diff data_manager/data_manager.py @ 2:b4c303665291 draft

planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit eec95ccc2189355061112ea2785b82f13a0fa077-dirty

--- a/data_manager/data_manager.py	Thu Mar 07 11:48:18 2019 -0500
+++ b/data_manager/data_manager.py	Fri Mar 08 05:38:44 2019 -0500
@@ -19,6 +19,15 @@
     "rdp16":"RDP trainset 16",
     "rdp14":"RDP trainset 14",
     "gg13.84":"GreenGenes version 13.8",
+    "unite8.0_fungi": "UNITE: General Fasta release 8.0 for Fungi",
+    "unite8.0_fungi_singletons": "UNITE: General Fasta release 8.0 for Fungi including global and 97% singletons",
+    "unite8.0_euka": "UNITE: General Fasta release 8.0 for all Eukaryotes",
+    "unite8.0_euka_singletons": "UNITE: General Fasta release 8.0 for all Eukaryotes including global and 97% singletons",
+    "RefSeq_RDP_2018_05": "NCBI RefSeq 16S rRNA database supplemented by RDP (05/2018)",
+    "gtdb_2018_11_20": "GTDB: Genome Taxonomy Database (Bacteria & Archaea) (11/2018)",
+    "hitdb1": "HitDB version 1 (Human InTestinal 16S rRNA)",
+    "silva132_euk_18S": "Silva version 132 Eukaryotic 18S",
+    "PR2v4.11.1": "Protist Ribosomal Reference database (PR2) 4.11.1"
 }
 
 FILE2TAXURL = {
@@ -26,7 +35,16 @@
     "silva128":"https://zenodo.org/record/824551/files/silva_nr_v128_train_set.fa.gz?download=1",
     "rdp16":"https://zenodo.org/record/801828/files/rdp_train_set_16.fa.gz?download=1",
     "rdp14":"https://zenodo.org/record/158955/files/rdp_train_set_14.fa.gz?download=1",
+    "unite8.0_fungi": "https://files.plutof.ut.ee/public/orig/EB/0C/EB0CCB3A871B77EA75E472D13926271076904A588D2E1C1EA5AFCF7397D48378.zip",
+    "unite8.0_fungi_singletons": "https://files.plutof.ut.ee/doi/06/A2/06A2C86256EED64085670EB0C54B7115F6DAC8F311C656A9CB33E386CFABA0D0.zip",
+    "unite8.0_euka": "https://files.plutof.ut.ee/public/orig/D6/96/D69658E99589D888A207805A744019DBA4EC0F603E67E53732767B3E03A5AA86.zip",
+    "unite8.0_euka_singletons": "https://files.plutof.ut.ee/doi/C2/20/C22034350E32D6AD7E5D1AF3F8BC487E34DA0BE25602B0E748906005CE6ADA97.zip",
     "gg13.84":"https://zenodo.org/record/158955/files/gg_13_8_train_set_97.fa.gz?download=1",
+    "RefSeq_RDP_2018_05": "https://zenodo.org/record/2541239/files/RefSeq-RDP16S_v2_May2018.fa.gz?download=1",
+    "gtdb_2018_11_20": "https://zenodo.org/record/2541239/files/GTDB_bac-arc_ssu_r86.fa.gz?download=1",
+    "hitdb1": "https://zenodo.org/record/159205/files/hitdb_v1.00.fa.gz?download=1",
+    "silva132_euk_18S": "https://zenodo.org/record/1447330/files/silva_132.18s.99_rep_set.dada2.fa.gz?download=1",
+    "PR2v4.11.1": "https://github.com/pr2database/pr2database/releases/download/4.11.1/pr2_version_4.11.1_dada2.fasta.gz"
 }
 
 FILE2SPECIESURL = {
@@ -37,6 +55,7 @@
 }
 
 FILE2TAXLEVELS = {
+    "PR2v4.11.1": "Kingdom,Supergroup,Division,Class,Order,Family,Genus,Species"
 }
 
 def url_download(url, fname, workdir):
@@ -63,7 +82,27 @@
     finally:
         if src:
             src.close()
-    return os.path.join(workdir, fname)
+
+    #special treatment of UNITE DBs: they are zip files containing two fasta (xyz.fasta and developer/xyz.fasta)
+    if fname.startswith("unite"):
+        import glob
+        import gzip
+        import shutil
+        import zipfile
+        # unzip download
+        zip_ref = zipfile.ZipFile(file_path, 'r')
+        zip_ref.extractall(workdir)
+        zip_ref.close()
+        # gzip top level fasta file
+        fastas = glob.glob("*fasta")
+        if len(fastas) != 1:
+            msg = "UNITE download %s contained more than one or no fasta file"
+            raise Exception(msg)
+        with open(fastas[0], 'rb') as f_in:
+            with gzip.open(file_path, 'wb') as f_out:
+                shutil.copyfileobj(f_in, f_out)
+
+    return fname
 
 def main(dataset, outjson):
 
@@ -73,28 +112,30 @@
     output_path = os.path.abspath(os.path.join(os.getcwd(), 'dada2'))
 
     workdir = os.path.join(os.getcwd(), 'dada2') 
-    path = url_download( FILE2TAXURL[dataset], taxdataset+".taxonomy", workdir)
+    path = url_download( FILE2TAXURL[dataset], dataset+".taxonomy", workdir)
 
     data_manager_json = {"data_tables":{}}
     data_manager_entry = {}
     data_manager_entry['value'] = dataset
     data_manager_entry['name'] = FILE2NAME[dataset]
-    data_manager_entry['path'] = path
+    data_manager_entry['path'] = dataset+".taxonomy"
     data_manager_entry['taxlevels'] = FILE2TAXLEVELS.get(dataset, DEFAULT_TAXLEVELS)
     data_manager_json["data_tables"]["dada2_taxonomy"] = data_manager_entry
 
 
-    if FILE2SPECIES.get(dataset, False ):
-        path = url_download( FILE2SPECIES[dataset], taxdataset+".species", workdir)
+    if FILE2SPECIESURL.get(dataset, False ):
+        path = url_download( FILE2SPECIESURL[dataset], dataset+".species", workdir)
     
         data_manager_entry = {}
         data_manager_entry['value'] = dataset
         data_manager_entry['name'] = FILE2NAME[dataset]
-        data_manager_entry['path'] = path
+        data_manager_entry['path'] = dataset+".species"
         data_manager_json["data_tables"]["dada2_species"] = data_manager_entry
     
     for filename in os.listdir(workdir):
         shutil.move(os.path.join(output_path, filename), target_directory)
+
+    sys.stderr.write("JSON %s" %json.dumps(data_manager_json))
     file(outjson, 'w').write(json.dumps(data_manager_json))
 
 if __name__ == '__main__':