updated to ensembl release 110; did some patching

popsim-consortium · Oct 25, 2023 · ce96648 · ce96648
1 parent a588724
commit ce96648
Show file tree

Hide file tree

Showing 17 changed files with 148 additions and 216 deletions.
diff --git a/maintenance/main.py b/maintenance/main.py
@@ -158,7 +158,10 @@ def black_format(code):
 
 
 def ensembl_stdpopsim_id(ensembl_id):
+    if ensembl_id == "canis_lupus_familiaris":
+        ensembl_id = "canis_familiaris"
     tmp = ensembl_id.split("_")[:2]
+    print(tmp, ensembl_id)
     sps_id = "".join([x[0:3].capitalize() for x in tmp])
     if len(sps_id) != 6:
         raise ValueError(f"Cannot extract six character id from {ensembl_id}")

diff --git a/stdpopsim/catalog/AnoCar/genome_data.py b/stdpopsim/catalog/AnoCar/genome_data.py
@@ -1,21 +1,20 @@
 # File autogenerated from Ensembl REST API. Do not edit.
 data = {
-    "assembly_accession": "GCA_000090745.1",
-    "assembly_name": "AnoCar2.0",
+    "assembly_accession": "GCA_000090745.2",
+    "assembly_name": "AnoCar2.0v2",
     "chromosomes": {
-        "1": {"length": 263920458, "synonyms": []},
-        "2": {"length": 199619895, "synonyms": []},
-        "3": {"length": 204416410, "synonyms": []},
-        "4": {"length": 156502444, "synonyms": []},
-        "5": {"length": 150641573, "synonyms": []},
-        "6": {"length": 80741955, "synonyms": []},
-        "LGa": {"length": 7025928, "synonyms": []},
-        "LGb": {"length": 3271537, "synonyms": []},
-        "LGc": {"length": 9478905, "synonyms": []},
-        "LGd": {"length": 1094478, "synonyms": []},
-        "LGf": {"length": 4257874, "synonyms": []},
-        "LGg": {"length": 424765, "synonyms": []},
-        "LGh": {"length": 248369, "synonyms": []},
-        "MT": {"length": 17223, "synonyms": []},
+        "1": {"length": 263920458, "synonyms": ["chr1"]},
+        "2": {"length": 199619895, "synonyms": ["chr2"]},
+        "3": {"length": 204416410, "synonyms": ["chr3"]},
+        "4": {"length": 156502444, "synonyms": ["chr4"]},
+        "5": {"length": 150641573, "synonyms": ["chr5"]},
+        "6": {"length": 80741955, "synonyms": ["chr6"]},
+        "a": {"length": 7025928, "synonyms": ["chrLGa"]},
+        "b": {"length": 3271537, "synonyms": ["chrLGb"]},
+        "c": {"length": 9478905, "synonyms": ["chrLGc"]},
+        "d": {"length": 1094478, "synonyms": ["chrLGd"]},
+        "f": {"length": 4257874, "synonyms": ["chrLGf"]},
+        "g": {"length": 424765, "synonyms": ["chrLGg"]},
+        "h": {"length": 248369, "synonyms": ["chrLGh"]},
     },
 }
diff --git a/stdpopsim/catalog/ApiMel/genome_data.py b/stdpopsim/catalog/ApiMel/genome_data.py
@@ -3,22 +3,22 @@
     "assembly_accession": "GCA_003254395.2",
     "assembly_name": "Amel_HAv3.1",
