def check_mapping_data(mapping_data, headers, filename_column):
""" Checks mapping data for MIMARKS SampleIDs, unique IDs, fasta file names
Also returns a dict of fasta file name: SampleID
mapping_data: list of lines of data from mapping file
headers: list of header strings
filename_column: Column of metadata mapping file containing fasta filenames
"""
# First make sure there is a SampleID and filename_column present
try:
sample_id_ix = headers.index("SampleID")
except ValueError:
raise ValueError(
"SampleID column not found in mapping file, please " + "check mapping file with validate_mapping_file.py"
)
try:
filename_col_ix = headers.index(filename_column)
except ValueError:
raise ValueError("Specified column %s not found in mapping file." % filename_column)
valid_mimarks = letters + digits + "."
fasta_name_to_sample_id = {}
fasta_names = []
sample_ids = []
for line in mapping_data:
try:
fasta_name_to_sample_id[basename(line[filename_col_ix].strip())] = line[sample_id_ix]
except IndexError:
raise IndexError("Missing filename column data in line %s " % line)
for curr_char in line[sample_id_ix]:
if curr_char not in valid_mimarks:
raise ValueError(
"Found invalid character in line: %s\n" % line
+ "SampleIDs must be alphanumeric and . characters "
+ "only"
)
sample_ids.append(line[sample_id_ix].strip())
fasta_names.append(line[filename_col_ix].strip())
fasta_name_dups = duplicates_indices(fasta_names)
if fasta_name_dups:
raise ValueError(
"Found duplicate fasta names: %s" % "\t".join([fasta_name for fasta_name in fasta_name_dups.keys()])
)
sample_id_dups = duplicates_indices(sample_ids)
if sample_id_dups:
raise ValueError(
"Found duplicate SampleID names: %s" % "\t".join([sample_id for sample_id in sample_id_dups.keys()])
)
return fasta_name_to_sample_id
def check_mapping_data(mapping_data, headers, filename_column):
""" Checks mapping data for MIMARKS SampleIDs, unique IDs, fasta file names
Also returns a dict of fasta file name: SampleID
mapping_data: list of lines of data from mapping file
headers: list of header strings
filename_column: Column of metadata mapping file containing fasta filenames
"""
# First make sure there is a SampleID and filename_column present
try:
sample_id_ix = headers.index("SampleID")
except ValueError:
raise ValueError("SampleID column not found in mapping file, please " +
"check mapping file with validate_mapping_file.py")
try:
filename_col_ix = headers.index(filename_column)
except ValueError:
raise ValueError("Specified column %s not found in mapping file." %
filename_column)
valid_mimarks = letters + digits + "."
fasta_name_to_sample_id = {}
fasta_names = []
sample_ids = []
for line in mapping_data:
try:
fasta_name_to_sample_id[basename(line[filename_col_ix].strip())] =\
line[sample_id_ix]
except IndexError:
raise IndexError("Missing filename column data in line %s " % line)
for curr_char in line[sample_id_ix]:
if curr_char not in valid_mimarks:
raise ValueError(
"Found invalid character in line: %s\n" % line +
"SampleIDs must be alphanumeric and . characters " +
"only")
sample_ids.append(line[sample_id_ix].strip())
fasta_names.append(line[filename_col_ix].strip())
fasta_name_dups = duplicates_indices(fasta_names)
if fasta_name_dups:
raise ValueError(
"Found duplicate fasta names: %s" %
"\t".join([fasta_name for fasta_name in fasta_name_dups.keys()]))
sample_id_dups = duplicates_indices(sample_ids)
if sample_id_dups:
raise ValueError(
"Found duplicate SampleID names: %s" %
"\t".join([sample_id for sample_id in sample_id_dups.keys()]))
return fasta_name_to_sample_id
def check_fixed_len_bcs_dups(header,
mapping_data,
errors):
""" Checks barcodes of same length for duplicates, adds to errors if found
header: list of header strings
mapping_data: list of lists of raw metadata mapping file data
errors: list of errors
"""
header_field_to_check = "BarcodeSequence"
# Skip if no field BarcodeSequence
try:
check_ix = header.index(header_field_to_check)
except ValueError:
return errors
barcodes = []
correction = 1
for curr_data in mapping_data:
barcodes.append(upper(curr_data[check_ix]))
dups = duplicates_indices(barcodes)
for curr_dup in dups:
for curr_loc in dups[curr_dup]:
errors.append('Duplicate barcode %s found.\t%d,%d' %
(curr_dup, curr_loc + correction, check_ix))
return errors
def check_fixed_len_bcs_dups(header,
mapping_data,
errors):
""" Checks barcodes of same length for duplicates, adds to errors if found
