changeset 2:370b56f8a02d draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"

--- a/format_metaphlan2_output.py	Mon Sep 14 09:52:15 2020 +0000
+++ b/format_metaphlan2_output.py	Wed Oct 19 14:39:16 2022 +0000
@@ -5,42 +5,43 @@
 
 
 taxo_level_corresp = {
-    'k': 'kingdom',
-    'p': 'phylum',
-    'c': 'class',
-    'o': 'order',
-    'f': 'family',
-    'g': 'genus',
-    's': 'species',
-    't': 'strains'}
-    
+    "k": "kingdom",
+    "p": "phylum",
+    "c": "class",
+    "o": "order",
+    "f": "family",
+    "g": "genus",
+    "s": "species",
+    "t": "strains",
+}
+
 
 def write_taxo_abundance(output_files, level, taxo, abundance):
     if level not in taxo_level_corresp:
-        raise ValueError(level + ' is not a know taxonomic level')
+        raise ValueError(level + " is not a know taxonomic level")
     f_n = taxo_level_corresp[level]
-    output_files[f_n].write(taxo + '\t')
-    output_files[f_n].write(abundance + '\n')
+    output_files[f_n].write(taxo + "\t")
+    output_files[f_n].write(abundance + "\n")
 
 
 def format_metaphlan2_output(args):
     taxo_levels_abund_f = {
-        'kingdom': open(args.kingdom_abundance_file, 'w'),
-        'phylum': open(args.phylum_abundance_file, 'w'),
-        'class': open(args.class_abundance_file, 'w'),
-        'order': open(args.order_abundance_file, 'w'),
-        'family': open(args.family_abundance_file, 'w'),
-        'genus': open(args.genus_abundance_file, 'w'),
-        'species': open(args.species_abundance_file, 'w'),
-        'strains': open(args.strains_abundance_file, 'w')
+        "kingdom": open(args.kingdom_abundance_file, "w"),
+        "phylum": open(args.phylum_abundance_file, "w"),
+        "class": open(args.class_abundance_file, "w"),
+        "order": open(args.order_abundance_file, "w"),
+        "family": open(args.family_abundance_file, "w"),
+        "genus": open(args.genus_abundance_file, "w"),
+        "species": open(args.species_abundance_file, "w"),
+        "strains": open(args.strains_abundance_file, "w"),
     }
 
     for taxo_level_f in taxo_levels_abund_f:
-        s = taxo_level_f + '\t' + 'abundance\n'
+        s = taxo_level_f + "\t" + "abundance\n"
         taxo_levels_abund_f[taxo_level_f].write(s)
 
-    with open(args.metaphlan2_output, 'r') as input_f:
-        with open(args.all_taxo_level_abundance_file, 'w') as output_f:
+    with open(args.metaphlan2_output, "r") as input_f:
+        with open(args.all_taxo_level_abundance_file, "w") as output_f:
             s = "kingdom\tphylum\tclass\torder\tfamily\t"
             s += "genus\tspecies\tstrains\tabundance\n"
             output_f.write(s)
@@ -50,46 +51,42 @@
                 if line.startswith("#"):
                     continue
 
-                split_line = line[:-1].split('\t')
+                split_line = line[:-1].split("\t")
                 all_taxo = split_line[0]
                 abundance = split_line[1]
 
-                split_taxo = all_taxo.split('|')
+                split_taxo = all_taxo.split("|")
                 for level in split_taxo:
-                    taxo = level.split('__')[1]
+                    taxo = level.split("__")[1]
                     taxo = taxo.replace("_", " ")
-                    output_f.write(taxo + '\t')
+                    output_f.write(taxo + "\t")
 
                 for i in range(len(split_taxo), levels_number):
-                    output_f.write('\t')
+                    output_f.write("\t")
 
                 output_f.write(abundance + "\n")
 
-                last_taxo_level = split_taxo[-1].split('__')
+                last_taxo_level = split_taxo[-1].split("__")
                 taxo = last_taxo_level[1].replace("_", " ")
                 level = last_taxo_level[0]
-                write_taxo_abundance(
-                    taxo_levels_abund_f,
-                    level,
-                    taxo,
-                    abundance)
+                write_taxo_abundance(taxo_levels_abund_f, level, taxo, abundance)
 
     for taxo_level_f in taxo_levels_abund_f:
         taxo_levels_abund_f[taxo_level_f].close()
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     parser = argparse.ArgumentParser()
-    parser.add_argument('--metaphlan2_output', required=True)
-    parser.add_argument('--all_taxo_level_abundance_file', required=True)
-    parser.add_argument('--kingdom_abundance_file', required=True)
-    parser.add_argument('--phylum_abundance_file', required=True)
-    parser.add_argument('--class_abundance_file', required=True)
-    parser.add_argument('--order_abundance_file', required=True)
-    parser.add_argument('--family_abundance_file', required=True)
-    parser.add_argument('--genus_abundance_file', required=True)
-    parser.add_argument('--species_abundance_file', required=True)
-    parser.add_argument('--strains_abundance_file', required=True)
+    parser.add_argument("--metaphlan2_output", required=True)
+    parser.add_argument("--all_taxo_level_abundance_file", required=True)
+    parser.add_argument("--kingdom_abundance_file", required=True)
+    parser.add_argument("--phylum_abundance_file", required=True)
+    parser.add_argument("--class_abundance_file", required=True)
+    parser.add_argument("--order_abundance_file", required=True)
+    parser.add_argument("--family_abundance_file", required=True)
+    parser.add_argument("--genus_abundance_file", required=True)
+    parser.add_argument("--species_abundance_file", required=True)
+    parser.add_argument("--strains_abundance_file", required=True)
     args = parser.parse_args()
 
     format_metaphlan2_output(args)