# HG changeset patch
# User bgruening
# Date 1689847632 0
# Node ID 01ac9954c27fd6b42092334e4dce4dd8400707de
# Parent fdfb357451044bcc1906859e49feba02eff4ebc6
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
diff -r fdfb35745104 -r 01ac9954c27f combine_metaphlan2_humann2.py
--- a/combine_metaphlan2_humann2.py Wed Oct 19 14:44:00 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,107 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import argparse
-
-
-def extract_clade_abundance(metaphlan2_fp):
- clade_abund = {}
- with open(metaphlan2_fp, "r") as metaphlan2_f:
- for line in metaphlan2_f.readlines():
- if line.find("g__") == -1:
- continue
-
- split_line = line[:-1].split("\t")
- taxo = split_line[0]
- abundance = split_line[1]
-
- genus = taxo[(taxo.find("g__") + 3):]
- if genus.find("|") != -1:
- genus = genus[: (genus.find("|"))]
- clade_abund.setdefault(genus, {"abundance": 0, "species": {}})
- if taxo.find("t__") != -1:
- continue
- elif taxo.find("s__") != -1:
- species = taxo[(taxo.find("s__") + 3):]
- clade_abund[genus]["species"].setdefault(species, abundance)
- else:
- clade_abund[genus]["abundance"] = abundance
- return clade_abund
-
-
-def compute_overall_abundance(humann2_fp):
- overall_abundance = 0
- with open(humann2_fp, "r") as humann2_f:
- for line in humann2_f.readlines():
- if line.find("|") != -1 or line.startswith("#"):
- continue
- split_line = line[:-1].split("\t")
- overall_abundance += float(split_line[1])
- return overall_abundance
-
-
-def format_characteristic_name(name):
- formatted_n = name
- formatted_n = formatted_n.replace("/", " ")
- formatted_n = formatted_n.replace("-", " ")
- formatted_n = formatted_n.replace("'", "")
- if formatted_n.find("(") != -1 and formatted_n.find(")") != -1:
- open_bracket = formatted_n.find("(")
- close_bracket = formatted_n.find(")") + 1
- formatted_n = formatted_n[:open_bracket] + formatted_n[close_bracket:]
- return formatted_n
-
-
-def combine_metaphlan2_humann2(args):
- clade_abund = extract_clade_abundance(args.metaphlan2_fp)
- overall_abund = compute_overall_abundance(args.humann2_fp)
-
- with open(args.output_fp, "w") as output_f:
- s = "genus\tgenus_abundance\tspecies\tspecies_abundance\t"
- s = "%s\t%s_id\t%s_name\t%s_abundance\n" % (s, args.type, args.type, args.type)
- output_f.write(s)
- with open(args.humann2_fp, "r") as humann2_f:
- for line in humann2_f.readlines():
- if line.find("|") == -1:
- continue
-
- split_line = line[:-1].split("\t")
- abundance = 100 * float(split_line[1]) / overall_abund
- annotation = split_line[0].split("|")
- charact = annotation[0].split(":")
- charact_id = charact[0]
- char_name = ""
- if len(charact) > 1:
- char_name = format_characteristic_name(charact[-1])
- taxo = annotation[1].split(".")
-
- if taxo[0] == "unclassified":
- continue
- genus = taxo[0][3:]
- species = taxo[1][3:]
-
- if genus not in clade_abund:
- print("no %s found in %s" % (genus, args.metaphlan2_fp))
- continue
- if species not in clade_abund[genus]["species"]:
- print(
- "no %s found in %s for % s"
- % (species, args.metaphlan2_fp, genus)
- )
- continue
-
- s = "%s\t%s\t" % (genus, clade_abund[genus]["abundance"])
- s += "%s\t%s\t" % (species, clade_abund[genus]["species"][species])
- s += "%s\t%s\t%s\n" % (charact_id, char_name, abundance)
- output_f.write(s)
-
-
-if __name__ == "__main__":
- parser = argparse.ArgumentParser()
- parser.add_argument("--humann2_fp", required=True)
- parser.add_argument("--metaphlan2_fp", required=True)
- parser.add_argument("--output_fp", required=True)
- parser.add_argument("--type", required=True, choices=["gene_families", "pathways"])
- args = parser.parse_args()
-
- combine_metaphlan2_humann2(args)
diff -r fdfb35745104 -r 01ac9954c27f combine_metaphlan2_humann2.xml
--- a/combine_metaphlan2_humann2.xml Wed Oct 19 14:44:00 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,81 +0,0 @@
-
- to relate genus/species abundances and gene families/pathways abundances
-
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- type=="gene_families"
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- type=="pathways"
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\ No newline at end of file
diff -r fdfb35745104 -r 01ac9954c27f combine_metaphlan_humann.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/combine_metaphlan_humann.py Thu Jul 20 10:07:12 2023 +0000
