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Commit 12b71e87 authored by Clara Moreno's avatar Clara Moreno
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Liens fonctionne car xref = cog donc https://www.ncbi.nlm.nih.gov/research/cog/cog/...

Renvoie dans l'html la liste mais pas le liens directement. Donc quelques modifications a faire. 
J'ai mis d'autres liens au cas ou on a un GFF qui a besoin de lien NCBI, Uniprot ou Ensembl. 

Ps : J'ai réussie a installé Busco, je l'avais deja fait j'ai repris l'ancien terminal. mais le code fonctionne pas vraiment. Pour tester les liens il faut mettre en commentaire les parties sur Busco  
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......@@ -47,22 +47,23 @@ def fusions_stat(count, avg):
return combined_df
#LIEN : marche pas il faut completer
def liens(feature):
base_urls = {
"gene": "https://www.ncbi.nlm.nih.gov/gene/",
"mRNA": "https://www.ncbi.nlm.nih.gov/nuccore/",
"CDS": "https://www.ncbi.nlm.nih.gov/protein/",
"exon": "https://www.ncbi.nlm.nih.gov/nuccore/",
"ncRNA": "https://www.ncbi.nlm.nih.gov/nuccore/",
"rRNA": "https://www.ncbi.nlm.nih.gov/nuccore/",
"tRNA": "https://www.ncbi.nlm.nih.gov/nuccore/"
}
if feature.featuretype in base_urls:
identifier = feature.attributes.get("ID", feature.attributes.get("db_xref", [None]))[0]
if identifier:
return f'<a href="{base_urls[feature.featuretype]}{identifier}" target="_blank">{identifier}</a>'
return "N/A"
if 'db_xref' in feature.attributes:
db_xrefs = feature.attributes['db_xref']
liens = {}
for xref in db_xrefs:
db_name, db_id = xref.split(':')
if db_name == "NCBI":
liens['NCBI'] = f"https://www.ncbi.nlm.nih.gov/{db_name}/{db_id}"
elif db_name == "UniProt":
liens['UniProt'] = f"https://www.uniprot.org/uniprot/{db_id}" #pas testé
elif db_name == "Ensembl":
liens['Ensembl'] = f"https://www.ensembl.org/id/{db_id}" #pas testé
elif db_name == "COG":
liens['COG'] = f"https://www.ncbi.nlm.nih.gov/research/cog/cog/{db_id}"
return liens
else:
return "NA"
def graphe(stats, output_plot):
"""
......
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