header: list of header strings
mapping_data: list of lists of raw metadata mapping file data
errors: list of errors
"""
header_field_to_check = "BarcodeSequence"
# Skip if no field BarcodeSequence
try:
check_ix = header.index(header_field_to_check)
except ValueError:
return errors
barcodes = []
correction = 1
for curr_data in mapping_data:
barcodes.append(curr_data[check_ix])
dups = duplicates_indices(barcodes)
for curr_dup in dups:
for curr_loc in dups[curr_dup]:
errors.append('Duplicate barcode %s found.\t%d,%d' %\
(curr_dup, curr_loc + correction, check_ix))
return errors
def check_variable_len_bcs_dups(header, mapping_data, errors):
""" Checks variable length barcodes plus sections of primers for dups
header: list of header strings
mapping_data: list of lists of raw metadata mapping file data
errors: list of errors
"""
header_field_to_check = "BarcodeSequence"
# Skip if no field BarcodeSequence
try:
check_ix = header.index(header_field_to_check)
except ValueError:
return errors
linker_primer_field = "LinkerPrimerSequence"
try:
linker_primer_ix = header.index(linker_primer_field)
no_primers = False
except ValueError:
no_primers = True
barcodes = []
bc_lens = []
correction = 1
for curr_data in mapping_data:
barcodes.append(upper(curr_data[check_ix]))
bc_lens.append(len(curr_data[check_ix]))
# Get max length of barcodes to determine how many primer bases to slice
barcode_max_len = max(bc_lens)
# Have to do second pass to append correct number of nucleotides to
# check for duplicates between barcodes and primer sequences
bcs_added_nts = []
for curr_data in mapping_data:
if no_primers:
bcs_added_nts.append(upper(curr_data[check_ix]))
else:
adjusted_len = barcode_max_len - len(curr_data[check_ix])
bcs_added_nts.append(upper(curr_data[check_ix] + curr_data[linker_primer_ix][0:adjusted_len]))
dups = duplicates_indices(bcs_added_nts)
for curr_dup in dups:
for curr_loc in dups[curr_dup]:
if no_primers:
errors.append("Duplicate barcode %s found.\t%d,%d" % (curr_dup, curr_loc + correction, check_ix))
else:
errors.append(
"Duplicate barcode and primer fragment sequence "
+ "%s found.\t%d,%d" % (curr_dup, curr_loc + correction, check_ix)
)
return errors
def check_variable_len_bcs_dups(header, mapping_data, errors):
""" Checks variable length barcodes plus sections of primers for dups
header: list of header strings
mapping_data: list of lists of raw metadata mapping file data
errors: list of errors
"""
header_field_to_check = "BarcodeSequence"
# Skip if no field BarcodeSequence
try:
check_ix = header.index(header_field_to_check)
except ValueError:
return errors
linker_primer_field = "LinkerPrimerSequence"
try:
linker_primer_ix = header.index(linker_primer_field)
no_primers = False
except ValueError:
no_primers = True
barcodes = []
bc_lens = []
correction = 1
for curr_data in mapping_data:
barcodes.append(upper(curr_data[check_ix]))
bc_lens.append(len(curr_data[check_ix]))
# Get max length of barcodes to determine how many primer bases to slice
barcode_max_len = max(bc_lens)
# Have to do second pass to append correct number of nucleotides to
# check for duplicates between barcodes and primer sequences
bcs_added_nts = []
for curr_data in mapping_data:
if no_primers:
bcs_added_nts.append(upper(curr_data[check_ix]))
else:
adjusted_len = barcode_max_len - len(curr_data[check_ix])
bcs_added_nts.append(upper(curr_data[check_ix] +\
curr_data[linker_primer_ix][0:adjusted_len]))
dups = duplicates_indices(bcs_added_nts)
for curr_dup in dups:
for curr_loc in dups[curr_dup]:
if no_primers:
errors.append('Duplicate barcode %s found.\t%d,%d' %\
(curr_dup, curr_loc + correction, check_ix))
else:
errors.append('Duplicate barcode and primer fragment sequence '+\
'%s found.\t%d,%d' % (curr_dup, curr_loc + correction, check_ix))
return errors
def check_sampleid_duplicates(header,
mapping_data,
errors):
""" Flags duplicate, missing SampleIDs as errors
header: list of header strings
mapping_data: list of lists of raw metadata mapping file data
errors: list of errors
"""
sample_id_field = "SampleID"
correction = 1
try:
sample_id_ix = header.index(sample_id_field)
except ValueError:
# Skip out at this point, header check will have error for missing
# field
return errors
sample_ids = []
# Need to save locations of missing IDs so they aren't flagged twice
missing_sample_ids = []
for curr_data in range(len(mapping_data)):
