac.uk/cosmic/file_download/GRCh37/cosmic/${version}/CosmicCompleteTargetedScreensMutantExport.tsv.gz | jq -r '.url')" -o cosmic/hg19/CosmicCompleteTargetedScreensMutantExport.tsv.gz
curl -sS "$(curl -H "Authorization: Basic $AUTH_TOKEN" https://cancer.sanger.ac.uk/cosmic/file_download/GRCh37/cosmic/${version}/CosmicFusionExport.tsv.gz | jq -r '.url')" -o cosmic_fusion/hg19/CosmicFusionExport.tsv.gz
curl -sS "$(curl -H "Authorization: Basic $AUTH_TOKEN" https://cancer.sanger.ac.uk/cosmic/file_download/GRCh38/cosmic/${version}/CosmicCompleteTargetedScreensMutantExport.tsv.gz | jq -r '.url')" -o cosmic/hg38/CosmicCompleteTargetedScreensMutantExport.tsv.gz
curl -sS "$(curl -H "Authorization: Basic $AUTH_TOKEN" https://cancer.sanger.ac.uk/cosmic/file_download/GRCh38/cosmic/${version}/CosmicFusionExport.tsv.gz | jq -r '.url')" -o cosmic_fusion/hg38/CosmicFusionExport.tsv.gz

echo "Retrieved COSMIC version ${version} on $(date) from sftp-cancer.sanger.ac.uk by: ${SCRIPTNAME}:" > cosmic/metadata.txt
echo "User: ${EMAIL}" >> cosmic/metadata.txt
Expand Down
2 changes: 1 addition & 1 deletion scripts/funcotator/data_sources/downloadHgncDataSource.sh
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Expand Up @@ -2,5 +2,5 @@

# Downloads the HGNC data source from the HGNC website.

curl 'https://www.genenames.org/cgi-bin/download?col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&col=gd_status&col=gd_locus_type&col=gd_locus_group&col=gd_prev_sym&col=gd_prev_name&col=gd_aliases&col=gd_name_aliases&col=gd_pub_chrom_map&col=gd_date_mod&col=gd_date_sym_change&col=gd_date_name_change&col=gd_pub_acc_ids&col=gd_enz_ids&col=gd_pub_eg_id&col=gd_pub_ensembl_id&col=gd_pubmed_ids&col=gd_pub_refseq_ids&col=family.id&col=family.name&col=gd_ccds_ids&col=gd_vega_ids&col=md_eg_id&col=md_mim_id&col=md_refseq_id&col=md_prot_id&col=md_ensembl_id&col=md_ucsc_id&status=Approved&status_opt=2&where=&order_by=gd_app_sym_sort&format=text&limit=&hgnc_dbtag=on&submit=submit' > hgnc_download_$(date +%b%d%Y).tsv
curl 'https://www.genenames.org/cgi-bin/download/custom?col=gd_hgnc_id&amp;col=gd_app_sym&amp;col=gd_app_name&amp;col=gd_status&amp;col=gd_locus_type&amp;col=gd_locus_group&amp;col=gd_prev_sym&amp;col=gd_prev_name&amp;col=gd_aliases&amp;col=gd_name_aliases&amp;col=gd_pub_chrom_map&amp;col=gd_date_mod&amp;col=gd_date_sym_change&amp;col=gd_date_name_change&amp;col=gd_pub_acc_ids&amp;col=gd_enz_ids&amp;col=gd_pub_eg_id&amp;col=gd_pub_ensembl_id&amp;col=gd_pubmed_ids&amp;col=gd_pub_refseq_ids&amp;col=family.id&amp;col=family.name&amp;col=gd_ccds_ids&amp;col=gd_vega_ids&amp;col=md_eg_id&amp;col=md_mim_id&amp;col=md_refseq_id&amp;col=md_prot_id&amp;col=md_ensembl_id&amp;col=md_ucsc_id&amp;status=Approved&amp;status_opt=2&amp;where=&amp;order_by=gd_app_sym_sort&amp;format=text&amp;limit=&amp;hgnc_dbtag=on&amp;submit=submi' > hgnc_download_$(date +%b%d%Y).tsv
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The last characters before the > look to be truncated.

