diff formatoutput.py @ 1:b89b0765695d draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/formatoutput.py	Mon May 17 20:10:24 2021 +0000
@@ -0,0 +1,144 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import argparse
+import re
+from pathlib import Path
+
+taxo_level = {
+    'k': 'kingdom',
+    'p': 'phylum',
+    'c': 'class',
+    'o': 'order',
+    'f': 'family',
+    'g': 'genus',
+    's': 'species',
+    't': 'strains'}
+
+
+def split_levels(metaphlan_output_fp, out_dp, legacy_output):
+    '''
+    Split default MetaPhlAn into a report for each taxonomic level
+
+    :param metaphlan_output_fp: Path default MetaPhlAn output
+    :param out_dp: Path to output directory
+    :param legacy_output: Boolean for legacy output
+    '''
+    # prepare output files
+    abund_f = {
+        'k': open(out_dp / Path('kingdom'), 'w'),
+        'p': open(out_dp / Path('phylum'), 'w'),
+        'c': open(out_dp / Path('class'), 'w'),
+        'o': open(out_dp / Path('order'), 'w'),
+        'f': open(out_dp / Path('family'), 'w'),
+        'g': open(out_dp / Path('genus'), 'w'),
+        's': open(out_dp / Path('species'), 'w'),
+        't': open(out_dp / Path('strains'), 'w')
+    }
+    for level in abund_f:
+        abund_f[level].write("%s\t" % taxo_level[level])
+        if not legacy_output:
+            abund_f[level].write("%s_id\t" % taxo_level[level])
+        abund_f[level].write("abundance\n")
+
+    levels_number = len(taxo_level)
+
+    with open(metaphlan_output_fp, 'r') as metaphlan_output_f:
+        with open(out_dp / Path('all'), 'w') as all_level_f:
+            # write header in all leve file
+            for level in ['k', 'p', 'c', 'o', 'f', 'g', 's', 't']:
+                all_level_f.write("%s\t" % taxo_level[level])
+                if not legacy_output:
+                    all_level_f.write("%s_id\t" % taxo_level[level])
+            all_level_f.write("abundance\n")
+
+            # parse metaphlan file
+            for line in metaphlan_output_f.readlines():
+                # skip headers
+                if line.startswith("#"):
+                    continue
+
+                # spit lines
+                split_line = line[:-1].split('\t')
+                taxo_n = split_line[0].split('|')
+                if legacy_output:
+                    abundance = split_line[1]
+                else:
+                    taxo_id = split_line[1].split('|')
+                    abundance = split_line[2]
+
+                # get taxon name and ids
+                for i in range(len(taxo_n)):
+                    taxo = taxo_n[i].split('__')[1]
+                    taxo = taxo.replace("_", " ")
+                    all_level_f.write("%s\t" % taxo)
+                    if not legacy_output:
+                        all_level_f.write("%s\t" % taxo_id[i])
+
+                # if not all taxon levels
+                for i in range(len(taxo_n), levels_number):
+                    all_level_f.write('\t')
+
+                all_level_f.write("%s\n" % abundance)
+
+                # write
+                last_taxo_level = taxo_n[-1].split('__')
+                taxo = last_taxo_level[1].replace("_", " ")
+                level = last_taxo_level[0]
+                abund_f[level].write("%s\t" % taxo)
+                if not legacy_output:
+                    abund_f[level].write("%s\t" % taxo_id[-1])
+                abund_f[level].write("%s\n" % abundance)
+
+    # close files
+    for taxo_level_f in abund_f:
+        abund_f[taxo_level_f].close()
+
+
+def format_for_krona(metaphlan_output_fp, krona_out_fp):
+    '''
+    Split default MetaPhlAn into a report for each taxonomic levKRONAel
+
+    :param metaphlan_output_fp: Path default MetaPhlAn output
+    :param krona_out: Path to output file for Krona
+    '''
+    re_replace = re.compile(r"\w__")
+    re_bar = re.compile(r"\|")
+    re_underscore = re.compile(r"_")
+
+    with open(metaphlan_output_fp, 'r') as metaphlan_output_f:
+        with open(krona_out_fp, 'w') as krona_out_f:
+            for line in metaphlan_output_f.readlines():
+                if "s__" in line:
+                    x = line.rstrip().split('\t')
+                    lineage = re.sub(re_bar, '', x[0])
+                    lineage = re.sub(re_replace, '\t', lineage)
+                    lineage = re.sub(re_underscore, ' ', lineage)
+                    krona_out_f.write("%s\t%s\n" % (x[-1], lineage))
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='Format MetaPhlAn output')
+    subparsers = parser.add_subparsers(dest='function')
+    # split_levels
+    split_levels_parser = subparsers.add_parser('split_levels', help='Split default MetaPhlAn into a report for each taxonomic level')
+    split_levels_parser.add_argument('--metaphlan_output', help="Path to default MetaPhlAn output")
+    split_levels_parser.add_argument('--outdir', help="Path to output directory")
+    split_levels_parser.add_argument('--legacy-output', dest='legacy_output', action='store_true', help="Old MetaPhlAn2 two columns output")
+    split_levels_parser.set_defaults(legacy_output=False)
+    # format_for_krona
+    format_for_krona_parser = subparsers.add_parser('format_for_krona', help='Split default MetaPhlAn into a report for each taxonomic level')
+    format_for_krona_parser.add_argument('--metaphlan_output', help="Path to default MetaPhlAn output")
+    format_for_krona_parser.add_argument('--krona_output', help="Path to Krona output directory")
+
+    args = parser.parse_args()
+
+    if args.function == 'split_levels':
+        split_levels(
+            Path(args.metaphlan_output),
+            Path(args.outdir),
+            args.legacy_output)
+    elif args.function == 'format_for_krona':
+        format_for_krona(
+            Path(args.metaphlan_output),
+            Path(args.krona_output))