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updated to ensembl release 110; did some patching #1536

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updated to ensembl release 110; did some patching #1536

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ce96648
updated to ensembl release 110; did some patching
andrewkern Oct 25, 2023
8962f3e
put back in manually added info
petrelharp Dec 12, 2023
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3 changes: 3 additions & 0 deletions maintenance/main.py
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Expand Up @@ -158,7 +158,10 @@ def black_format(code):


def ensembl_stdpopsim_id(ensembl_id):
if ensembl_id == "canis_lupus_familiaris":
ensembl_id = "canis_familiaris"
Comment on lines +161 to +162
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this is a horrible, terrible thing that i've done, but i've done it because this single ensembl shift disagrees with all the other ensembl ids....

tmp = ensembl_id.split("_")[:2]
print(tmp, ensembl_id)
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stray print

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oops-- debugging

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}")
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31 changes: 15 additions & 16 deletions stdpopsim/catalog/AnoCar/genome_data.py
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@@ -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"]},
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wtf, the previous chromosome names (e.g., LGa) are not included in the synonyms. I vote to leave well enough alone there. But - why no mitochondria?

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And gee, the mitochondria shows on ensembl:
Screenshot from 2023-12-12 09-15-25

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ah I see what happened here: consulting http://rest.ensembl.org/info/assembly/anolis_carolinensis they've removed the mitochondria from the "karyotype" list of chromosomes, but it's still there, at the end of a list of a bajillion tiny contigs:

  - 
    coord_system: primary_assembly
    length: 17223
    name: MT

},
}
34 changes: 17 additions & 17 deletions stdpopsim/catalog/ApiMel/genome_data.py
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Expand Up @@ -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"]},
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ensembl dropping the MT label here

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@petrelharp petrelharp Dec 12, 2023 •
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and those synonyms are still there, labeled "RefSeq" or "GenBank":

  - 
    coord_system: primary_assembly
    length: 16343
    name: CM009947.2
    synonyms: 
      - 
        dbname: ensembl_internal_synonym
        name: NC_001566
      - 
        dbname: GenBank
        name: MT
      - 
        dbname: INSDC
        name: CM009947.2
      - 
        dbname: ensembl_internal_synonym
        name: CM009947
      - 
        dbname: RefSeq
        name: NC_001566.1

"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": []},
},
}
2 changes: 1 addition & 1 deletion stdpopsim/catalog/CaeEle/genome_data.py
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@@ -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": []},
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84 changes: 42 additions & 42 deletions stdpopsim/catalog/CanFam/genome_data.py
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@@ -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": []},
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Looks like the chromosome lengths changed between these two builds of CanFam, and new build doesn't have a mitochondrial genome. We probably want to stick with old version to avoid conflicts with recombination map.

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Hm - unlike in other species, it appears to legit not have MT any more.

"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": []},
},
}
2 changes: 1 addition & 1 deletion stdpopsim/catalog/CanFam/species.py
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Expand Up @@ -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,
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2 changes: 1 addition & 1 deletion stdpopsim/catalog/DroMel/genome_data.py
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# 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": []},
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30 changes: 1 addition & 29 deletions stdpopsim/catalog/GasAcu/genome_data.py
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# 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": {}}
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uh-oh, what happened to this one?

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wow that's not good

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it looks to have all the info there: http://rest.ensembl.org/info/assembly/gasterosteus_aculeatus?synonyms=1

2 changes: 1 addition & 1 deletion stdpopsim/catalog/GasAcu/species.py
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Expand Up @@ -116,7 +116,7 @@

_species = stdpopsim.Species(
id="GasAcu",
ensembl_id="9307941",
ensembl_id="gasterosteus_aculeatus",
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perhaps this is why the assembly dissappeared?

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no, the original ensembl_id was incompatible with the REST API and the maintenance script...

name="Gasterosteus aculeatus",
common_name="Three-spined stickleback",
genome=_genome,
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4 changes: 2 additions & 2 deletions stdpopsim/catalog/HomSap/genome_data.py
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@@ -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"]},
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51 changes: 26 additions & 25 deletions stdpopsim/catalog/PanTro/genome_data.py
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Expand Up @@ -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": []},
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looks like they just removed those synonyms, oh well

