Mercurial > repos > bebatut > combine_metaphlan2_humann2

annotate combine_metaphlan2_humann2.py @ 2:fdfb35745104 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
author bgruening
date Wed, 19 Oct 2022 14:44:00 +0000
parents e25efca0a49c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
bebatut
parents:
diff changeset
1 #!/usr/bin/env python
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
bebatut
parents:
diff changeset
2 # -*- coding: utf-8 -*-
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
bebatut
parents:
diff changeset
3
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
bebatut
parents:
diff changeset
4 import argparse
1
e25efca0a49c "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit 4a40a73a6eb981310a3c1c54dfa98b5460a843f9"
bebatut
parents: 0
diff changeset
5
0
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
bebatut
parents:
diff changeset
6
1
e25efca0a49c "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit 4a40a73a6eb981310a3c1c54dfa98b5460a843f9"
bebatut
parents: 0
diff changeset
7 def extract_clade_abundance(metaphlan2_fp):
e25efca0a49c "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit 4a40a73a6eb981310a3c1c54dfa98b5460a843f9"
bebatut
parents: 0
diff changeset
8 clade_abund = {}
2
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
9 with open(metaphlan2_fp, "r") as metaphlan2_f:
1
e25efca0a49c "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit 4a40a73a6eb981310a3c1c54dfa98b5460a843f9"
bebatut
parents: 0
diff changeset
10 for line in metaphlan2_f.readlines():
2
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
11 if line.find("g__") == -1:
0
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
bebatut
parents:
diff changeset
12 continue
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
bebatut
parents:
diff changeset
13
2
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
14 split_line = line[:-1].split("\t")
0
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
bebatut
parents:
diff changeset
15 taxo = split_line[0]
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
bebatut
parents:
diff changeset
16 abundance = split_line[1]
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
bebatut
parents:
diff changeset
17
2
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
18 genus = taxo[(taxo.find("g__") + 3):]
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
19 if genus.find("|") != -1:
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
20 genus = genus[: (genus.find("|"))]
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
21 clade_abund.setdefault(genus, {"abundance": 0, "species": {}})
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
22 if taxo.find("t__") != -1:
0
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
bebatut
parents:
diff changeset
23 continue
2
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
24 elif taxo.find("s__") != -1:
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
25 species = taxo[(taxo.find("s__") + 3):]
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
26 clade_abund[genus]["species"].setdefault(species, abundance)
0
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
bebatut
parents:
diff changeset
27 else:
2
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
28 clade_abund[genus]["abundance"] = abundance
1
e25efca0a49c "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit 4a40a73a6eb981310a3c1c54dfa98b5460a843f9"
bebatut
parents: 0
diff changeset
29 return clade_abund
0
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
bebatut
parents:
diff changeset
30
1
e25efca0a49c "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit 4a40a73a6eb981310a3c1c54dfa98b5460a843f9"
bebatut
parents: 0
diff changeset
31
e25efca0a49c "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit 4a40a73a6eb981310a3c1c54dfa98b5460a843f9"
bebatut
parents: 0
diff changeset
32 def compute_overall_abundance(humann2_fp):
0
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
bebatut
parents:
diff changeset
33 overall_abundance = 0
2
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
34 with open(humann2_fp, "r") as humann2_f:
1
e25efca0a49c "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit 4a40a73a6eb981310a3c1c54dfa98b5460a843f9"
bebatut
parents: 0
diff changeset
35 for line in humann2_f.readlines():
2
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
36 if line.find("|") != -1 or line.startswith("#"):
0
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
bebatut
parents:
diff changeset
37 continue
2
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
38 split_line = line[:-1].split("\t")
0
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
bebatut
parents:
diff changeset
39 overall_abundance += float(split_line[1])
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
bebatut
parents:
diff changeset
40 return overall_abundance
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
bebatut
parents:
diff changeset
41
1
e25efca0a49c "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit 4a40a73a6eb981310a3c1c54dfa98b5460a843f9"
bebatut
parents: 0
diff changeset
42
0
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
bebatut
parents:
diff changeset
43 def format_characteristic_name(name):
1
e25efca0a49c "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit 4a40a73a6eb981310a3c1c54dfa98b5460a843f9"
bebatut
parents: 0
diff changeset
44 formatted_n = name
2
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
45 formatted_n = formatted_n.replace("/", " ")
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
46 formatted_n = formatted_n.replace("-", " ")
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
47 formatted_n = formatted_n.replace("'", "")
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
48 if formatted_n.find("(") != -1 and formatted_n.find(")") != -1:
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
49 open_bracket = formatted_n.find("(")
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
50 close_bracket = formatted_n.find(")") + 1
1
e25efca0a49c "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit 4a40a73a6eb981310a3c1c54dfa98b5460a843f9"
bebatut
parents: 0
diff changeset
51 formatted_n = formatted_n[:open_bracket] + formatted_n[close_bracket:]
e25efca0a49c "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit 4a40a73a6eb981310a3c1c54dfa98b5460a843f9"
bebatut
parents: 0
diff changeset
52 return formatted_n
e25efca0a49c "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit 4a40a73a6eb981310a3c1c54dfa98b5460a843f9"
bebatut
parents: 0
diff changeset
53
0
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
bebatut
parents:
