1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
|
#cython: language_level=3
from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
from obitools3.dms.dms cimport DMS
from obitools3.dms.view import RollbackException
from obitools3.dms.capi.obiecotag cimport obi_ecotag
from obitools3.apps.optiongroups import addMinimalInputOption, addTaxonomyOption, addMinimalOutputOption, addNoProgressBarOption
from obitools3.uri.decode import open_uri
from obitools3.apps.config import logger
from obitools3.utils cimport tobytes, str2bytes
from obitools3.dms.view.view cimport View
from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
import sys
from io import BufferedWriter
__title__="Taxonomic assignment of sequences"
def addOptions(parser):
addMinimalInputOption(parser)
addTaxonomyOption(parser)
addMinimalOutputOption(parser)
addNoProgressBarOption(parser)
group = parser.add_argument_group('obi ecotag specific options')
group.add_argument('--ref-database','-R',
action="store", dest="ecotag:ref_view",
metavar='<REF_VIEW>',
type=str,
help="URI of the view containing the reference database as built by the build_ref_db command.")
group.add_argument('--minimum-identity','-m',
action="store", dest="ecotag:threshold",
metavar='<THRESHOLD>',
default=0.0,
type=float,
help="Minimum identity to consider for assignment, as a normalized identity, e.g. 0.95 for an identity of 95%%. "
"Default: 0.00 (no threshold).")
group.add_argument('--minimum-circle','-c',
action="store", dest="ecotag:bubble_threshold",
metavar='<CIRCLE_THRESHOLD>',
default=0.99,
type=float,
help="Minimum identity considered for the assignment circle "
"(sequence is assigned to the LCA of all sequences within a similarity circle of the best matches; "
"the threshold for this circle is the highest value between <CIRCLE_THRESHOLD> and the best assignment score found for the query sequence). "
"Give value as a normalized identity, e.g. 0.95 for an identity of 95%%. "
"Default: 0.99.")
def run(config):
DMS.obi_atexit()
logger("info", "obi ecotag")
# Open the query view: only the DMS
input = open_uri(config['obi']['inputURI'],
dms_only=True)
if input is None:
raise Exception("Could not read input")
i_dms = input[0]
i_dms_name = input[0].name
i_view_name = input[1]
# Open the reference view: only the DMS
ref = open_uri(config['ecotag']['ref_view'],
dms_only=True)
if ref is None:
raise Exception("Could not read reference view URI")
ref_dms = ref[0]
ref_dms_name = ref[0].name
ref_view_name = ref[1]
# Check that the threshold demanded is greater than or equal to the threshold used to build the reference database
if config['ecotag']['bubble_threshold'] < eval(ref_dms[ref_view_name].comments["ref_db_threshold"]) :
raise Exception(f"Error: The threshold demanded ({config['ecotag']['bubble_threshold']}) is lower than the threshold used to build the reference database ({float(ref_dms[ref_view_name].comments['ref_db_threshold'])}).")
# Open the output: only the DMS
output = open_uri(config['obi']['outputURI'],
input=False,
dms_only=True)
if output is None:
raise Exception("Could not create output")
o_dms = output[0]
output_0 = output[0]
final_o_view_name = output[1]
# If stdout output or the input and output DMS are not the same, create a temporary view that will be exported and deleted.
if i_dms != o_dms or type(output_0)==BufferedWriter:
temporary_view_name = b"temp"
i=0
while temporary_view_name in i_dms: # Making sure view name is unique in input DMS
temporary_view_name = temporary_view_name+b"_"+str2bytes(str(i))
i+=1
o_view_name = temporary_view_name
if type(output_0)==BufferedWriter:
o_dms = i_dms
else:
o_view_name = final_o_view_name
# Read taxonomy DMS and name
taxo = open_uri(config['obi']['taxoURI'],
dms_only=True)
taxo_dms_name = taxo[0].name
taxo_dms = taxo[0]
taxonomy_name = config['obi']['taxoURI'].split("/")[-1] # Robust in theory
# Save command config in View comments
command_line = " ".join(sys.argv[1:])
input_dms_name=[i_dms_name]
input_view_name= [i_view_name]
input_dms_name.append(ref_dms_name)
input_view_name.append(ref_view_name)
input_dms_name.append(config['obi']['taxoURI'].split("/")[-3])
input_view_name.append("taxonomy/"+config['obi']['taxoURI'].split("/")[-1])
comments = View.print_config(config, "ecotag", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
if obi_ecotag(i_dms.name_with_full_path, tobytes(i_view_name), \
ref_dms.name_with_full_path, tobytes(ref_view_name), \
taxo_dms.name_with_full_path, tobytes(taxonomy_name), \
tobytes(o_view_name), comments, \
config['ecotag']['threshold'], \
config['ecotag']['bubble_threshold']) < 0:
raise Exception("Error running ecotag")
# If the input and output DMS are not the same, export result view to output DMS
if i_dms != o_dms:
View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, final_o_view_name)
# Save command config in DMS comments
o_dms.record_command_line(command_line)
# stdout output: write to buffer
if type(output_0)==BufferedWriter:
logger("info", "Printing to output...")
o_view = o_dms[o_view_name]
o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
o_view.close()
#print("\n\nOutput view:\n````````````", file=sys.stderr)
#print(repr(o_dms[final_o_view_name]), file=sys.stderr)
# If the input and the output DMS are different or if stdout output, delete the temporary imported view used to create the final view
if i_dms != o_dms or type(output_0)==BufferedWriter:
View.delete_view(i_dms, o_view_name)
o_dms.close(force=True)
taxo_dms.close(force=True)
ref_dms.close(force=True)
i_dms.close(force=True)
logger("info", "Done.")
|