Is it really submit=submi?

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i just checked and that link works... ask the HGNC devs? Evidently both submi and submit work there...


28 changes: 28 additions & 0 deletions scripts/funcotator/data_sources/finalizeFuncotatorReleaseDirectory.sh
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@@ -0,0 +1,28 @@
#!/usr/bin/env bash

#NOTE: This script has been checked in to aid in the release process for future Funcotator datasource bundles.

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echo "Making Tarballs of each Datasource Directory..."

tar -zcvf funcotator_dataSources.v1.8.hg38.20230908s.tar.gz funcotator_dataSources.v1.8.hg38.20230908s
tar -zcvf funcotator_dataSources.v1.8.hg38.20230908g.tar.gz funcotator_dataSources.v1.8.hg38.20230908g
tar -zcvf funcotator_dataSources.v1.8.hg19.20230908s.tar.gz funcotator_dataSources.v1.8.hg19.20230908s
tar -zcvf funcotator_dataSources.v1.8.hg19.20230908g.tar.gz funcotator_dataSources.v1.8.hg19.20230908g

echo "Making the various hashfiles for release"

find funcotator_dataSources.v1.8.hg38.20230908s -type f | xargs md5sum > funcotator_dataSources.v1.8.hg38.20230908s.dir.long.md5sum
md5sum funcotator_dataSources.v1.8.hg38.20230908s.tar.gz | awk '{print $1}' > funcotator_dataSources.v1.8.hg38.20230908s.dir.md5sum
sha256sum funcotator_dataSources.v1.8.hg38.20230908s.tar.gz > funcotator_dataSources.v1.8.hg38.20230908s.sha256

find funcotator_dataSources.v1.8.hg38.20230908g -type f | xargs md5sum > funcotator_dataSources.v1.8.hg38.20230908g.dir.long.md5sum
md5sum funcotator_dataSources.v1.8.hg38.20230908g.tar.gz | awk '{print $1}' > funcotator_dataSources.v1.8.hg38.20230908g.dir.md5sum
sha256sum funcotator_dataSources.v1.8.hg38.20230908g.tar.gz > funcotator_dataSources.v1.8.hg38.20230908g.sha256

find funcotator_dataSources.v1.8.hg19.20230908s -type f | xargs md5sum > funcotator_dataSources.v1.8.hg19.20230908s.dir.long.md5sum
md5sum funcotator_dataSources.v1.8.hg19.20230908s.tar.gz | awk '{print $1}' > funcotator_dataSources.v1.8.hg19.20230908s.dir.md5sum
sha256sum funcotator_dataSources.v1.8.hg19.20230908s.tar.gz > funcotator_dataSources.v1.8.hg19.20230908s.sha256

find funcotator_dataSources.v1.8.hg19.20230908g -type f | xargs md5sum > funcotator_dataSources.v1.8.hg19.20230908g.dir.long.md5sum
md5sum funcotator_dataSources.v1.8.hg19.20230908g.tar.gz | awk '{print $1}' > funcotator_dataSources.v1.8.hg19.20230908g.dir.md5sum
sha256sum funcotator_dataSources.v1.8.hg19.20230908g.tar.gz > funcotator_dataSources.v1.8.hg19.20230908g.sha256
2 changes: 1 addition & 1 deletion scripts/funcotator/data_sources/getGencode.sh
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Expand Up @@ -15,7 +15,7 @@ MAXARGS=0

# Latest release numbers for our references.
# Update these numbers when a new Gencode is released.
LATEST_RELEASE=34
LATEST_RELEASE=43