     "chromosomes": {
-        "CM009931.2": {"length": 27754200, "synonyms": ["NC_037638.1"]},
-        "CM009932.2": {"length": 16089512, "synonyms": ["NC_037639.1"]},
-        "CM009933.2": {"length": 13619445, "synonyms": ["NC_037640.1"]},
-        "CM009934.2": {"length": 13404451, "synonyms": ["NC_037641.1"]},
-        "CM009935.2": {"length": 13896941, "synonyms": ["NC_037642.1"]},
-        "CM009936.2": {"length": 17789102, "synonyms": ["NC_037643.1"]},
-        "CM009937.2": {"length": 14198698, "synonyms": ["NC_037644.1"]},
-        "CM009938.2": {"length": 12717210, "synonyms": ["NC_037645.1"]},
-        "CM009939.2": {"length": 12354651, "synonyms": ["NC_037646.1"]},
-        "CM009940.2": {"length": 12360052, "synonyms": ["NC_037647.1"]},
-        "CM009941.2": {"length": 16352600, "synonyms": ["NC_037648.1"]},
-        "CM009942.2": {"length": 11514234, "synonyms": ["NC_037649.1"]},
-        "CM009943.2": {"length": 11279722, "synonyms": ["NC_037650.1"]},
-        "CM009944.2": {"length": 10670842, "synonyms": ["NC_037651.1"]},
-        "CM009945.2": {"length": 9534514, "synonyms": ["NC_037652.1"]},
-        "CM009946.2": {"length": 7238532, "synonyms": ["NC_037653.1"]},
-        "CM009947.2": {"length": 16343, "synonyms": ["NC_001566.1", "MT"]},
+        "CM009931.2": {"length": 27754200, "synonyms": []},
+        "CM009932.2": {"length": 16089512, "synonyms": []},
+        "CM009933.2": {"length": 13619445, "synonyms": []},
+        "CM009934.2": {"length": 13404451, "synonyms": []},
+        "CM009935.2": {"length": 13896941, "synonyms": []},
+        "CM009936.2": {"length": 17789102, "synonyms": []},
+        "CM009937.2": {"length": 14198698, "synonyms": []},
+        "CM009938.2": {"length": 12717210, "synonyms": []},
+        "CM009939.2": {"length": 12354651, "synonyms": []},
+        "CM009940.2": {"length": 12360052, "synonyms": []},
+        "CM009941.2": {"length": 16352600, "synonyms": []},
+        "CM009942.2": {"length": 11514234, "synonyms": []},
+        "CM009943.2": {"length": 11279722, "synonyms": []},
+        "CM009944.2": {"length": 10670842, "synonyms": []},
+        "CM009945.2": {"length": 9534514, "synonyms": []},
+        "CM009946.2": {"length": 7238532, "synonyms": []},
+        "CM009947.2": {"length": 16343, "synonyms": []},
     },
 }
diff --git a/stdpopsim/catalog/CaeEle/genome_data.py b/stdpopsim/catalog/CaeEle/genome_data.py
@@ -1,7 +1,7 @@
 # File autogenerated from Ensembl REST API. Do not edit.
 data = {
     "assembly_accession": "GCA_000002985.3",
-    "assembly_name": "ce11",
+    "assembly_name": "WBcel235",
     "chromosomes": {
         "I": {"length": 15072434, "synonyms": []},
         "II": {"length": 15279421, "synonyms": []},

