diff data_manager/ariba_database_builder.py @ 4:be46816110b4 draft

planemo upload for repository https://github.com/thanhleviet/galaxy-tools commit 98648bbb7796db528b5685d44a2a5b761c53c19b-dirty

--- a/data_manager/ariba_database_builder.py	Mon Jan 14 07:01:15 2019 -0500
+++ b/data_manager/ariba_database_builder.py	Sun May 19 08:10:45 2019 -0400
@@ -1,33 +1,236 @@
-# Thanh Le Viet
-# 7-Jan-2019
-
+import sys
+import subprocess
+import shlex
+import shutil
 import argparse
 import json
 import os
 import shutil
+import errno
 
 
-def main(args):
-    output_path = os.getcwd()
-    db_folder = [d for d in os.listdir(output_path) if os.path.isdir(d)]
-    params = json.loads(open(args.output).read())
-    target_directory = params['output_data'][0]['extra_files_path']
-    os.mkdir(target_directory)
-    data_manager_entry = []
-    for db in db_folder:
-        print("Current: ".format(os.path.join(output_path, d)))
-        print("Target: {}".format(target_directory))
-        shutil.move(os.path.join(output_path, d), os.path.join(target_directory, d))
-        data_manager_entry.append(dict(value=db.lower(),
-                                  name=db,
-                                  path=target_directory)
-                                    )
-    data_manager_json = dict(data_tables=dict(ariba_databases=data_manager_entry))
-    file(args.output, 'w').write(json.dumps(data_manager_json))
+data_table_name = "ariba_databases"
+
+mlst_dict = {
+    "achs"	: "Achromobacter spp.",
+    "acib1"	: "Acinetobacter baumannii#1",
+    "acib2"	: "Acinetobacter baumannii#2",
+    "aers"	: "Aeromonas spp.",
+    "anap"	: "Anaplasma phagocytophilum",
+    "arcs"	: "Arcobacter spp.",
+    "aspf"	: "Aspergillus fumigatus",
+    "bacc"	: "Bacillus cereus",
+    "bacl"	: "Bacillus licheniformis",
+    "bacs"	: "Bacillus subtilis",
+    "barb"	: "Bartonella bacilliformis",
+    "barh"	: "Bartonella henselae",
+    "bors"	: "Bordetella spp.",
+    "borr"	: "Borrelia spp.",
+    "brah"	: "Brachyspira hampsonii",
+    "brach"	: "Brachyspira hyodysenteriae",
+    "brai"	: "Brachyspira intermedia",
+    "brap"	: "Brachyspira pilosicoli",
+    "bras"	: "Brachyspira spp.",
+    "brus"	: "Brucella spp.",
+    "bucc"	: "Burkholderia cepacia complex",
+    "burp"	: "Burkholderia pseudomallei",
+    "camc"	: "Campylobacter concisus/curvus",
+    "camf"	: "Campylobacter fetus",
+    "camh"	: "Campylobacter helveticus",
+    "rlis"	: "Campylobacter hyointestinalis",
+    "cami"	: "Campylobacter insulaenigrae",
+    "camj"	: "Campylobacter jejuni",
+    "caml"	: "Campylobacter lanienae",
+    "rari"	: "Campylobacter lari",
+    "cams"	: "Campylobacter sputorum",
+    "camu"	: "Campylobacter upsaliensis",
+    "cana"	: "Candida albicans",
+    "cang"	: "Candida glabrata",
+    "cank"	: "Candida krusei",
+    "cant"	: "Candida tropicalis",
+    "cals"	: "Candidatus Liberibacter solanacearum",
+    "carm"	: "Carnobacterium maltaromaticum",
+    "chls"	: "Chlamydiales spp.",
+    "citf"	: "Citrobacter freundii",
+    "clos"	: "Clonorchis sinensis",
+    "clob"	: "Clostridium botulinum",
+    "clod"	: "Clostridium difficile",
+    "mcum"	: "Clostridium septicum",
+    "cord"	: "Corynebacterium diphtheriae",
+    "cros"	: "Cronobacter spp.",
+    "dicn"	: "Dichelobacter nodosus",
+    "edws"	: "Edwardsiella spp.",
+    "entc"	: "Enterobacter cloacae",
+    "entf"	: "Enterococcus faecalis",
+    "sium"	: "Enterococcus faecium",
+    "escc1"	: "Escherichia coli#1",