diff changeset
54
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
bebatut
parents:
diff changeset
55 def combine_metaphlan2_humann2(args):
1
e25efca0a49c "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit 4a40a73a6eb981310a3c1c54dfa98b5460a843f9"
bebatut
parents: 0
diff changeset
56 clade_abund = extract_clade_abundance(args.metaphlan2_fp)
e25efca0a49c "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit 4a40a73a6eb981310a3c1c54dfa98b5460a843f9"
bebatut
parents: 0
diff changeset
57 overall_abund = compute_overall_abundance(args.humann2_fp)
0
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
bebatut
parents:
diff changeset
58
2
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
59 with open(args.output_fp, "w") as output_f:
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
60 s = "genus\tgenus_abundance\tspecies\tspecies_abundance\t"
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
61 s = "%s\t%s_id\t%s_name\t%s_abundance\n" % (s, args.type, args.type, args.type)
1
e25efca0a49c "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit 4a40a73a6eb981310a3c1c54dfa98b5460a843f9"
bebatut
parents: 0
diff changeset
62 output_f.write(s)
2
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
63 with open(args.humann2_fp, "r") as humann2_f:
1
e25efca0a49c "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit 4a40a73a6eb981310a3c1c54dfa98b5460a843f9"
bebatut
parents: 0
diff changeset
64 for line in humann2_f.readlines():
2
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
65 if line.find("|") == -1:
0
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
bebatut
parents:
diff changeset
66 continue
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
bebatut
parents:
diff changeset
67
2
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
68 split_line = line[:-1].split("\t")
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
69 abundance = 100 * float(split_line[1]) / overall_abund
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
70 annotation = split_line[0].split("|")
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
71 charact = annotation[0].split(":")
1
e25efca0a49c "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit 4a40a73a6eb981310a3c1c54dfa98b5460a843f9"
bebatut
parents: 0
diff changeset
72 charact_id = charact[0]
2
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
73 char_name = ""
1
e25efca0a49c "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit 4a40a73a6eb981310a3c1c54dfa98b5460a843f9"
bebatut
parents: 0
diff changeset
74 if len(charact) > 1:
e25efca0a49c "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit 4a40a73a6eb981310a3c1c54dfa98b5460a843f9"
bebatut
parents: 0
diff changeset
75 char_name = format_characteristic_name(charact[-1])
2
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
76 taxo = annotation[1].split(".")
1
e25efca0a49c "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit 4a40a73a6eb981310a3c1c54dfa98b5460a843f9"
bebatut
parents: 0
diff changeset
77
2
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
78 if taxo[0] == "unclassified":
0
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
bebatut
parents:
diff changeset
79 continue
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
bebatut
parents:
diff changeset
80 genus = taxo[0][3:]
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
bebatut
parents:
diff changeset
81 species = taxo[1][3:]
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
bebatut
parents:
diff changeset
82
1
e25efca0a49c "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit 4a40a73a6eb981310a3c1c54dfa98b5460a843f9"
bebatut
parents: 0
diff changeset
83 if genus not in clade_abund:
e25efca0a49c "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit 4a40a73a6eb981310a3c1c54dfa98b5460a843f9"
bebatut
parents: 0
diff changeset
84 print("no %s found in %s" % (genus, args.metaphlan2_fp))
0
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
bebatut
parents:
diff changeset
85 continue
2
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
86 if species not in clade_abund[genus]["species"]:
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
87 print(
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
88 "no %s found in %s for % s"
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
89 % (species, args.metaphlan2_fp, genus)
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
90 )
0
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
bebatut
parents:
diff changeset
91 continue
1
e25efca0a49c "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit 4a40a73a6eb981310a3c1c54dfa98b5460a843f9"
bebatut
parents: 0
diff changeset
92
2
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
93 s = "%s\t%s\t" % (genus, clade_abund[genus]["abundance"])
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
94 s += "%s\t%s\t" % (species, clade_abund[genus]["species"][species])
1
e25efca0a49c "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit 4a40a73a6eb981310a3c1c54dfa98b5460a843f9"
bebatut
parents: 0
diff changeset
95 s += "%s\t%s\t%s\n" % (charact_id, char_name, abundance)
e25efca0a49c "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit 4a40a73a6eb981310a3c1c54dfa98b5460a843f9"
bebatut
parents: 0
diff changeset
96 output_f.write(s)
e25efca0a49c "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit 4a40a73a6eb981310a3c1c54dfa98b5460a843f9"
bebatut
parents: 0
diff changeset
97
0
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
bebatut
parents:
diff changeset
98
2
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
99 if __name__ == "__main__":
0
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
bebatut
parents:
diff changeset
100 parser = argparse.ArgumentParser()
2
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
101 parser.add_argument("--humann2_fp", required=True)
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
102 parser.add_argument("--metaphlan2_fp", required=True)
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
103 parser.add_argument("--output_fp", required=True)
fdfb35745104 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
bgruening
parents: 1
diff changeset
104 parser.add_argument("--type", required=True, choices=["gene_families", "pathways"])
0
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
bebatut
parents:
diff changeset
105 args = parser.parse_args()
31394a0c0242 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
bebatut
parents:
diff changeset
106
1
e25efca0a49c "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit 4a40a73a6eb981310a3c1c54dfa98b5460a843f9"
bebatut
parents: 0
diff changeset
107 combine_metaphlan2_humann2(args)