DATA_SOURCE_NAME="Gencode"
OUT_DIR_NAME='gencode'
Expand Down
4 changes: 2 additions & 2 deletions scripts/funcotator/data_sources/getGencodeXHGNC.sh
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Expand Up @@ -8,10 +8,10 @@ outFileBaseName="gencode_xhgnc"
outExt=".tsv"

hg19db="homo_sapiens_core_75_37"
hg38db="homo_sapiens_core_90_38"
hg38db="homo_sapiens_core_110_38"

hg19FileName=${outFileBaseName}_v75_37.hg19${outExt}
hg38FileName=${outFileBaseName}_v90_38.hg38${outExt}
hg38FileName=${outFileBaseName}_v110_38.hg38${outExt}

################################################################################

Expand Down
4 changes: 2 additions & 2 deletions scripts/funcotator/data_sources/getGencodeXRefseq.sh
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Expand Up @@ -8,10 +8,10 @@ outFileBaseName="gencode_xrefseq"
outExt=".tsv"

hg19db="homo_sapiens_core_75_37"
hg38db="homo_sapiens_core_90_38"
hg38db="homo_sapiens_core_110_38"

hg19FileName=${outFileBaseName}_v75_37.hg19${outExt}
hg38FileName=${outFileBaseName}_v90_38.hg38${outExt}
hg38FileName=${outFileBaseName}_v110_38.hg38${outExt}

################################################################################

Expand Down
77 changes: 61 additions & 16 deletions ...n/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorDataSourceDownloader.java
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Expand Up @@ -32,8 +32,8 @@
* <p>
* To download and extract the data sources, you can invoke {@link FuncotatorDataSourceDownloader} in the following ways:
* <ul>
* <li>For <strong>somatic</strong> data sources:<br /><pre>{@code ./gatk FuncotatorDataSourceDownloader --somatic --validate-integrity --extract-after-download}</pre></li>
* <li>For <strong>germline</strong> data sources:<br /><pre>{@code ./gatk FuncotatorDataSourceDownloader --germline --validate-integrity --extract-after-download}</pre></li>
* <li>For <strong>somatic</strong> data sources:<br /><pre>{@code ./gatk FuncotatorDataSourceDownloader --somatic --validate-integrity --hg38 --extract-after-download}</pre></li>
* <li>For <strong>germline</strong> data sources:<br /><pre>{@code ./gatk FuncotatorDataSourceDownloader --germline --validate-integrity --hg19 --extract-after-download}</pre></li>
* </ul>
* </p>
*
Expand Down Expand Up @@ -63,6 +63,8 @@ public class FuncotatorDataSourceDownloader extends CommandLineProgram {
public static final String GERMLINE_ARG_LONG_NAME = "germline";
public static final String OVERWRITE_ARG_LONG_NAME = "overwrite-output-file";
public static final String EXTRACT_AFTER_DOWNLOAD = "extract-after-download";
public static final String HG38_ARG_LONG_NAME = "hg38";
public static final String HG19_ARG_LONG_NAME = "hg19";

//==================================================================================================================
// Private Static Members:
Expand All @@ -73,18 +75,27 @@ public class FuncotatorDataSourceDownloader extends CommandLineProgram {
// Private Static Members:

// Set to always get the latest version of the data sources:
private static final String BASE_URL = DataSourceUtils.DATA_SOURCES_BUCKET_PATH +
DataSourceUtils.DATA_SOURCES_NAME_PREFIX + "." + DataSourceUtils.getDataSourceMaxVersionString();
private static final String HG38_BASE_URL = DataSourceUtils.DATA_SOURCES_BUCKET_PATH +
DataSourceUtils.DATA_SOURCES_NAME_PREFIX + "." + DataSourceUtils.getDataSourceMaxVersionString(38);
private static final String HG19_BASE_URL = DataSourceUtils.DATA_SOURCES_BUCKET_PATH +
DataSourceUtils.DATA_SOURCES_NAME_PREFIX + "." + DataSourceUtils.getDataSourceMaxVersionString(19);

