def create_snp_reference_seq(options_dict):
"""Write reference sequence bases at SNP locations to a fasta file.
Description:
Write reference sequence bases at SNP locations to a fasta file.
This function expects, or creates '(*)', the following files:
reference.fasta
snplist.txt
referenceSNP.fasta (*)
The files are used as follows:
1. The reference.fasta input file contains the whole-genome reference
bases.
2. The snplist.txt input file contains the list of SNP positions across
all the samples.
2. The referenceSNP.fasta output file contains the reference bases at
the identified SNP locations.
The snplist.txt file is created outside of this function. The package
documentation provides an example of creating this file based on the
lambda_virus sequence that is used as one test for this package.
Args:
referenceFile: File path (not just file name) for reference sequence
(in fasta format
snpListFile: File path (not just file name) of text format list of SNP
positions
snpRefFile: File path (not just file name) for the SNP reference
sequence file.
Raises:
Examples:
options_dict = {'referenceFile':'reference.fasta',
'snpListFile':'snplist.txt',
'snpRefFile':'referenceSNP.fasta'
}
create_snp_reference_seq(options_dict)
"""
print_log_header()
verbose_print("# %s %s" % (timestamp(), command_line_short()))
verbose_print("# %s version %s" % (program_name(), __version__))
print_arguments(options_dict)
#==========================================================================
# Write reference sequence bases at SNP locations to a fasta file.
#==========================================================================
reference_file = options_dict['referenceFile']
snp_list_file_path = options_dict['snpListFile']
snp_ref_seq_path = options_dict['snpRefFile']
source_files = [reference_file, snp_list_file_path]
if options_dict['forceFlag'] or utils.target_needs_rebuild(source_files, snp_ref_seq_path):
utils.write_reference_snp_file(reference_file, snp_list_file_path, snp_ref_seq_path)
verbose_print("")
else:
verbose_print("SNP reference sequence %s has already been freshly built. Use the -f option to force a rebuild." % snp_ref_seq_path)
verbose_print("# %s %s finished" % (timestamp(), program_name()))
def create_snp_list(options_dict):
"""Create SNP list file
Description:
Create the SNP list -- the list of positions where variants were found
and the corresponding list of samples having a variant at each position.
This function expects, or creates '(*)', the following files arranged
in the following way:
sampleDirectories.txt
samples
sample_name_one/var.flt.vcf
...
snplist.txt (*)
The files are used as follows:
1. The sampleDirectories.txt input file contains a list of the paths to
the sample directories.
2. The var.flt.vcf variant input files are used to construct the
SNP position list.
3. The snplist.txt output file contains the union of the SNP positions
and sample names extracted from all the var.flt.vcf files.
The sampleDirectories.txt and var.flt.vcf files are created outside of
this function. The package documentation provides an example of creating
these files based on the lambda_virus sequence that is used as one test
for this package.
Args:
sampleDirsFile: File path (not just file name) of file containing paths
to directories containing var.flt.vcf file for each sequence.
vcfFileName: File name of the VCF files which must exist in each of the
sample directories
snpListFile: File path (not just file name) of text format list
of SNP positions
Raises:
Examples:
options_dict = {'sampleDirsFile':'sampleDirectories.txt',
'vcfFileName':'var.flt.vcf'
'snpListFile':'snplist.txt',
}
create_snp_list(options_dict)
"""
print_log_header()
verbose_print("# %s %s" % (timestamp(), command_line_short()))
verbose_print("# %s version %s" % (program_name(), __version__))
print_arguments(options_dict)
#==========================================================================
# Prep work
# Note use of filter on list_of_sample_directories to remove blank lines.
#==========================================================================
sample_directories_list_filename = options_dict['sampleDirsFile']
list_of_sample_directories = [line.rstrip() for line in open(sample_directories_list_filename, "r")]
list_of_sample_directories = sorted(filter(None, list_of_sample_directories))
#==========================================================================
# Read in all vcf files and process into dict of SNPs passing various
# criteria. Do this for each sample. Write to file.
#==========================================================================
snp_list_file_path = options_dict['snpListFile']
vcf_file_name = options_dict['vcfFileName']
list_of_vcf_files = [os.path.join(dir, vcf_file_name) for dir in list_of_sample_directories]
if options_dict['forceFlag'] or utils.target_needs_rebuild(list_of_vcf_files, snp_list_file_path):
snp_dict = utils.convert_vcf_files_to_snp_dict(list_of_vcf_files)
verbose_print('Found %d snp positions across %d sample vcf files.' % (len(snp_dict), len(list_of_vcf_files)))
utils.write_list_of_snps(snp_list_file_path, snp_dict)
verbose_print("")
else:
verbose_print("SNP list %s has already been freshly built. Use the -f option to force a rebuild." % snp_list_file_path)
verbose_print("# %s %s finished" % (timestamp(), program_name()))
def create_snp_matrix(options_dict):
"""Create SNP matrix
Description:
Create the SNP matrix containing the consensus base for each of the samples
at the positions where SNPs were found in any of the samples. The matrix
contains one row per sample and one column per SNP position. Non-SNP
positions are not included in the matrix.