},
}
57 changes: 26 additions & 31 deletions stdpopsim/catalog/PonAbe/genome_data.py
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@@ -1,36 +1,31 @@
# File autogenerated from Ensembl REST API.
# WARNING: autogenerated file has been edited!
# File autogenerated from Ensembl REST API. Do not edit.
data = {
"assembly_accession": "GCA_002880775.3",
"assembly_name": "ponAbe3", # Also known as Susie_PABv2.
"assembly_name": "Susie_PABv2",
"chromosomes": {
"1": {"length": 227913704, "synonyms": []},
# Capitalisation of 2A/2B changed from the previous assembly,
# so the old names are here as synonyms.
"2A": {"length": 109511694, "synonyms": ["2a", "chr2a"]},
"2B": {"length": 129937803, "synonyms": ["2b", "chr2b"]},
"3": {"length": 193656255, "synonyms": []},
"4": {"length": 189387572, "synonyms": []},
"5": {"length": 179185813, "synonyms": []},
"6": {"length": 169501136, "synonyms": []},
"7": {"length": 145408105, "synonyms": []},
"8": {"length": 144036388, "synonyms": []},
"9": {"length": 112206110, "synonyms": []},
"10": {"length": 132178492, "synonyms": []},
"11": {"length": 128122151, "synonyms": []},
"12": {"length": 132184051, "synonyms": []},
"13": {"length": 98475126, "synonyms": []},
"14": {"length": 88963417, "synonyms": []},
"15": {"length": 82547911, "synonyms": []},
"16": {"length": 68237989, "synonyms": []},
"17": {"length": 75914007, "synonyms": []},
"18": {"length": 75923960, "synonyms": []},
"19": {"length": 57575784, "synonyms": []},
"20": {"length": 60841859, "synonyms": []},
"21": {"length": 34683425, "synonyms": []},
"22": {"length": 35308119, "synonyms": []},
"X": {"length": 151242693, "synonyms": []},
# Mitochondria absent in ponAbe3, so length taken from ponAbe2.
"MT": {"length": 16499, "synonyms": []},
"1": {"length": 227913704, "synonyms": ["chr1"]},
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looks like we need to stick in this manually again?

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nope - it's there, just not listed in the karyotype:

  - 
    coord_system: primary_assembly
    length: 16499
    name: MT

"2A": {"length": 109511694, "synonyms": ["chr2A"]},
"2B": {"length": 129937803, "synonyms": ["chr2B"]},
"3": {"length": 193656255, "synonyms": ["chr3"]},
"4": {"length": 189387572, "synonyms": ["chr4"]},
"5": {"length": 179185813, "synonyms": ["chr5"]},
"6": {"length": 169501136, "synonyms": ["chr6"]},
"7": {"length": 145408105, "synonyms": ["chr7"]},
"8": {"length": 144036388, "synonyms": ["chr8"]},
"9": {"length": 112206110, "synonyms": ["chr9"]},
"10": {"length": 132178492, "synonyms": ["chr10"]},
"11": {"length": 128122151, "synonyms": ["chr11"]},
"12": {"length": 132184051, "synonyms": ["chr12"]},
"13": {"length": 98475126, "synonyms": ["chr13"]},
"14": {"length": 88963417, "synonyms": ["chr14"]},
"15": {"length": 82547911, "synonyms": ["chr15"]},
"16": {"length": 68237989, "synonyms": ["chr16"]},
"17": {"length": 75914007, "synonyms": ["chr17"]},
"18": {"length": 75923960, "synonyms": ["chr18"]},
"19": {"length": 57575784, "synonyms": ["chr19"]},
"20": {"length": 60841859, "synonyms": ["chr20"]},
"21": {"length": 34683425, "synonyms": ["chr21"]},
"22": {"length": 35308119, "synonyms": ["chr22"]},
"X": {"length": 151242693, "synonyms": ["chrX"]},
},
}
6 changes: 3 additions & 3 deletions stdpopsim/catalog/StrAga/genome_data.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
# File autogenerated from Ensembl REST API. Do not edit.
data = {
"assembly_accession": "GCA_000689235.1",
"assembly_name": "GBCO_p1",
"chromosomes": {"1": {"length": 2065074, "synonyms": ["I"]}},
"assembly_accession": "GCA_001017915.1",
"assembly_name": "ASM101791v1",
"chromosomes": {},
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another empty one?

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yep - the current build for this has no chromosome-level assembly

}
2 changes: 1 addition & 1 deletion stdpopsim/catalog/StrAga/species.py
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Original file line number Diff line number Diff line change
Expand Up @@ -93,7 +93,7 @@

_species = stdpopsim.Species(
id="StrAga",
ensembl_id="NA",
ensembl_id="streptococcus_agalactiae_GCA_001017915",
name="Streptococcus agalactiae",
common_name="Group B Streptococcus",
genome=_genome,
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2 changes: 1 addition & 1 deletion stdpopsim/catalog/ensembl_info.py
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Original file line number Diff line number Diff line change
@@ -1,2 +1,2 @@
# File autogenerated from Ensembl REST API. Do not edit.
release = 103
release = 110
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