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feat: add ucsc browser url to genomes built from ncbi (#159)
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@hunterckx
hunterckx committed Nov 16, 2024
1 parent b0e23c9 commit 9acf716
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Showing 2 changed files with 32 additions and 23 deletions.
13 changes: 11 additions & 2 deletions files/build-genomes-files-from-ncbi.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,8 @@
"Coccidioides immitis"
]

ASSEMBLIES_URL = "https://hgdownload.soe.ucsc.edu/hubs/BRC/assemblyList.json"

OUTPUT_PATH = "files/source/genomes-from-ncbi.tsv"

def build_taxonomy_request_body(taxa):
Expand Down Expand Up @@ -45,6 +47,7 @@ def get_genome_row(genome_info):
"coverage": genome_info["assembly_stats"].get("genome_coverage"),
"gcPercent": genome_info["assembly_stats"]["gc_percent"],
"annotationStatus": genome_info["annotation_info"].get("status"),
"pairedAccession": genome_info["paired_accession"],
}

def get_genomes_df(tax_ids):
Expand All @@ -53,9 +56,15 @@ def get_genomes_df(tax_ids):
def build_genomes_files():
print("Building files")

df = get_genomes_df(get_tax_ids(TAXA))
genomes_source_df = get_genomes_df(get_tax_ids(TAXA))
assemblies_df = pd.DataFrame(requests.get(ASSEMBLIES_URL).json()["data"])[["ucscBrowser", "genBank", "refSeq"]]

gen_bank_merge_df = genomes_source_df.merge(assemblies_df, how="left", left_on="pairedAccession", right_on="genBank")
ref_seq_merge_df = genomes_source_df.merge(assemblies_df, how="left", left_on="accession", right_on="refSeq")

result_df = gen_bank_merge_df.combine_first(ref_seq_merge_df)

df.to_csv(OUTPUT_PATH, index=False, sep="\t")
result_df.to_csv(OUTPUT_PATH, index=False, sep="\t")

print(f"Wrote to {OUTPUT_PATH}")

