Add support for Illumina NextSeq 2000 GEO platforms

PavlidisLab · Jan 12, 2023 · c94118f · c94118f
1 parent 1cc7af9
commit c94118f
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Showing 2 changed files with 10 additions and 1 deletion.
diff --git a/rnaseq_pipeline/sources/geo.py b/rnaseq_pipeline/sources/geo.py
@@ -47,7 +47,7 @@ def match_geo_platform(geo_platform):
         return BgiPlatform(geo_platform_title.split(' ')[0])
 
     # Illumina HiSeq X and NextSeq 550 platforms are not prefixed with Illumina
-    illumina_regex = [r'Illumina (.+) \(.+\)', r'(HiSeq X .+) \(.+\)', r'(NextSeq 550) \(.+\)']
+    illumina_regex = [r'Illumina (.+) \(.+\)', r'(HiSeq X .+) \(.+\)', r'(NextSeq 550) \(.+\)', r'(NextSeq 2000) \(.+\)']
 
     for r in illumina_regex:
         illumina_match = re.match(r, geo_platform_title)

diff --git a/tests/test_geo.py b/tests/test_geo.py
@@ -0,0 +1,9 @@
+from rnaseq_pipeline.sources.geo import match_geo_platform
+from rnaseq_pipeline.platforms import IlluminaPlatform
+
+def test_parse_illumina_platform():
+    platform = match_geo_platform('GPL30172')
+    assert isinstance(platform, IlluminaPlatform)
+    assert platform.name == 'Illumina'
+    assert platform.instrument == 'NextSeq 2000'
+