+    "escc2"	: "Escherichia coli#2",
+    "flap"	: "Flavobacterium psychrophilum",
+    "gala"	: "Gallibacterium anatis",
+    "haei"	: "Haemophilus influenzae",
+    "haep"	: "Haemophilus parasuis",
+    "helc"	: "Helicobacter cinaedi",
+    "help"	: "Helicobacter pylori",
+    "hels"	: "Helicobacter suis",
+    "kink"	: "Kingella kingae",
+    "klea"	: "Klebsiella aerogenes",
+    "kleo"	: "Klebsiella oxytoca",
+    "klep"	: "Klebsiella pneumoniae",
+    "kuds"	: "Kudoa septempunctata",
+    "lacs"	: "Lactobacillus salivarius",
+    "leps"	: "Leptospira spp.",
+    "leps2"	: "Leptospira spp.#2",
+    "leps3"	: "Leptospira spp.#3",
+    "lism"	: "Listeria monocytogenes",
+    "macc"	: "Macrococcus canis",
+    "scus"	: "Macrococcus caseolyticus",
+    "manh"	: "Mannheimia haemolytica",
+    "melp"	: "Melissococcus plutonius",
+    "morc"	: "Moraxella catarrhalis",
+    "mycs"	: "Mycobacteria spp.",
+    "myca"	: "Mycobacterium abscessus",
+    "mycm"	: "Mycobacterium massiliense",
+    "mycoa"	: "Mycoplasma agalactiae",
+    "mycb"	: "Mycoplasma bovis",
+    "mych"	: "Mycoplasma hyopneumoniae",
+    "anis"	: "Mycoplasma hyorhinis",
+    "myci"	: "Mycoplasma iowae",
+    "mycp"	: "Mycoplasma pneumoniae",
+    "mycos"	: "Mycoplasma synoviae",
+    "neis"	: "Neisseria spp.",
+    "orit"	: "Orientia tsutsugamushi",
+    "ornr"	: "Ornithobacterium rhinotracheale",
+    "pael"	: "Paenibacillus larvae",
+    "pasm1"	: "Pasteurella multocida#1",
+    "pasm2"	: "Pasteurella multocida#2",
+    "pedp"	: "Pediococcus pentosaceus",
+    "phod"	: "Photobacterium damselae",
+    "piss"	: "Piscirickettsia salmonis",
+    "porg"	: "Porphyromonas gingivalis",
+    "proa"	: "Propionibacterium acnes",
+    "psea"	: "Pseudomonas aeruginosa",
+    "psef"	: "Pseudomonas fluorescens",
+    "psep"	: "Pseudomonas putida",
+    "rhos"	: "Rhodococcus spp.",
+    "riea"	: "Riemerella anatipestifer",
+    "sale"	: "Salmonella enterica",
+    "sapp"	: "Saprolegnia parasitica",
+    "sins"	: "Sinorhizobium spp.",
+    "staa"	: "Staphylococcus aureus",
+    "stae"	: "Staphylococcus epidermidis",
+    "stah"	: "Staphylococcus haemolyticus",
+    "snis"	: "Staphylococcus hominis",
+    "stal"	: "Staphylococcus lugdunensis",
+    "stap"	: "Staphylococcus pseudintermedius",
+    "stem"	: "Stenotrophomonas maltophilia",
+    "stra"	: "Streptococcus agalactiae",
+    "sbcx"	: "Streptococcus bovis/equinus complex (SBSEC)",
+    "strc"	: "Streptococcus canis",
+    "stde"	: "Streptococcus dysgalactiae equisimilis",
+    "strg"	: "Streptococcus gallolyticus",
+    "stro"	: "Streptococcus oralis",
+    "strp"	: "Streptococcus pneumoniae",
+    "snes"	: "Streptococcus pyogenes",
+    "strs"	: "Streptococcus suis",
+    "strt"	: "Streptococcus thermophilus",
+    "strt2"	: "Streptococcus thermophilus#2",
+    "stru"	: "Streptococcus uberis",
+    "strz"	: "Streptococcus zooepidemicus",
+    "sspp"	: "Streptomyces spp",
+    "tays"	: "Taylorella spp.",
+    "tens"	: "Tenacibaculum spp.",
+    "trep"	: "Treponema pallidum",
+    "triv"	: "Trichomonas vaginalis",
+    "ures"	: "Ureaplasma spp.",
+    "vibc"	: "Vibrio cholerae",
+    "vibc2"	: "Vibrio cholerae#2",
+    "vibp"	: "Vibrio parahaemolyticus",
+    "vibs"	: "Vibrio spp.",
+    "vibt"	: "Vibrio tapetis",
+    "vibv"	: "Vibrio vulnificus",
+    "wolb"	: "Wolbachia",
+    "xylf"	: "Xylella fastidiosa",
+    "yerp"	: "Yersinia pseudotuberculosis",
+    "yerr"	: "Yersinia ruckeri",
+    "yers"	: "Yersinia spp."
