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
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
|
#!/usr/bin/env python
# File created on 27 Oct 2009.
from __future__ import division
__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.4.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
__status__ = "Release"
from qiime.util import make_option
from os import makedirs
from qiime.util import (load_qiime_config,
parse_command_line_parameters,
get_options_lookup)
from qiime.parse import parse_qiime_parameters
from qiime.workflow import (run_core_qiime_analyses, print_commands,
call_commands_serially, print_to_stdout, no_status_updates,
validate_and_set_jobs_to_start)
qiime_config = load_qiime_config()
options_lookup = get_options_lookup()
script_info={}
script_info['brief_description'] = """A workflow for running a core set of QIIME analyses."""
script_info['script_description'] = """This script plugs several QIIME steps together to form a basic full data analysis workflow. The steps include quality filtering and demultiplexing sequences (optional), running the pick_otus_through_otu_table.py workflow (pick otus and representative sequences, assign taxonomy, align representative sequences, build a tree, and build the OTU table), generating 2d and 3d beta diversity PCoA plots, generating alpha rarefaction plots, identifying OTUs that are differentially represented in different categories, and several additional analysis. Beta diversity calculations will be run both with and without an even sampling step, where the depth of sampling can either be passed to the script or QIIME will try to make a reasonable guess."""
script_info['script_usage'] = [("","Run serial analysis using default parameters, and guess the even sampling depth (no -e provided)","%prog -i Fasting_Example.fna -q Fasting_Example.qual -o FastingStudy -m Fasting_Map.txt -c Treatment,DOB"),("","Run serial analysis, and guess the even sampling depth (no -e provided). Skip split libraries by starting with already demultiplexed sequences.","%prog -i seqs.fna -o FastingStudy -p custom_parameters.txt -m Fasting_Map.txt -c Treatment,DOB")]
script_info['output_description'] =""""""
script_info['required_options'] = [
make_option('-i','--input_fnas',
help='the input fasta file(s) -- comma-separated '+\
'if more than one [REQUIRED]'),
make_option('-o','--output_dir',
help='the output directory [REQUIRED]'),
make_option('-m','--mapping_fp',
help='the mapping filepath [REQUIRED]'),
]
script_info['optional_options'] = [\
make_option('-p','--parameter_fp',
help='path to the parameter file, which specifies changes'+\
' to the default behavior. '+\
'See http://www.qiime.org/documentation/file_formats.html#qiime-parameters.'+\
' [if omitted, default values will be used]'),
make_option('-q','--input_quals',
help='The 454 qual files. Comma-separated'+\
' if more than one, and must correspond to the '+\
' order of the fasta files. Not relevant if passing '+\
' --suppress_split_libraries. [default: %default]'),
make_option('-f','--force',action='store_true',\
dest='force',help='Force overwrite of existing output directory'+\
' (note: existing files in output_dir will not be removed)'+\
' [default: %default]'),
# make_option('-w','--print_only',action='store_true',
# dest='print_only',help='Print the commands but don\'t call them -- '+\
# 'useful for debugging [default: %default]',default=False),
make_option('-a','--parallel',action='store_true',
dest='parallel',default=False,
help='Run in parallel where available. Specify number of'+\
' jobs to start with -O or in the parameters file. [default: %default]'),
make_option('-e','--seqs_per_sample',type='int',
help='Depth of coverage for diversity analyses that incorporate'+\
' subsampling the OTU table to an equal number of sequences per'+\
' sample. [default: determined automatically - bad choices can be'+\
' made in some circumstances]'),
make_option('--even_sampling_keeps_all_samples',
help='if -e/--seqs_per_sample is not provided, chose the even sampling'+\
' depth to force retaining all samples (rather then default which will'+\
' choose a sampling depth which may favor keeping '+\
' more sequences by excluding some samples) [default: %default]',
default=False, action='store_true'),
make_option('-t','--reference_tree_fp',
help='Path to the tree file if one should be used.'+\
' Relevant for closed-reference-based OTU picking'+\
' methods only (i.e., uclust_ref -C and BLAST)'+\
' [default: de novo tree will be used]'),
make_option('-c','--categories',
help='The metadata category or categories to compare'+\
' (i.e., column headers in the mapping file)' +\
' for the otu_category_significance,'+\
' supervised_learning.py, and cluster_quality.py steps.'+\
' Pass a comma-separated list if more than one category'+\
' [default: %default; skip these steps]'),
make_option('--suppress_split_libraries',action='store_true',default=False,
help='Skip demultiplexing/quality filtering (i.e. split_libraries).'+\
' This assumes that sequence identifiers are in post-split_libraries'+\
' format (i.e., sampleID_seqID) [default: %default]'),
options_lookup['jobs_to_start_workflow']
]
script_info['version'] = __version__
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
verbose = opts.verbose
input_fnas = opts.input_fnas
input_quals = opts.input_quals
output_dir = opts.output_dir
sampling_depth = opts.seqs_per_sample
categories = opts.categories
reference_tree_fp = opts.reference_tree_fp
mapping_fp = opts.mapping_fp
verbose = opts.verbose
print_only = False # This feature is not currently supported
suppress_split_libraries = opts.suppress_split_libraries
even_sampling_keeps_all_samples = opts.even_sampling_keeps_all_samples
parallel = opts.parallel
if suppress_split_libraries and len(input_fnas.split(',')) > 1:
option_parser.error("Only a single fasta file can be passed with "+\
"--suppress_split_libraries")
if opts.parameter_fp != None:
try:
parameter_f = open(opts.parameter_fp)
except IOError:
raise IOError,\
"Can't open parameters file (%s). Does it exist? Do you have read access?"\
% opts.parameter_fp
params = parse_qiime_parameters(parameter_f)
else:
params = parse_qiime_parameters([])
jobs_to_start = opts.jobs_to_start
default_jobs_to_start = qiime_config['jobs_to_start']
validate_and_set_jobs_to_start(params,
jobs_to_start,
default_jobs_to_start,
parallel,
option_parser)
try:
makedirs(output_dir)
except OSError:
if opts.force:
pass
else:
# Since the analysis can take quite a while, I put this check
# in to help users avoid overwriting previous output.
print "Output directory already exists. Please choose "+\
"a different directory, or force overwrite with -f."
exit(1)
if print_only:
command_handler = print_commands
else:
command_handler = call_commands_serially
if verbose:
status_update_callback = print_to_stdout
else:
status_update_callback = no_status_updates
run_core_qiime_analyses(
fna_fps=input_fnas,
qual_fps=input_quals,
mapping_fp=mapping_fp,
output_dir=output_dir,
command_handler=command_handler,
params=params,
qiime_config=qiime_config,
categories=categories,
sampling_depth=sampling_depth,
suppress_split_libraries=suppress_split_libraries,
even_sampling_keeps_all_samples=even_sampling_keeps_all_samples,
arare_min_rare_depth=10,
arare_num_steps=10,
reference_tree_fp=reference_tree_fp,
parallel=parallel,
status_update_callback=status_update_callback)
if __name__ == "__main__":
main()
|