diff --git a/stdpopsim/catalog/CanFam/genome_data.py b/stdpopsim/catalog/CanFam/genome_data.py
@@ -1,47 +1,47 @@
 # File autogenerated from Ensembl REST API. Do not edit.
 data = {
-    "assembly_accession": "GCA_000002285.2",
-    "assembly_name": "CanFam3.1",
+    "assembly_accession": "GCA_014441545.1",
+    "assembly_name": "ROS_Cfam_1.0",
     "chromosomes": {
-        "1": {"length": 122678785, "synonyms": []},
-        "2": {"length": 85426708, "synonyms": []},
-        "3": {"length": 91889043, "synonyms": []},
-        "4": {"length": 88276631, "synonyms": []},
-        "5": {"length": 88915250, "synonyms": []},
-        "6": {"length": 77573801, "synonyms": []},
-        "7": {"length": 80974532, "synonyms": []},
-        "8": {"length": 74330416, "synonyms": []},
-        "9": {"length": 61074082, "synonyms": []},
-        "10": {"length": 69331447, "synonyms": []},
-        "11": {"length": 74389097, "synonyms": []},
-        "12": {"length": 72498081, "synonyms": []},
-        "13": {"length": 63241923, "synonyms": []},
-        "14": {"length": 60966679, "synonyms": []},
-        "15": {"length": 64190966, "synonyms": []},
-        "16": {"length": 59632846, "synonyms": []},
-        "17": {"length": 64289059, "synonyms": []},
-        "18": {"length": 55844845, "synonyms": []},
-        "19": {"length": 53741614, "synonyms": []},
-        "20": {"length": 58134056, "synonyms": []},
-        "21": {"length": 50858623, "synonyms": []},
-        "22": {"length": 61439934, "synonyms": []},
-        "23": {"length": 52294480, "synonyms": []},
-        "24": {"length": 47698779, "synonyms": []},
-        "25": {"length": 51628933, "synonyms": []},
-        "26": {"length": 38964690, "synonyms": []},
-        "27": {"length": 45876710, "synonyms": []},
-        "28": {"length": 41182112, "synonyms": []},
-        "29": {"length": 41845238, "synonyms": []},
-        "30": {"length": 40214260, "synonyms": []},
-        "31": {"length": 39895921, "synonyms": []},
-        "32": {"length": 38810281, "synonyms": []},
-        "33": {"length": 31377067, "synonyms": []},
-        "34": {"length": 42124431, "synonyms": []},
-        "35": {"length": 26524999, "synonyms": []},
-        "36": {"length": 30810995, "synonyms": []},
-        "37": {"length": 30902991, "synonyms": []},
-        "38": {"length": 23914537, "synonyms": []},
-        "X": {"length": 123869142, "synonyms": []},
-        "MT": {"length": 16727, "synonyms": []},
+        "1": {"length": 123313939, "synonyms": []},
+        "2": {"length": 86187811, "synonyms": []},
+        "3": {"length": 92870237, "synonyms": []},
+        "4": {"length": 89007665, "synonyms": []},
+        "5": {"length": 89573405, "synonyms": []},
+        "6": {"length": 78268176, "synonyms": []},
+        "7": {"length": 81039452, "synonyms": []},
+        "8": {"length": 75260524, "synonyms": []},
+        "9": {"length": 62002293, "synonyms": []},
+        "10": {"length": 70361000, "synonyms": []},
+        "11": {"length": 75541347, "synonyms": []},
+        "12": {"length": 73497294, "synonyms": []},
+        "13": {"length": 64037277, "synonyms": []},
+        "14": {"length": 61043064, "synonyms": []},
+        "15": {"length": 65200600, "synonyms": []},
+        "16": {"length": 62021213, "synonyms": []},
+        "17": {"length": 65471548, "synonyms": []},
+        "18": {"length": 56883407, "synonyms": []},
+        "19": {"length": 55265241, "synonyms": []},
+        "20": {"length": 58896461, "synonyms": []},
+        "21": {"length": 52140716, "synonyms": []},
+        "22": {"length": 62106979, "synonyms": []},
+        "23": {"length": 53282923, "synonyms": []},
+        "24": {"length": 48838997, "synonyms": []},
+        "25": {"length": 51941001, "synonyms": []},
+        "26": {"length": 40674351, "synonyms": []},
+        "27": {"length": 46248802, "synonyms": []},
+        "28": {"length": 41862212, "synonyms": []},
+        "29": {"length": 42049852, "synonyms": []},
+        "30": {"length": 40414903, "synonyms": []},
+        "31": {"length": 39518933, "synonyms": []},
+        "32": {"length": 39023732, "synonyms": []},
+        "33": {"length": 31649084, "synonyms": []},
+        "34": {"length": 42263871, "synonyms": []},
+        "35": {"length": 26942268, "synonyms": []},
+        "36": {"length": 31065185, "synonyms": []},
+        "37": {"length": 30932408, "synonyms": []},
+        "38": {"length": 24102048, "synonyms": []},
+        "X": {"length": 127069619, "synonyms": []},
+        "Y": {"length": 3937623, "synonyms": []},
     },
 }
diff --git a/stdpopsim/catalog/CanFam/species.py b/stdpopsim/catalog/CanFam/species.py
@@ -152,7 +152,7 @@
 
