def read_gene2fam(pangenome, gene2fam, disable_bar=False):
logging.getLogger().info(
f"Adding {len(gene2fam)} genes to the gene families")
link = True if pangenome.status["genomesAnnotated"] in [
"Computed", "Loaded"
] else False
if link:
if len(gene2fam) != len(
pangenome.genes
): # then maybe there are genes with identical IDs
raise Exception(
"Something unexpected happened during clustering "
"(have less genes clustered than genes in the pangenome). "
"A probable reason is that two genes in two different organisms have the same IDs;"
" If you are sure that all of your genes have non identical IDs, "
"please post an issue at https://github.com/labgem/PPanGGOLiN/"
)
bar = tqdm(gene2fam.items(), unit="gene", disable=disable_bar)
for gene, (family, is_frag) in bar:
fam = pangenome.addGeneFamily(family)
if link: # doing the linking if the annotations are loaded.
geneObj = pangenome.getGene(gene)
else:
geneObj = Gene(gene)
geneObj.is_fragment = is_frag
fam.addGene(geneObj)
bar.close()
def readOrganism(pangenome, orgName, contigDict, circularContigs, link=False):
org = Organism(orgName)
for contigName, geneList in contigDict.items():
contig = org.getOrAddContig(contigName,
is_circular=circularContigs[contigName])
for row in geneList:
if link: #if the gene families are already computed/loaded the gene exists.
gene = pangenome.getGene(row["ID"].decode())
else: #else creating the gene.
gene_type = row["type"].decode()
if gene_type == "CDS":
gene = Gene(row["ID"].decode())
elif "RNA" in gene_type:
gene = RNA(row["ID"].decode())
try:
local = row["local"].decode()
except ValueError:
local = ""
gene.fill_annotations(start=row["start"],
stop=row["stop"],
strand=row["strand"].decode(),
geneType=row["type"].decode(),
position=row["position"],
genetic_code=row["genetic_code"],
name=row["name"].decode(),
product=row["product"].decode(),
local_identifier=local)
gene.is_fragment = row["is_fragment"]
gene.fill_parents(org, contig)
if gene_type == "CDS":
contig.addGene(gene)
elif "RNA" in gene_type:
contig.addRNA(gene)
else:
raise Exception(
f"A strange type '{gene_type}', which we do not know what to do with, was met."
)
pangenome.addOrganism(org)