This function expects, or creates '(*)', the following
files arranged in the following way:
sampleDirectories.txt
snplist.txt
samples
sample_name_one/reads.snp.pileup
...
snpma.fasta (*)
The files are used as follows:
1. The sampleDirectories.txt input file contains a list of the paths to
the sample directories.
2. The snplist.txt input file contains the list of SNP positions
extracted from the var.flt.vcf file.
3. The reads.snp.pileup input files are pileups at the SNP positions
only, used to determine the nucleotide base at each SNP position
for each sample to construct the SNP matrix fasta file.
4. The snpma.fasta output file contains the SNP calls for each
sequence, arranged as a fasta file with one sequence per sample.
The snplist.txt, sampleDirectories.txt, and reads.snp.pileup are created
outside of this function. The package documentation provides an example
of creating these files based on the lambda_virus sequence that is used
as one test for this package.
Args:
sampleDirsFile: File path (not just file name) of file containing paths
to directories containing reads.snp.pileup file for each sequence.
snpListFile: File path (not just file name) of text format list
of SNP positions
pileupFileName: File name of the SNP pileup files which must exist in
each of the sample directories')
snpmaFile: File path (not just file name) of the output snp matrix,
formatted as a fasta file, with each sequence (all of identical
length) corresponding to the SNPs in the correspondingly named
sequence.
Raises:
Examples:
options_dict = {'sampleDirsFile':'sampleDirectories.txt',
'snpListFile':'snplist.txt',
'pileupFileName':'reads.snp.pileup',
'snpmaFile':'snpma.fasta',
'minConsFreq':0.6,
}
create_snp_matrix(options_dict)
"""
print_log_header()
verbose_print("# %s %s" % (timestamp(), command_line_short()))
verbose_print("# %s version %s" % (program_name(), __version__))
print_arguments(options_dict)
#==========================================================================
# Prep work
# Note use of filter on list_of_sample_directories to remove blank lines.
#==========================================================================
sample_directories_list_filename = options_dict['sampleDirsFile']
list_of_sample_directories = [line.rstrip() for line in open(sample_directories_list_filename, "r")]
list_of_sample_directories = sorted(filter(None, list_of_sample_directories))
#==========================================================================
# Check if the result is already fresh
#==========================================================================
snpma_file_path = options_dict['snpmaFile']
snp_list_file_path = options_dict['snpListFile']
source_files = [snp_list_file_path]
if not options_dict['forceFlag']:
for sample_directory in list_of_sample_directories:
snp_pileup_file_path = os.path.join(sample_directory, options_dict['pileupFileName'])
source_files.append(snp_pileup_file_path)
if not utils.target_needs_rebuild(source_files, snpma_file_path):
verbose_print("SNP matrix %s has already been freshly built. Use the -f option to force a rebuild." % snpma_file_path)
verbose_print("# %s %s finished" % (timestamp(), program_name()))
return
#==========================================================================
# Read the list of SNP positions.
#==========================================================================
sorted_snp_position_list = utils.read_snp_position_list(snp_list_file_path)
snplist_length = len(sorted_snp_position_list)
verbose_print("snp position list length = %d" % snplist_length)
#==========================================================================
# Create snp matrix. Write results to file.
#==========================================================================
snp_sequence_records_list = []
for sample_directory in list_of_sample_directories:
sample_name = os.path.basename(sample_directory)
snp_pileup_file_path = os.path.join(sample_directory, options_dict['pileupFileName'])
position_consensus_base_dict = utils.create_consensus_dict(snp_pileup_file_path, options_dict['minConsFreq'])
if snplist_length > 0:
verbose_print("Sample %s consensus base coverage = %.2f%%" % (sample_name, 100.0 * len(position_consensus_base_dict) / snplist_length))
snp_seq_string = ""
for key in sorted_snp_position_list:
if position_consensus_base_dict.has_key(key):
snp_seq_string += position_consensus_base_dict[key]
else:
snp_seq_string += "-"
snp_seq_record = SeqRecord(Seq(snp_seq_string), id=sample_name, description="")
snp_sequence_records_list.append(snp_seq_record)
#Write bases for snps for each sequence to a fasta file
with open(snpma_file_path, "w") as fasta_file_object:
SeqIO.write(snp_sequence_records_list, fasta_file_object, "fasta")
verbose_print("")
verbose_print("# %s %s finished" % (timestamp(), program_name()))
def create_snp_pileup(options_dict):
"""Create the SNP pileup file for a sample.