if len(mapping_data[curr_data][sample_id_ix]) == 0:
errors.append('Missing SampleID.\t%d,%d' %
(curr_data + correction, sample_id_ix))
missing_sample_ids.append(curr_data + correction)
sample_ids.append(mapping_data[curr_data][sample_id_ix])
dups = duplicates_indices(sample_ids)
for curr_dup in dups:
for curr_loc in dups[curr_dup]:
if (curr_loc + correction) not in missing_sample_ids:
errors.append('Duplicate SampleID %s found.\t%d,%d' %
(curr_dup, curr_loc + correction, sample_id_ix))
return errors
def check_sampleid_duplicates(header,
mapping_data,
errors):
""" Flags duplicate, missing SampleIDs as errors
header: list of header strings
mapping_data: list of lists of raw metadata mapping file data
errors: list of errors
"""
sample_id_field = "SampleID"
correction = 1
try:
sample_id_ix = header.index(sample_id_field)
except ValueError:
# Skip out at this point, header check will have error for missing
# field
return errors
sample_ids = []
# Need to save locations of missing IDs so they aren't flagged twice
missing_sample_ids = []
for curr_data in range(len(mapping_data)):
if len(mapping_data[curr_data][sample_id_ix]) == 0:
errors.append('Missing SampleID.\t%d,%d' %\
(curr_data + correction, sample_id_ix))
missing_sample_ids.append(curr_data + correction)
sample_ids.append(mapping_data[curr_data][sample_id_ix])
dups = duplicates_indices(sample_ids)
for curr_dup in dups:
for curr_loc in dups[curr_dup]:
if (curr_loc + correction) not in missing_sample_ids:
errors.append('Duplicate SampleID %s found.\t%d,%d' %\
(curr_dup, curr_loc + correction, sample_id_ix))
return errors
def check_mapping_data(mapping_data):
""" Checks mapping data for MIMARKS SampleIDs, unique IDs, fasta file names
Also returns a dict of fasta file name: SampleID
mapping_data: list of lines of data from mapping file
"""
valid_mimarks = letters + digits + "."
fasta_name_to_sample_id = {}
fasta_names = []
for line in mapping_data:
curr_line = line.strip().split('\t')
if not curr_line or line.startswith("#"):
continue
try:
fasta_name_to_sample_id[basename(curr_line[1].strip())] =\
curr_line[0]
except IndexError:
raise IndexError,("Found non-tab separated line in mapping "+\
"data. Offending line is: %s" % line)
for curr_char in curr_line[0]:
if curr_char not in valid_mimarks:
raise ValueError,("Found invalid character in line: %s\n" %\
line + "SampleIDs must be alphanumeric and . characters "+\
"only")
fasta_names.append(curr_line[1].strip())
fasta_name_dups = duplicates_indices(fasta_names)
if fasta_name_dups:
raise ValueError,("Found duplicate fasta names: %s" %\
"\t".join([fasta_name for fasta_name in fasta_name_dups.keys()]))
return fasta_name_to_sample_id
def check_mapping_data(mapping_data):
""" Checks mapping data for MIMARKS SampleIDs, unique IDs, fasta file names
Also returns a dict of fasta file name: SampleID
mapping_data: list of lines of data from mapping file
"""
valid_mimarks = letters + digits + "."
fasta_name_to_sample_id = {}
fasta_names = []
for line in mapping_data:
curr_line = line.strip().split('\t')
if not curr_line or line.startswith("#"):
continue
try:
fasta_name_to_sample_id[basename(curr_line[1].strip())] =\
curr_line[0]
except IndexError:
raise IndexError,("Found non-tab separated line in mapping "+\
"data. Offending line is: %s" % line)
for curr_char in curr_line[0]:
if curr_char not in valid_mimarks:
raise ValueError,("Found invalid character in line: %s\n" %\
line + "SampleIDs must be alphanumeric and . characters "+\
"only")
fasta_names.append(curr_line[1].strip())
fasta_name_dups = duplicates_indices(fasta_names)
if fasta_name_dups:
raise ValueError,("Found duplicate fasta names: %s" %\
"\t".join([fasta_name for fasta_name in fasta_name_dups.keys()]))
return fasta_name_to_sample_id
def check_added_demultiplex_dups(header,
mapping_data,
errors,
has_barcodes=True,
added_demultiplex_field=None):
""" Checks that all barcodes and added demultiplex fields are unique
header: list of header strings
mapping_data: list of lists of raw metadata mapping file data
errors: list of errors
has_barcodes: True if barcode fields are to be used.
added_demultiplex_field: If specified, references a field in the mapping
file to use for demultiplexing. These are to be read from fasta labels
during the actual demultiplexing step. All combinations of barcodes,
primers, and the added_demultiplex_field must be unique.
