Mercurial > repos > estrain > data_manager_amrfinderplus_database_builder
changeset 14:d57fecce2d3b draft
Uploaded
| author | estrain |
|---|---|
| date | Tue, 08 Mar 2022 16:54:50 +0000 |
| parents | 9b71d79ff903 |
| children | c74ed5f206bd |
| files | data_manager_amrfinderplus_database_builder/data_manager/data_manager_amrfinderplus_database_builder.py |
| diffstat | 1 files changed, 6 insertions(+), 6 deletions(-) [+] |
line wrap: on
line diff
--- a/data_manager_amrfinderplus_database_builder/data_manager/data_manager_amrfinderplus_database_builder.py Tue Mar 08 10:52:29 2022 +0000 +++ b/data_manager_amrfinderplus_database_builder/data_manager/data_manager_amrfinderplus_database_builder.py Tue Mar 08 16:54:50 2022 +0000 @@ -30,12 +30,12 @@ for f in files: ftp.retrbinary("RETR " + f, open(f, 'wb').write) - ftp.quit() - - #find species specific point mutation files + files = ftp.nlst() + files = filter(lambda x: re.search(r'^((?!allele|(?:invokername=allele)).)*$', x), files) pointmuts = filter(lambda x: re.search(r'^((?!tab|(?:invokername=tab)).)*$', x), files) pointmuts = filter(lambda x: re.search(r'AMR_DNA-', x), pointmuts) + # Make blast databases blastcmd = "makeblastdb -in AMRProt -dbtype prot -logfile /dev/null" os.system(blastcmd) @@ -43,6 +43,7 @@ os.system(blastcmd) for f in pointmuts: + print(f) blastcmd = "makeblastdb -in " + f +" -dbtype nucl -logfile /dev/null" os.system(blastcmd) @@ -54,6 +55,8 @@ with open("version.txt") as f: version = f.readline().rstrip() + ftp.quit() + return version def print_json (version,argspath): @@ -65,7 +68,6 @@ 'amrfinder_databases': [ { "value":valueentry, - "dbkey":valueentry, "name":version, "path":argspath, } @@ -90,8 +92,6 @@ os.chdir("..") shutil.copytree("output",args.path[0]) - shutil.rmtree("output") - print_json(version,args.path[0]) if __name__ == "__main__": main()