Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

ENH specific version for NCBI in db_harmonisation & clean up harmonisation code #46

Merged
merged 1 commit into from
May 28, 2024
Merged

ENH specific version for NCBI in db_harmonisation & clean up harmonisation code #46

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
5 changes: 0 additions & 5 deletions db_harmonisation/construct_megares_mapping.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -161,17 +161,12 @@ def merge_megares_mappings(cds_mapping, contig_mapping):
cds_mapping = pd.read_csv(cds_mapping, sep='\t')
contig_mapping = pd.read_csv(contig_mapping, sep='\t')

print(cds_mapping)
print(contig_mapping)

cds_mapping['Original ID'] = cds_mapping['ORF_ID']
contig_mapping['Original ID'] = contig_mapping['Contig'].apply(lambda x: '_'.join(x.split('_')[:-1]))

cds_mapping = cds_mapping[['Original ID', 'ARO']]
contig_mapping = contig_mapping[['Original ID', 'ARO']]

print(megares_mappings)

megares_mappings.set_index('Original ID').drop(index=set(cds_mapping['Original ID']) & set(megares_mappings.index), inplace=True)
megares_mappings.set_index('Original ID').drop(index=set(contig_mapping['Original ID']) & set(megares_mappings.index), inplace=True)
megares_mappings = pd.concat([megares_mappings, cds_mapping, contig_mapping])
Expand Down
7 changes: 1 addition & 6 deletions db_harmonisation/crude_db_harmonisation.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@ def get_resfinderfg_db():

def get_ncbi_db():
ofile = 'dbs/ncbi_amr_raw.faa'
url = 'https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/latest/AMRProt'
url = 'https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/3.12/2024-01-31.1/AMRProt'
return download_file(url, ofile)

def get_resfinder_db():
Expand All @@ -55,10 +55,6 @@ def get_argannot_db():
url = 'https://www.mediterranee-infection.com/wp-content/uploads/2019/06/ARG_ANNOT_V5_AA_JUNE2019.txt'
return download_file(url, 'dbs/argannot.faa')

def get_megares_db():
url = 'https://www.meglab.org/downloads/megares_v3.00/megares_database_v3.00.fasta'
return download_file(url, 'dbs/megares.fna')

# NCBI db has '*' at end of each protein sequence. RGI can't handle that, so '*' is removed
@TaskGenerator
def fix_ncbi(ncbi_amr_faa):
Expand Down Expand Up @@ -128,7 +124,6 @@ def move_mappings_to_argnorm(aro_mapping):
get_sarg_db(),
get_resfinderfg_db(),
get_deeparg_db(),
get_megares_db(),
get_argannot_db()
]:
move_mappings_to_argnorm(run_rgi(db))
Expand Down
Loading