Merge branch 'hotfix/0.7.2'

Author: simonvh

CHANGELOG.md

@@ -6,6 +6,12 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 
 ## [Unreleased]
 
+## [0.7.2] - 2019-03-31
+
+### Fixes
+- Fix minor issue with hg19 wrong blacklist url
+- Ensembl downloads over http instead of https (release 99 no longer has https)
+
 ## [0.7.1] - 2019-11-20
 
 ### Fixes

genomepy/__about__.py

@@ -1,3 +1,3 @@
 """Metadata"""
-__version__ = "0.7.1"
+__version__ = "0.7.2"
 __author__ = "Simon van Heeringen"

genomepy/plugins/blacklist.py

@@ -11,7 +11,8 @@ class BlacklistPlugin(Plugin):
         "ce10": base_url + "ce10-C.elegans/ce10-blacklist.bed.gz",
         "dm3": base_url + "dm3-D.melanogaster/dm3-blacklist.bed.gz",
         "hg38": base_url + "hg38-human/hg38.blacklist.bed.gz",
-        "hg19": base_url + "hg38-human/hg19.blacklist.bed.gz",
+        "hg19": base_url
+        + "hg19-human/wgEncodeHg19ConsensusSignalArtifactRegions.bed.gz",
         "mm9": base_url + "mm9-mouse/mm9-blacklist.bed.gz",
         "mm10": base_url + "mm10-mouse/mm10.blacklist.bed.gz",
     }

genomepy/provider.py

@@ -434,7 +434,7 @@ def get_genome_download_link(self, name, mask="soft", **kwargs):
 
         ftp_site = "ftp://ftp.ensemblgenomes.org/pub"
         if division == "vertebrates":
-            ftp_site = "https://ftp.ensembl.org/pub"
+            ftp_site = "http://ftp.ensembl.org/pub"
 
         version = self.version
         if kwargs.get("version", None):
@@ -510,7 +510,7 @@ def download_annotation(self, name, genome_dir, localname=None, **kwargs):
         # Get the base link depending on division
         ftp_site = "ftp://ftp.ensemblgenomes.org/pub"
         if division == "vertebrates":
-            ftp_site = "https://ftp.ensembl.org/pub"
+            ftp_site = "http://ftp.ensembl.org/pub"
 
         version = self.version
         if kwargs.get("version", None):

tests/test_2_links.py

@@ -30,7 +30,7 @@ def test_ensemblgenomes_genome_download_links():
     """
     p = genomepy.provider.ProviderBase.create("Ensembl")
 
-    for genome in ["AgamP4", "WBcel235"]:
+    for genome in ["Amel_4.5", "WBcel235"]:
         p.get_genome_download_link(genome)