@@ -0,0 +1,118 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import argparse
+
+
+def extract_clade_abundance(metaphlan_fp):
+ clade_abund = {}
+ with open(metaphlan_fp, "r") as metaphlan_f:
+ is_metaphlan_v4 = False
+ for line in metaphlan_f.readlines():
+ if 'SGB' in line:
+ # New versions of metaphlan against a recent DB contain a header line with DB name, which contains SGB
+ is_metaphlan_v4 = True
+ if line.find("g__") == -1:
+ continue
+
+ split_line = line[:-1].split("\t")
+ taxo = split_line[0]
+ if is_metaphlan_v4:
+ # Column order in new metaphlan versions:
+ # clade_name NCBI_tax_id relative_abundance additional_species
+ abundance = split_line[2]
+ else:
+ # Column order in the old metaphlan versions:
+ # clade_name relative_abundance coverage average_genome_length_in_the_clade estimated_number_of_reads_from_the_clade
+ abundance = split_line[1]
+
+ genus = taxo[(taxo.find("g__") + 3):]
+ if genus.find("|") != -1:
+ genus = genus[: (genus.find("|"))]
+ clade_abund.setdefault(genus, {"abundance": 0, "species": {}})
+ if taxo.find("t__") != -1:
+ continue
+ elif taxo.find("s__") != -1:
+ species = taxo[(taxo.find("s__") + 3):]
+ clade_abund[genus]["species"].setdefault(species, abundance)
+ else:
+ clade_abund[genus]["abundance"] = abundance
+ return clade_abund
+
+
+def compute_overall_abundance(humann_fp):
+ overall_abundance = 0
+ with open(humann_fp, "r") as humann_f:
+ for line in humann_f.readlines():
+ if line.find("|") != -1 or line.startswith("#"):
+ continue
+ split_line = line[:-1].split("\t")
+ overall_abundance += float(split_line[1])
+ return overall_abundance
+
+
+def format_characteristic_name(name):
+ formatted_n = name
+ formatted_n = formatted_n.replace("/", " ")
+ formatted_n = formatted_n.replace("-", " ")
+ formatted_n = formatted_n.replace("'", "")
+ if formatted_n.find("(") != -1 and formatted_n.find(")") != -1:
+ open_bracket = formatted_n.find("(")
+ close_bracket = formatted_n.find(")") + 1
+ formatted_n = formatted_n[:open_bracket] + formatted_n[close_bracket:]
+ return formatted_n
+
+
+def combine_metaphlan_humann(args):
+ clade_abund = extract_clade_abundance(args.metaphlan_fp)
+ overall_abund = compute_overall_abundance(args.humann_fp)
+
+ with open(args.output_fp, "w") as output_f:
+ s = "genus\tgenus_abundance\tspecies\tspecies_abundance\t"
+ s = "%s\t%s_id\t%s_name\t%s_abundance\n" % (s, args.type, args.type, args.type)
+ output_f.write(s)
+ with open(args.humann_fp, "r") as humann_f:
+ for line in humann_f.readlines():
+ if line.find("|") == -1:
+ continue
+
+ split_line = line[:-1].split("\t")
+ abundance = 100 * float(split_line[1]) / overall_abund
+ annotation = split_line[0].split("|")
+ charact = annotation[0].split(":")
+ charact_id = charact[0]
+ char_name = ""
+ if len(charact) > 1:
+ char_name = format_characteristic_name(charact[-1])
+ taxo = annotation[1].split(".")
+
+ if taxo[0] == "unclassified":
+ continue
+ genus = taxo[0][3:]
+ species = taxo[1][3:]
+
+ if genus not in clade_abund:
+ print("no %s found in %s" % (genus, args.metaphlan_fp))
+ continue
+ if species not in clade_abund[genus]["species"]:
+ print(
+ "No %s found in %s for % s"
+ % (species, args.metaphlan_fp, genus)
+ )
+ continue
+
+ s = "%s\t%s\t" % (genus, clade_abund[genus]["abundance"])
+ s += "%s\t%s\t" % (species, clade_abund[genus]["species"][species])
+ s += "%s\t%s\t%s\n" % (charact_id, char_name, abundance)
+ output_f.write(s)
+
+
+if __name__ == "__main__":
+ parser = argparse.ArgumentParser()
+ parser.add_argument("--humann_fp", required=True)
+ parser.add_argument("--metaphlan_fp", required=True)
+ parser.add_argument("--output_fp", required=True)
+ parser.add_argument("--type", required=True, choices=["gene_families", "pathways"])
+ args = parser.parse_args()
+
+ combine_metaphlan_humann(args)
diff -r fdfb35745104 -r 01ac9954c27f combine_metaphlan_humann.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/combine_metaphlan_humann.xml Thu Jul 20 10:07:12 2023 +0000
@@ -0,0 +1,109 @@
+
+ to relate genus/species abundances and gene families/pathways abundances
+
+ python
+
+
+
+
+
+
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+
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+
+
+ type=="gene_families"
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+
+ type=="pathways"
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+ 10.7554/eLife.65088
+
+