wip

varfish-org · Dec 28, 2023 · 92e7d34 · 92e7d34
1 parent 68aeb44
commit 92e7d34
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Showing 4 changed files with 11 additions and 3 deletions.
diff --git 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
diff --git a/excerpt-data/58d3599d2c8b6c3d/url.txt b/excerpt-data/58d3599d2c8b6c3d/url.txt
diff --git 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):