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42 changes: 21 additions & 21 deletions files/source/genomes-from-ncbi.tsv
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@@ -1,21 +1,21 @@
taxon taxonomyId accession isRef level chromosomeCount length scaffoldCount scaffoldN50 scaffoldL50 coverage gcPercent annotationStatus
Mycobacterium tuberculosis H37Rv 83332 GCF_000195955.2 True Complete Genome 1.0 4411532 1 4411532 1 65.5
Plasmodium falciparum 3D7 36329 GCF_000002765.6 True Complete Genome 14.0 23292622 14 1687656 5 100.0x 19.5 Full annotation
Plasmodium yoelii 5861 GCF_900002385.2 True Complete Genome 14.0 23043114 14 2046250 5 100.0x 21.5 Full annotation
Coccidioides posadasii str. Silveira 443226 GCF_018416015.2 True Complete Genome 9.0 28193268 9 8079863 2 475.0x 46.5 Full annotation
Plasmodium vinckei vinckei 54757 GCF_900681995.1 True Complete Genome 14.0 18338688 14 1692345 5 155.0x 23.0 Full annotation
Toxoplasma gondii ME49 508771 GCF_000006565.2 True Chromosome 14.0 65633124 2276 4973582 6 26.5x 52.5
Anopheles gambiae 7165 GCF_943734735.2 True Chromosome 3.0 264451381 190 99149756 2 54.0x 44.5 Full annotation
Plasmodium vivax 5855 GCF_000002415.2 True Chromosome 14.0 27007701 2747 1678596 6 42.5 Full annotation
Culex pipiens pallens 42434 GCF_016801865.2 True Chromosome 3.0 566339288 289 186194774 2 250.0x 37.0 Full annotation
Coccidioides immitis RS 246410 GCF_000149335.2 True Scaffold 28947925 6 4323945 3 46.0 Full annotation
Mycobacterium tuberculosis H37Rv 83332 GCF_000277735.2 False Complete Genome 1.0 4411709 1 4411709 1 65.5
Mycobacterium tuberculosis 1773 GCF_030566675.1 False Complete Genome 1.0 4516435 1 4516435 1 20.0x 65.5
Mycobacterium tuberculosis 1773 GCF_963525475.1 False Complete Genome 1.0 4469156 1 4469156 1 100.0x 65.5
Mycobacterium tuberculosis 1773 GCF_017901095.1 False Complete Genome 1.0 4459449 1 4459449 1 111.0x 65.5
Mycobacterium tuberculosis 1773 GCF_030566105.1 False Complete Genome 1.0 4459087 1 4459087 1 20.0x 65.0
Mycobacterium tuberculosis 1773 GCF_033124885.1 False Complete Genome 1.0 4456234 1 4456234 1 257.0x 65.5
Mycobacterium tuberculosis 1773 GCF_014899985.1 False Complete Genome 1.0 4450340 1 4450340 1 92.0x 65.5
Mycobacterium tuberculosis 1773 GCF_040208995.1 False Complete Genome 1.0 4448271 1 4448271 1 208.6x 65.5
Mycobacterium tuberculosis 1773 GCF_014899965.1 False Complete Genome 1.0 4447644 1 4447644 1 51.0x 65.5
Mycobacterium tuberculosis 1773 GCF_040208985.1 False Complete Genome 1.0 4445673 1 4445673 1 232.2x 65.5
taxon taxonomyId accession isRef level chromosomeCount length scaffoldCount scaffoldN50 scaffoldL50 coverage gcPercent annotationStatus pairedAccession ucscBrowser genBank refSeq
Mycobacterium tuberculosis H37Rv 83332 GCF_000195955.2 True Complete Genome 1.0 4411532 1 4411532 1 65.5 GCA_000195955.2
Plasmodium falciparum 3D7 36329 GCF_000002765.6 True Complete Genome 14.0 23292622 14 1687656 5 100.0x 19.5 Full annotation GCA_000002765.3 https://genome.ucsc.edu/h/GCF_000002765.5 GCA_000002765.3 GCF_000002765.5
Plasmodium yoelii 5861 GCF_900002385.2 True Complete Genome 14.0 23043114 14 2046250 5 100.0x 21.5 Full annotation GCA_900002385.2 https://genome.ucsc.edu/h/GCF_900002385.2 GCA_900002385.2 GCF_900002385.2
Coccidioides posadasii str. Silveira 443226 GCF_018416015.2 True Complete Genome 9.0 28193268 9 8079863 2 475.0x 46.5 Full annotation GCA_018416015.2 https://genome.ucsc.edu/h/GCA_018416015.2 GCA_018416015.2 GCF_018416015.1
Plasmodium vinckei vinckei 54757 GCF_900681995.1 True Complete Genome 14.0 18338688 14 1692345 5 155.0x 23.0 Full annotation GCA_900681995.1 https://genome.ucsc.edu/h/GCF_900681995.1 GCA_900681995.1 GCF_900681995.1
Toxoplasma gondii ME49 508771 GCF_000006565.2 True Chromosome 14.0 65633124 2276 4973582 6 26.5x 52.5 GCA_000006565.2 https://genome.ucsc.edu/h/GCF_000006565.2 GCA_000006565.2 GCF_000006565.2
Anopheles gambiae 7165 GCF_943734735.2 True Chromosome 3.0 264451381 190 99149756 2 54.0x 44.5 Full annotation GCA_943734735.2 https://genome.ucsc.edu/h/GCF_943734735.2 GCA_943734735.2 GCF_943734735.2
Plasmodium vivax 5855 GCF_000002415.2 True Chromosome 14.0 27007701 2747 1678596 6 42.5 Full annotation GCA_000002415.2 https://genome.ucsc.edu/h/GCF_000002415.2 GCA_000002415.2 GCF_000002415.2
Culex pipiens pallens 42434 GCF_016801865.2 True Chromosome 3.0 566339288 289 186194774 2 250.0x 37.0 Full annotation GCA_016801865.2
Coccidioides immitis RS 246410 GCF_000149335.2 True Scaffold 28947925 6 4323945 3 46.0 Full annotation GCA_000149335.2 https://genome.ucsc.edu/h/GCF_000149335.2 GCA_000149335.2 GCF_000149335.2
Mycobacterium tuberculosis H37Rv 83332 GCF_000277735.2 False Complete Genome 1.0 4411709 1 4411709 1 65.5 GCA_000277735.2
Mycobacterium tuberculosis 1773 GCF_030566675.1 False Complete Genome 1.0 4516435 1 4516435 1 20.0x 65.5 GCA_030566675.1
Mycobacterium tuberculosis 1773 GCF_963525475.1 False Complete Genome 1.0 4469156 1 4469156 1 100.0x 65.5 GCA_963525475.1
Mycobacterium tuberculosis 1773 GCF_017901095.1 False Complete Genome 1.0 4459449 1 4459449 1 111.0x 65.5 GCA_017901095.1
Mycobacterium tuberculosis 1773 GCF_030566105.1 False Complete Genome 1.0 4459087 1 4459087 1 20.0x 65.0 GCA_030566105.1
Mycobacterium tuberculosis 1773 GCF_033124885.1 False Complete Genome 1.0 4456234 1 4456234 1 257.0x 65.5 GCA_033124885.1
Mycobacterium tuberculosis 1773 GCF_014899985.1 False Complete Genome 1.0 4450340 1 4450340 1 92.0x 65.5 GCA_014899985.1
Mycobacterium tuberculosis 1773 GCF_040208995.1 False Complete Genome 1.0 4448271 1 4448271 1 208.6x 65.5 GCA_040208995.1
Mycobacterium tuberculosis 1773 GCF_014899965.1 False Complete Genome 1.0 4447644 1 4447644 1 51.0x 65.5 GCA_014899965.1
Mycobacterium tuberculosis 1773 GCF_040208985.1 False Complete Genome 1.0 4445673 1 4445673 1 232.2x 65.5 GCA_040208985.1

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