 _species = stdpopsim.Species(
     id="CanFam",
-    ensembl_id="canis_familiaris",
+    ensembl_id="canis_lupus_familiaris",
     name="Canis familiaris",
     common_name="Dog",
     genome=_genome,

diff --git a/stdpopsim/catalog/DroMel/genome_data.py b/stdpopsim/catalog/DroMel/genome_data.py
@@ -1,7 +1,7 @@
 # File autogenerated from Ensembl REST API. Do not edit.
 data = {
     "assembly_accession": "GCA_000001215.4",
-    "assembly_name": "BDGP6.32",
+    "assembly_name": "BDGP6.46",
     "chromosomes": {
         "2L": {"length": 23513712, "synonyms": []},
         "2R": {"length": 25286936, "synonyms": []},

diff --git a/stdpopsim/catalog/DroSec/genome_data.py b/stdpopsim/catalog/DroSec/genome_data.py
@@ -1,13 +1,6 @@
-# File created manually from https://www.ncbi.nlm.nih.gov/assembly/GCF_004382195.1
+# File autogenerated from Ensembl REST API. Do not edit.
 data = {
-    "assembly_accession": "GCA_004382195.1",
-    "assembly_name": "ASM438219v1",
-    "chromosomes": {
-        "2L": {"length": 24956976, "synonyms": []},
-        "2R": {"length": 21536224, "synonyms": []},
-        "3L": {"length": 28131630, "synonyms": []},
-        "3R": {"length": 30464902, "synonyms": []},
-        "X": {"length": 22909512, "synonyms": []},
-        "4": {"length": 1277805, "synonyms": []},
-    },
+    "assembly_accession": "GCA_000005215.1",
+    "assembly_name": "dsec_caf1",
+    "chromosomes": {},
 }
diff --git a/stdpopsim/catalog/GasAcu/genome_data.py b/stdpopsim/catalog/GasAcu/genome_data.py
@@ -1,30 +1,2 @@
 # File autogenerated from Ensembl REST API. Do not edit.
-data = {
-    "assembly_accession": "GCF_016920845.1",
-    "assembly_name": "GAculeatus_UGA_version5",
-    "chromosomes": {
-        "1": {"length": 29619991, "synonyms": []},
-        "2": {"length": 23686546, "synonyms": []},
-        "3": {"length": 17759012, "synonyms": []},
-        "4": {"length": 34181212, "synonyms": []},
-        "5": {"length": 15550311, "synonyms": []},
-        "6": {"length": 18825451, "synonyms": []},
-        "7": {"length": 30776923, "synonyms": []},
-        "8": {"length": 20553084, "synonyms": []},
-        "9": {"length": 20843631, "synonyms": []},
-        "10": {"length": 17985176, "synonyms": []},
-        "11": {"length": 17651971, "synonyms": []},
-        "12": {"length": 20694444, "synonyms": []},
-        "13": {"length": 20748428, "synonyms": []},
-        "14": {"length": 16147532, "synonyms": []},
-        "15": {"length": 17318724, "synonyms": []},
-        "16": {"length": 19507025, "synonyms": []},
-        "17": {"length": 20195758, "synonyms": []},
-        "18": {"length": 15939336, "synonyms": []},
-        "19": {"length": 20580295, "synonyms": []},
-        "20": {"length": 20445003, "synonyms": []},
-        "21": {"length": 17421465, "synonyms": []},
-        "Y": {"length": 15859692, "synonyms": []},
-        "MT": {"length": 16543, "synonyms": []},
-    },
-}
+data = {"assembly_accession": None, "assembly_name": "BROAD S1", "chromosomes": {}}
diff --git a/stdpopsim/catalog/GasAcu/species.py b/stdpopsim/catalog/GasAcu/species.py
@@ -116,7 +116,7 @@
 
 _species = stdpopsim.Species(
     id="GasAcu",
-    ensembl_id="9307941",
+    ensembl_id="gasterosteus_aculeatus",
     name="Gasterosteus aculeatus",
     common_name="Three-spined stickleback",
     genome=_genome,

diff --git a/stdpopsim/catalog/HelMel/genome_data.py b/stdpopsim/catalog/HelMel/genome_data.py
@@ -1,37 +1,6 @@
 # File autogenerated from Ensembl REST API. Do not edit.
-#
-# Manually edited. See
-# https://github.com/popsim-consortium/stdpopsim/issues/835#issuecomment-815854055
-#
-# Data source:
-# http://ensembl.lepbase.org/Heliconius_melpomene_melpomene_hmel25/Info/Index
-#
-# Chromosomes lengths from Davey et al. 2017
-#
 data = {
-    "assembly_accession": None,  # No accession number available
-    "assembly_name": "Hmel2.5",
-    "chromosomes": {
-        "1": {"length": 17206585, "synonyms": []},
-        "2": {"length": 9045316, "synonyms": []},
-        "3": {"length": 10541528, "synonyms": []},
-        "4": {"length": 9662098, "synonyms": []},
-        "5": {"length": 9908586, "synonyms": []},
-        "6": {"length": 14054175, "synonyms": []},
-        "7": {"length": 14308859, "synonyms": []},
-        "8": {"length": 9320449, "synonyms": []},
-        "9": {"length": 8708747, "synonyms": []},
-        "10": {"length": 17965481, "synonyms": []},
-        "11": {"length": 11759272, "synonyms": []},
-        "12": {"length": 16327298, "synonyms": []},
-        "13": {"length": 18127314, "synonyms": []},
-        "14": {"length": 9174305, "synonyms": []},
-        "15": {"length": 10235750, "synonyms": []},
-        "16": {"length": 10083215, "synonyms": []},
-        "17": {"length": 14773299, "synonyms": []},
-        "18": {"length": 16803890, "synonyms": []},
-        "19": {"length": 16399344, "synonyms": []},
-        "20": {"length": 14871695, "synonyms": []},
-        "21": {"length": 13359691, "synonyms": []},
-    },
+    "assembly_accession": "GCA_000313835.1",
+    "assembly_name": "Hmel1",
+    "chromosomes": {},
 }
diff --git a/stdpopsim/catalog/HomSap/genome_data.py b/stdpopsim/catalog/HomSap/genome_data.py
@@ -1,7 +1,7 @@
 # File autogenerated from Ensembl REST API. Do not edit.
 data = {
-    "assembly_accession": "GCA_000001405.28",
-    "assembly_name": "GRCh38.p13",
+    "assembly_accession": "GCA_000001405.29",
+    "assembly_name": "GRCh38.p14",
     "chromosomes": {
         "1": {"length": 248956422, "synonyms": ["chr1"]},
         "2": {"length": 242193529, "synonyms": ["chr2"]},

