Rename fixing profile script

metaphlan/utils/fix_relab_mpa4.py

@@ -1,5 +1,6 @@
 #!/usr/bin/env python
-__author__ = 'Aitor Blanco Miguez ([email protected])'
+__author__ = ('Aitor Blanco Miguez ([email protected]), '
+              'Claudia Mengoni ([email protected])')
 __version__ = '4.1.1'
 __date__ = '11 Mar 2024'
 
@@ -11,6 +12,8 @@
     from util_fun import info, error, warning
 import argparse as ap
 
+script_install_folder = os.path.dirname(os.path.abspath(__file__))
+OCT22_FIXES=os.path.join(script_install_folder,'oct22_fix_tax.tsv')
 
 def read_params():
     """ Reads and parses the command line arguments of the script
@@ -19,11 +22,23 @@ def read_params():
         namespace: The populated namespace with the command line arguments
     """
     p = ap.ArgumentParser(formatter_class=ap.RawTextHelpFormatter, add_help=False)   
-    requiredNamed = p.add_argument_group('requiered arguments')
+    requiredNamed = p.add_argument_group('required arguments')
     requiredNamed.add_argument('--input', type=str, default=None, help="The path to the input profile")
     requiredNamed.add_argument('--output', type=str, default=None, help="The path to the output profile")
     return p.parse_args()
 
+def read_oct22_fixes(file):
+    """Reads the tab separated file with old and new taxonomies of Oct22
+    Args:
+        file: file with Oct22 fixes
+    """
+    oct_fixes=dict()
+    with open(file) as inf:
+        for l in inf.readlines()[1:]:
+            old_tax, new_tax, new_tax_id = l.split('\t') 
+            oct_fixes[old_tax]= (new_tax, new_tax_id.strip())
+    return oct_fixes
+
 
 def check_params(args):
     """Checks the mandatory command line arguments of the script
@@ -38,9 +53,6 @@ def check_params(args):
             args.input), exit=True)           
     if not args.output:
         error('--output must be specified', exit=True)
-    elif not os.path.exists(args.output):
-        error('The file {} does not exist'.format(
-            args.output), exit=True)   
 
 def fix_relab_mpa4(input, output):
     taxa_levs = [{},{},{},{},{},{},{},{}] 
@@ -59,15 +71,20 @@ def fix_relab_mpa4(input, output):
                                 line = line.replace('p__Bacillota', 'p__Firmicutes')
                             elif 'f__Saccharomycetales_unclassified' in line:
                                 line = line.replace('f__Saccharomycetales_unclassified','f__Debaryomycetaceae')
+                            line = line.strip().split('\t') 
+
                         elif release == 'mpa_vOct22_CHOCOPhlAnSGB_202212':
-                            pass
-                        line = line.strip().split('\t') 
-                        taxa_levs[-1][line[0]] = [line[1], float(line[2]), line[3] if len(line)==4 else '']
+                                line = line.strip().split('\t')
+                                if line[0] in oct_fixes:
+                                    line[0],line[1] = oct_fixes[line[0]]
+
+                        taxa_levs[-1][line[0]] = [line[1], round(float(line[2]),5), line[3] if len(line)==4 else '']
+
             for i in range(1,8):
                 j = i+1
                 for ss in taxa_levs[-i]:
                     gg = ss.replace('|{}'.format(ss.split('|')[-1]), '')
-                    gg_n = taxa_levs[-i][ss][0].replace('|{}'.format(taxa_levs[-i][ss][0].split('|')[-1]), '')
+                    gg_n = '|'.join(taxa_levs[-i][ss][0].split('|')[:-1])
                     if gg not in taxa_levs[-j]:
                         taxa_levs[-j][gg] = [gg_n, taxa_levs[-i][ss][1], '']
                     else:
@@ -77,10 +94,12 @@ def fix_relab_mpa4(input, output):
                     wf.write(tax + '\t' + '\t'.join([str(x) for x in level[tax]]) + '\n')
 
 def main():
+    global oct_fixes
     t0 = time.time()
     args = read_params()
     info("Start fixing profile")
     check_params(args)
+    oct_fixes = read_oct22_fixes(OCT22_FIXES) 
     fix_relab_mpa4(args.input, args.output)
     exec_time = time.time() - t0
     info("Finish fixing profile ({} seconds)".format(round(exec_time, 2)))