"""
# Treat as variable length to test combinations of barcodes and the
# added demultiplex field (should return the same result for the barcode
# component)
correction = 1
header_field_to_check = "BarcodeSequence"
bc_found = False
# Skip if no field BarcodeSequence
if has_barcodes:
try:
bc_ix = header.index(header_field_to_check)
bc_found = True
except ValueError:
pass
linker_primer_field = "LinkerPrimerSequence"
try:
linker_primer_ix = header.index(linker_primer_field)
no_primers = False
except ValueError:
no_primers = True
try:
added_demultiplex_ix = header.index(added_demultiplex_field)
except ValueError:
# Skip out at this point, header check will have error for missing
# field
return errors
barcodes = []
bc_lens = []
bcs_added_field = []
if has_barcodes and bc_found:
for curr_data in mapping_data:
barcodes.append(upper(curr_data[bc_ix]))
bc_lens.append(len(curr_data[bc_ix]))
# Get max length of barcodes to determine how many primer bases to
# slice
barcode_max_len = max(bc_lens)
# Have to do second pass to append correct number of nucleotides to
# check for duplicates between barcodes and primer sequences
for curr_data in mapping_data:
if no_primers:
bcs_added_field.append(curr_data[bc_ix] +
curr_data[added_demultiplex_ix])
else:
adjusted_len = barcode_max_len - len(curr_data[bc_ix])
bcs_added_field.append(curr_data[bc_ix] +
curr_data[linker_primer_ix][0:adjusted_len] +
curr_data[added_demultiplex_ix])
else:
for curr_data in mapping_data:
bcs_added_field.append(curr_data[added_demultiplex_ix])
dups = duplicates_indices(bcs_added_field)
for curr_dup in dups:
if has_barcodes and bc_found:
for curr_loc in dups[curr_dup]:
errors.append('Duplicate barcode and added demultiplex field ' +
'%s found.\t%d,%d' % (curr_dup, curr_loc + correction, bc_ix))
else:
for curr_loc in dups[curr_dup]:
errors.append('Duplicate added demultiplex field ' +
'%s found.\t%d,%d' % (curr_dup, curr_loc + correction,
added_demultiplex_ix))
return errors
def check_added_demultiplex_dups(header,
mapping_data,
errors,
has_barcodes=True,
added_demultiplex_field=None):
""" Checks that all barcodes and added demultiplex fields are unique
header: list of header strings
mapping_data: list of lists of raw metadata mapping file data
errors: list of errors
has_barcodes: True if barcode fields are to be used.
added_demultiplex_field: If specified, references a field in the mapping
file to use for demultiplexing. These are to be read from fasta labels
during the actual demultiplexing step. All combinations of barcodes,
primers, and the added_demultiplex_field must be unique.
"""
# Treat as variable length to test combinations of barcodes and the
# added demultiplex field (should return the same result for the barcode
# component)
correction = 1
header_field_to_check = "BarcodeSequence"
bc_found = False
# Skip if no field BarcodeSequence
if has_barcodes:
try:
bc_ix = header.index(header_field_to_check)
bc_found = True
except ValueError:
pass
linker_primer_field = "LinkerPrimerSequence"
try:
linker_primer_ix = header.index(linker_primer_field)
no_primers = False
except ValueError:
no_primers = True
try:
added_demultiplex_ix = header.index(added_demultiplex_field)
except ValueError:
# Skip out at this point, header check will have error for missing
# field
return errors
barcodes = []
bc_lens = []
bcs_added_field = []
if has_barcodes and bc_found:
for curr_data in mapping_data:
barcodes.append(curr_data[bc_ix])
bc_lens.append(len(curr_data[bc_ix]))
# Get max length of barcodes to determine how many primer bases to slice
barcode_max_len = max(bc_lens)
# Have to do second pass to append correct number of nucleotides to
# check for duplicates between barcodes and primer sequences
for curr_data in mapping_data:
if no_primers:
bcs_added_field.append(curr_data[bc_ix] +\
curr_data[added_demultiplex_ix])
else:
adjusted_len = barcode_max_len - len(curr_data[bc_ix])
bcs_added_field.append(curr_data[bc_ix] +\
curr_data[linker_primer_ix][0:adjusted_len] +\
curr_data[added_demultiplex_ix])
else:
for curr_data in mapping_data:
bcs_added_field.append(curr_data[added_demultiplex_ix])
dups = duplicates_indices(bcs_added_field)
for curr_dup in dups:
if has_barcodes and bc_found:
for curr_loc in dups[curr_dup]:
errors.append('Duplicate barcode and added demultiplex field '+\
'%s found.\t%d,%d' % (curr_dup, curr_loc + correction, bc_ix))
else:
for curr_loc in dups[curr_dup]:
errors.append('Duplicate added demultiplex field '+\
'%s found.\t%d,%d' % (curr_dup, curr_loc + correction,
added_demultiplex_ix))
return errors