private static final String HG38_GERMLINE_GCLOUD_DATASOURCES_BASEURL = HG38_BASE_URL + DataSourceUtils.DS_GERMLINE_NAME_MODIFIER;
private static final String HG19_GERMLINE_GCLOUD_DATASOURCES_BASEURL = HG19_BASE_URL + DataSourceUtils.DS_GERMLINE_NAME_MODIFIER;

private static final String GERMLINE_GCLOUD_DATASOURCES_BASEURL = BASE_URL + DataSourceUtils.DS_GERMLINE_NAME_MODIFIER;
@VisibleForTesting
static final Path GERMLINE_GCLOUD_DATASOURCES_PATH = IOUtils.getPath(GERMLINE_GCLOUD_DATASOURCES_BASEURL + DataSourceUtils.DS_EXTENSION);
private static final Path GERMLINE_GCLOUD_DATASOURCES_SHA256_PATH = IOUtils.getPath(GERMLINE_GCLOUD_DATASOURCES_BASEURL + DataSourceUtils.DS_CHECKSUM_EXTENSION);
static final Path HG38_GERMLINE_GCLOUD_DATASOURCES_PATH = IOUtils.getPath(HG38_GERMLINE_GCLOUD_DATASOURCES_BASEURL + DataSourceUtils.DS_EXTENSION);
static final Path HG19_GERMLINE_GCLOUD_DATASOURCES_PATH = IOUtils.getPath(HG19_GERMLINE_GCLOUD_DATASOURCES_BASEURL + DataSourceUtils.DS_EXTENSION);
private static final Path HG38_GERMLINE_GCLOUD_DATASOURCES_SHA256_PATH = IOUtils.getPath(HG38_GERMLINE_GCLOUD_DATASOURCES_BASEURL + DataSourceUtils.DS_CHECKSUM_EXTENSION);
private static final Path HG19_GERMLINE_GCLOUD_DATASOURCES_SHA256_PATH = IOUtils.getPath(HG19_GERMLINE_GCLOUD_DATASOURCES_BASEURL + DataSourceUtils.DS_CHECKSUM_EXTENSION);

public static final String SOMATIC_GCLOUD_DATASOURCES_BASEURL = BASE_URL + DataSourceUtils.DS_SOMATIC_NAME_MODIFIER;;
public static final String HG38_SOMATIC_GCLOUD_DATASOURCES_BASEURL = HG38_BASE_URL + DataSourceUtils.DS_SOMATIC_NAME_MODIFIER;;
public static final String HG19_SOMATIC_GCLOUD_DATASOURCES_BASEURL = HG19_BASE_URL + DataSourceUtils.DS_SOMATIC_NAME_MODIFIER;;

public static final Path SOMATIC_GCLOUD_DATASOURCES_PATH = IOUtils.getPath(SOMATIC_GCLOUD_DATASOURCES_BASEURL + DataSourceUtils.DS_EXTENSION);
private static final Path SOMATIC_GCLOUD_DATASOURCES_SHA256_PATH = IOUtils.getPath(SOMATIC_GCLOUD_DATASOURCES_BASEURL + DataSourceUtils.DS_CHECKSUM_EXTENSION);
public static final Path HG38_SOMATIC_GCLOUD_DATASOURCES_PATH = IOUtils.getPath(HG38_SOMATIC_GCLOUD_DATASOURCES_BASEURL + DataSourceUtils.DS_EXTENSION);
public static final Path HG19_SOMATIC_GCLOUD_DATASOURCES_PATH = IOUtils.getPath(HG19_SOMATIC_GCLOUD_DATASOURCES_BASEURL + DataSourceUtils.DS_EXTENSION);
private static final Path HG38_SOMATIC_GCLOUD_DATASOURCES_SHA256_PATH = IOUtils.getPath(HG38_SOMATIC_GCLOUD_DATASOURCES_BASEURL + DataSourceUtils.DS_CHECKSUM_EXTENSION);
private static final Path HG19_SOMATIC_GCLOUD_DATASOURCES_SHA256_PATH = IOUtils.getPath(HG19_SOMATIC_GCLOUD_DATASOURCES_BASEURL + DataSourceUtils.DS_CHECKSUM_EXTENSION);

