diff --git a/download_urls.yml b/download_urls.yml index c52baee..665cabd 100644 --- a/download_urls.yml +++ b/download_urls.yml @@ -213,6 +213,7 @@ count: null - url: https://storage.googleapis.com/gcp-public-data--gnomad/release/2.1.1/constraint/gnomad.v2.1.1.lof_metrics.by_gene.txt.bgz +- url: https://storage.googleapis.com/gcp-public-data--gnomad/release/v4.0/constraint/gnomad.v4.0.constraint_metrics.tsv - url: https://ftp.ncbi.nih.gov/gene/DATA/mim2gene_medgen - comment: We replace the linux64.gene2.xml binary with a wrapper to zcat... diff --git a/excerpt-data/58d3599d2c8b6c3d/gnomad.v4.0.constraint_metrics.tsv b/excerpt-data/58d3599d2c8b6c3d/gnomad.v4.0.constraint_metrics.tsv new file mode 100644 index 0000000..48b39bf --- /dev/null +++ b/excerpt-data/58d3599d2c8b6c3d/gnomad.v4.0.constraint_metrics.tsv @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:b9489dcef84265243314f42c29236f05a9e9e7caa78cdd8726a209df20abf91b +size 41407 diff --git a/excerpt-data/58d3599d2c8b6c3d/url.txt b/excerpt-data/58d3599d2c8b6c3d/url.txt new file mode 100644 index 0000000..0b909db --- /dev/null +++ b/excerpt-data/58d3599d2c8b6c3d/url.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:2926e12f06bdca84a986c3293e04b3bbf8bcf4341be327e698adf04d3d2edb93 +size 114 diff --git a/varfish_db_downloader/wget.py b/varfish_db_downloader/wget.py index 970284b..b71a93e 100644 --- a/varfish_db_downloader/wget.py +++ b/varfish_db_downloader/wget.py @@ -87,9 +87,10 @@ def excerpt_head(url: str, path_out: str, count: int): break f_out.write(line.encode("utf-8")) f_out.write(b"\n") - # Fixup resulting compressed files so they are proper bgzip. - subprocess.check_call(["gzip", "-d", path_out]) - subprocess.check_call(["bgzip", path_out.replace(".gz", "")]) + if try_gzip: + # Fixup resulting compressed files so they are proper bgzip. + subprocess.check_call(["gzip", "-d", path_out]) + subprocess.check_call(["bgzip", path_out.replace(".gz", "")]) def excerpt_copy_tbi(url: str, path_out: str, count: int):