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#!/usr/bin/env python
# File created on 09 Feb 2010
from __future__ import division
__author__ = "William Walters"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["William Walters"]
__license__ = "GPL"
__version__ = "1.4.0"
__maintainer__ = "William Walters"
__email__ = "William.A.Walters@colorado.edu"
__status__ = "Release"
from qiime.util import parse_command_line_parameters, get_options_lookup
from qiime.util import make_option
from qiime.check_id_map import check_mapping_file
from string import letters, digits
#check_id_map.py
options_lookup = get_options_lookup()
script_info={}
script_info['brief_description']="""Checks user's metadata mapping file for required data, valid format"""
script_info['script_description']="""Specifically, we check that:
- The filename does not contain spaces (warn + rewrite if it does)
- There are headers for SampleID, LinkerPrimerSequence, and BarcodeSequence if barcodes are used (returns errors if these are absent or misspelled)
- The BarcodeSequence and LinkerPrimerSequences fields have valid IUPAC DNA characters
- There are not duplicate header fields (error)
- There are not duplicate near-unique but not exactly unique values within each column (warning)
- The headers do not contain invalid characters (alphanumeric and underscore only)
- The data fields do not contain invalid characters (alphanumeric, underscore, space, and +-%./:,; characters)
- SampleID fields are MIENS compliant (only alphanumeric and . characters)
- There are no duplicates when the primer and barcodes are appended
- If there is a field ReversePrimer for reverse primers (for removal with split_libraries), the characters are DNA IUPAC compliant and no fields are empty
Errors and warnings are saved to a log file. Errors are generally caused
by problems with the headers, and should be resolved before attempting to
correct any warnings. Warnings can arise from invalid characters,
near-duplicate metadata, duplicate sample descriptions/barcodes, or missing
data fields. Warnings will contain a reference to the cell (row,column)
that the warning arose from.
In addition to the log file, a "corrected_mapping" file will be created.
Invalid characters will be replaced by underscores in this corrected mapping
file if there were any such characters in the input metadata mapping file.
If there were no invalid characters to replace, the corrected mapping file
will contain comments saying as much.
check_id_map.py should not raise exceptions itself under normal
circumstances, except for situations such as having a misformatted input
metadata mapping file.
If pooled primers are used, separate with a comma. For instance, a pooled
set of three 27f primers (used to increase taxonomic coverage) could be
specified in the LinkerPrimerSequence fields as such:
AGGGTTCGATTCTGGCTCAG,AGAGTTTGATCCTGGCTTAG,AGAATTTGATCTTGGTTCAG
"""
script_info['script_usage']=[]
script_info['script_usage'].append(("""Example:""","""Check the test_mapping.txt mapping file for problems, supplying the required mapping file and output directory (in this case mapping_info)""","""check_id_map.py -m test_mapping.txt -o mapping_info/"""))
script_info['output_description']="""A log file and corrected_mapping.txt file will be written to the mapping_info directory."""
script_info['required_options']= [\
make_option('-m', '--map', dest='map_fname',
help='Metadata mapping file filepath'),
make_option('-o', '--output_dir',
help='Required output directory for log file and corrected mapping '+\
'file (by default, invalid characters will be '+\
'converted to underscores)')
]
script_info['optional_options']= [\
make_option('-c', '--char_replace', dest='char_replace',
help='Changes the default character used to replace invalid '+\
'characters found in the mapping file. Must be a valid character ('+\
'alphanumeric or underscore). NOT IMPLEMENTED CURRENTLY '+\
'[default: %default]', default="_"),
make_option('-b', '--not_barcoded',
action='store_true', default=False,
help='Use -b if barcodes are not present. [default: %default]'),
make_option('-B', '--variable_len_barcodes',
action='store_true', default=False,
help='Use -B if variable length barcodes are present to suppress '+\
'warnings about barcodes of unequal length. [default: %default]'),
make_option('-p', '--disable_primer_check',
action='store_true', default=False,
help='Use -p to disable checks for primers. [default: %default]'),
make_option('-v', '--verbose',
action='store_false', default=True,
help='Turn on this flag to disable verbose output. '+\
' [default: %default]'),
make_option('-j', '--added_demultiplex_field',
action='store', default=None,
help='Use -j to add a field to use in the mapping file as an '+\
'additional demultiplexing option to the barcode. All combinations '+\
'of barcodes and the values in these fields must be unique. The '+\
'fields must contain values that can be parsed from the fasta labels '+\
'such as "plate=R_2008_12_09". In this case, "plate" would be the '+\
'column header and "R_2008_12_09" would be the field data (minus '+\
'quotes) in the mapping file. To use the run prefix from the fasta '+\
'label, such as ">FLP3FBN01ELBSX", where "FLP3FBN01" is generated '+\
'from the run ID, use "-j run_prefix" and set the run prefix to '+\
'be used as the data under the column headerr "run_prefix". '+\
' [default: %default]')]
script_info['version'] = __version__
def main():
option_parser, opts, args =\
parse_command_line_parameters(suppress_verbose=True, **script_info)
infile_name = opts.map_fname
has_barcodes = not opts.not_barcoded
output_dir = opts.output_dir
char_replace = opts.char_replace
var_len_barcodes = opts.variable_len_barcodes
verbose = opts.verbose
disable_primer_check = opts.disable_primer_check
added_demultiplex_field = opts.added_demultiplex_field
valid_replacement_chars=digits+letters+"_"
if char_replace not in valid_replacement_chars:
option_parser.error('-c option requires alphanumeric or '+\
'underscore character')
if len(char_replace) != 1:
option_parser.error('-c parameter must be a single character.')
check_mapping_file(infile_name, output_dir, has_barcodes, char_replace,\
verbose, var_len_barcodes, disable_primer_check, added_demultiplex_field)
if __name__ == "__main__":
main()
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