diff --git a/stdpopsim/catalog/PanTro/genome_data.py b/stdpopsim/catalog/PanTro/genome_data.py
@@ -3,30 +3,31 @@
     "assembly_accession": "GCA_000001515.5",
     "assembly_name": "Pan_tro_3.0",
     "chromosomes": {
-        "1": {"length": 228573443, "synonyms": ["chr1"]},
-        "2A": {"length": 111504155, "synonyms": ["chr2A"]},
-        "2B": {"length": 133216015, "synonyms": ["chr2B"]},
-        "3": {"length": 202621043, "synonyms": ["chr3"]},
-        "4": {"length": 194502333, "synonyms": ["chr4"]},
-        "5": {"length": 181907262, "synonyms": ["chr5"]},
-        "6": {"length": 175400573, "synonyms": ["chr6"]},
-        "7": {"length": 166211670, "synonyms": ["chr7"]},
-        "8": {"length": 147911612, "synonyms": ["chr8"]},
-        "9": {"length": 116767853, "synonyms": ["chr9"]},
-        "10": {"length": 135926727, "synonyms": ["chr10"]},
-        "11": {"length": 135753878, "synonyms": ["chr11"]},
-        "12": {"length": 137163284, "synonyms": ["chr12"]},
-        "13": {"length": 100452976, "synonyms": ["chr13"]},
-        "14": {"length": 91965084, "synonyms": ["chr14"]},
-        "15": {"length": 83230942, "synonyms": ["chr15"]},
-        "16": {"length": 81586097, "synonyms": ["chr16"]},
-        "17": {"length": 83181570, "synonyms": ["chr17"]},
-        "18": {"length": 78221452, "synonyms": ["chr18"]},
-        "19": {"length": 61309027, "synonyms": ["chr19"]},
-        "20": {"length": 66533130, "synonyms": ["chr20"]},
-        "21": {"length": 33445071, "synonyms": ["chr21"]},
-        "22": {"length": 37823149, "synonyms": ["chr22"]},
-        "X": {"length": 155549662, "synonyms": ["chrX"]},
-        "Y": {"length": 26350515, "synonyms": ["chrY"]},
+        "1": {"length": 228573443, "synonyms": []},
+        "2A": {"length": 111504155, "synonyms": []},
+        "2B": {"length": 133216015, "synonyms": []},
+        "3": {"length": 202621043, "synonyms": []},
+        "4": {"length": 194502333, "synonyms": []},
+        "5": {"length": 181907262, "synonyms": []},
+        "6": {"length": 175400573, "synonyms": []},
+        "7": {"length": 166211670, "synonyms": []},
+        "8": {"length": 147911612, "synonyms": []},
+        "9": {"length": 116767853, "synonyms": []},
+        "10": {"length": 135926727, "synonyms": []},
+        "11": {"length": 135753878, "synonyms": []},
+        "12": {"length": 137163284, "synonyms": []},
+        "13": {"length": 100452976, "synonyms": []},
+        "14": {"length": 91965084, "synonyms": []},
+        "15": {"length": 83230942, "synonyms": []},
+        "16": {"length": 81586097, "synonyms": []},
+        "17": {"length": 83181570, "synonyms": []},
+        "18": {"length": 78221452, "synonyms": []},
+        "19": {"length": 61309027, "synonyms": []},
+        "20": {"length": 66533130, "synonyms": []},
+        "21": {"length": 33445071, "synonyms": []},
+        "22": {"length": 37823149, "synonyms": []},
+        "X": {"length": 155549662, "synonyms": []},
+        "Y": {"length": 26350515, "synonyms": []},
+        "MT": {"length": 16554, "synonyms": []},
     },
 }