+}
 
 
-if __name__ == '__main__':
-    parser = argparse.ArgumentParser(description='Create data manager json.')
-    parser.add_argument('--out', dest='output', action='store', help='JSON filename')
+genes_dict = {
+    "card" : "CARD",
+    "resfinder" : "Resfinder",
+    "plasmidfinder" : "Plasmidfinder",
+    "megares" : "Megares",
+    "argannot" : "Argannot",
+    "vfdb_core" : "vfdb_core",
+    "vfdb_full" : "vfdb_full",
+    "virulencefinder" : "virulencefinder"
+}
+
+def run_ariba(cmd):
+    _cmd = shlex.split(cmd)
+    subprocess.check_call(_cmd)
+
+def build_mlst(mlst_db):
+    mlst_species = mlst_dict[mlst_db]
+    run_ariba("ariba pubmlstget '{}' out".format(mlst_species))
+    output_path = os.getcwd()
+    old = "{}/out/ref_db".format(output_path, mlst_db)
+    new = "{}/{}".format(output_path, mlst_db)
+    shutil.move(old, new)
+
+def build_curated_db(gen_db):
+    run_ariba("ariba getref {} out".format(gen_db))
+    run_ariba("ariba prepareref -f out.fa -m out.tsv {}".format(gen_db))
+
+def build_custom_db(fasta, coding, db_name):
+    run_ariba("ariba prepareref --all_coding {} -f {} {}".format(coding, fasta, db_name))
+
+def _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry):
+    data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
+    data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] )
+    data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry )
+    return data_manager_dict
+
+def main():
+    parser = argparse.ArgumentParser()
+    parser.add_argument('params')
+    parser.add_argument( '-t', '--dbtype', dest='database_type', help='database type' )
+    parser.add_argument( '-d', '--db', dest='db_name', help='database name' )
+    parser.add_argument( '-c', '--coding', dest='coding', help='' )
+    parser.add_argument( '-f', '--fasta', dest='fasta', help='' )
     args = parser.parse_args()
-    main(args)
\ No newline at end of file
+
+    if args.database_type == "curated":
+        build_curated_db(args.db_name)
+        name = genes_dict[args.db_name]
+    elif args.database_type == "mlst":
+        build_mlst(args.db_name)
+        name = mlst_dict[args.db_name]
+    elif args.database_type == "fasta":
+        build_custom_db(args.fasta, args.coding, args.db_name)
+        name = args.db_name
+
+    params = json.loads(open(args.params).read())
+        
+    target_directory = params['output_data'][0]['extra_files_path']
+    
+    if not os.path.isdir(target_directory):
+      os.mkdir(target_directory)
+
+    output_path = os.getcwd()
+    shutil.copytree(os.path.join(output_path, args.db_name), os.path.join(target_directory, args.db_name))
+    
+    data_manager_dict = {}
+
+    data_table_entry = {
+        "value": args.db_name,
+        "name": name,
+        "path": os.path.join(target_directory, args.db_name)
+    }
+    _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry)
+    open(args.params, 'wb').write(json.dumps(data_manager_dict))
+
+if __name__ == "__main__":
+    main()
+    
\ No newline at end of file