//==================================================================================================================
// Private Members:
Expand Down Expand Up @@ -129,6 +140,23 @@ public class FuncotatorDataSourceDownloader extends CommandLineProgram {
optional = true)
protected boolean extractDataSourcesAfterDownload = false;

@Argument(
shortName = HG38_ARG_LONG_NAME,
fullName = HG38_ARG_LONG_NAME,
mutex = {HG19_ARG_LONG_NAME, TESTING_OVERRIDE_PATH_FOR_DATA_SOURCES_SHA256_ARG},
doc = "If set, will extract data from the HG38 data sources bucket.",
optional = true)
protected boolean getHg38Datasources = false;

@Argument(
//TODO should these be MUTEX or should one be allowed to download either?
shortName = HG19_ARG_LONG_NAME,
fullName = HG19_ARG_LONG_NAME,
mutex = {HG38_ARG_LONG_NAME, TESTING_OVERRIDE_PATH_FOR_DATA_SOURCES_SHA256_ARG},
doc = "If set, will extract data from the HG19 data sources bucket.",
optional = true)
protected boolean getHg19Datasources = false;

// Testing arguments:
@Hidden
@Advanced
Expand Down Expand Up @@ -164,6 +192,11 @@ protected void onStartup() {
throw new UserException("Must select either somatic or germline datasources.");
}

// Make sure the user specified at least one reference source to download:
if ((!getHg38Datasources) && (!getHg19Datasources) && (testingOverrideDataSourcesPath == null)) {
throw new UserException("Must select either HG19 or HG38 datasources.");
}

// Make sure the testing inputs are correct:
if ( ((testingOverrideDataSourcesPath == null) && (testingOverrideDataSourcesSha256Path != null)) ||
((testingOverrideDataSourcesSha256Path == null) && (testingOverrideDataSourcesPath != null)) ) {
Expand All @@ -184,14 +217,26 @@ protected Object doWork() {

// Get the correct data source:
if ( getSomaticDataSources ) {
dataSourceDescription = "Somatic";
dataSourcesPath = SOMATIC_GCLOUD_DATASOURCES_PATH;
dataSourcesSha256Path = SOMATIC_GCLOUD_DATASOURCES_SHA256_PATH;
if (getHg38Datasources) {
dataSourceDescription = "HG38_Somatic";
dataSourcesPath = HG38_SOMATIC_GCLOUD_DATASOURCES_PATH;
dataSourcesSha256Path = HG38_SOMATIC_GCLOUD_DATASOURCES_SHA256_PATH;
} else { // Okay because HG38 and HG19 datasources are currently MUTEX and at least one is required
dataSourceDescription = "HG19_Somatic";
dataSourcesPath = HG19_SOMATIC_GCLOUD_DATASOURCES_PATH;
dataSourcesSha256Path = HG19_SOMATIC_GCLOUD_DATASOURCES_SHA256_PATH;
}
}
else if ( getGermlineDataSources ) {
dataSourceDescription = "Germline";
dataSourcesPath = GERMLINE_GCLOUD_DATASOURCES_PATH;
dataSourcesSha256Path = GERMLINE_GCLOUD_DATASOURCES_SHA256_PATH;
if (getHg38Datasources) {
dataSourceDescription = "HG38_Germline";
dataSourcesPath = HG38_GERMLINE_GCLOUD_DATASOURCES_PATH;
dataSourcesSha256Path = HG38_GERMLINE_GCLOUD_DATASOURCES_SHA256_PATH;
} else {
dataSourceDescription = "HG19_Germline";
dataSourcesPath = HG19_GERMLINE_GCLOUD_DATASOURCES_PATH;
dataSourcesSha256Path = HG19_GERMLINE_GCLOUD_DATASOURCES_SHA256_PATH;
}
}
else {
// Test case:
Expand Down
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