Description:
Create the SNP pileup file for a sample -- the pileup file restricted to
only positions where variants were found in any sample.
This function expects, or creates '(*)', the following files arranged
in the following way:
snplist.txt
samples
sample_name_one/reads.all.pileup
sample_name_one/reads.snp.pileup (*)
...
The files are used as follows:
1. The snplist.txt input file contains the list of SNP positions
extracted from the var.flt.vcf file.
2. The reads.all.pileup input file is the genome-wide pileup file
for this sample.
3. The reads.snp.pileup output file is the pileup file for this sample,
restricted to only positions where variants were found in any
sample.
The snplist.txt and reads.all.pileup files are created outside of this
function. The package documentation provides an example of creating these
files based on the lambda_virus sequence that is used as one test for
this package.
Args:
snpListFile: File path (not just file name) of text format list
of SNP positions across all samples
allPileupFile: File path (not just file name) of the whole-genome
pileup file fot this sample
snpPileupFile: File path (not just file name) of the snp pileup file
Raises:
Examples:
options_dict = {'snpListFile':'snplist.txt',
'allPileupFile':'samples/SRR555888/reads.all.pileup'
'snpPileupFile':'samples/SRR555888/reads.snp.pileup'
}
create_snp_pileup(options_dict)
"""
print_log_header()
verbose_print("# %s %s" % (timestamp(), command_line_short()))
verbose_print("# %s version %s" % (program_name(), __version__))
print_arguments(options_dict)
snp_list_file_path = options_dict['snpListFile']
all_pileup_file_path = options_dict['allPileupFile']
snp_pileup_file_path = options_dict['snpPileupFile']
source_files = [snp_list_file_path, all_pileup_file_path]
if options_dict['forceFlag'] or utils.target_needs_rebuild(source_files, snp_pileup_file_path):
# Create a pileup file with a subset of the whole-genome pileup restricted
# to locations with SNPs only.
snp_list = utils.read_snp_position_list(snp_list_file_path)
utils.create_snp_pileup(all_pileup_file_path, snp_pileup_file_path, set(snp_list))
verbose_print("")
else:
verbose_print("SNP pileup %s has already been freshly built. Use the -f option to force a rebuild." % snp_pileup_file_path)
verbose_print("# %s %s finished" % (timestamp(), program_name()))
def create_snp_matrix(options_dict):
"""Create SNP matrix
Description:
Create the SNP matrix containing the consensus base for each of the samples
at the positions where SNPs were found in any of the samples. The matrix
contains one row per sample and one column per SNP position. Non-SNP
positions are not included in the matrix.
This function expects, or creates '(*)', the following
files arranged in the following way:
sampleDirectories.txt
samples
sample_name_one/consensus.fasta
...
snpma.fasta (*)
The files are used as follows:
1. The sampleDirectories.txt input file contains a list of the paths to
the sample directories.
2. The consensus.fasta input files are previously called consensus
for each sample to construct the SNP matrix fasta file.
3. The snpma.fasta output file contains the SNP calls for each
sequence, arranged as a multi-fasta file with one sequence per
sample.
The sampleDirectories.txt, and consensus.fasta are created outside of this
function. The package documentation provides an example of creating
these files based on the lambda_virus sequence that is used as one
test for this package.
Args:
sampleDirsFile : str
File path (not just file name) of file containing paths
to directories containing consensus.fasta file for each sequence.
snpListFile : str
File path (not just file name) of text format list of SNP positions
consFileName : str
File name of the previously called consensus fasta files which must
exist in each of the sample directories
snpmaFile : str
File path (not just file name) of the output snp matrix, formatted
as a fasta file, with each sequence (all of identical length)
corresponding to the SNPs in the correspondingly named sequence.
Raises:
Examples:
options_dict = {'sampleDirsFile':'sampleDirectories.txt',
'consFileName':'consensus.fasta',
'snpmaFile':'snpma.fasta',
'minConsFreq':0.6,
}
create_snp_matrix(options_dict)
"""
print_log_header()
verbose_print("# %s %s" % (timestamp(), command_line_short()))
verbose_print("# %s version %s" % (program_name(), __version__))
print_arguments(options_dict)
#==========================================================================
# Prep work
# Note use of filter on list_of_sample_directories to remove blank lines.
#==========================================================================
sample_directories_list_filename = options_dict['sampleDirsFile']
list_of_sample_directories = [line.rstrip() for line in open(sample_directories_list_filename, "r")]
list_of_sample_directories = sorted(filter(None, list_of_sample_directories))
#==========================================================================
# Check if the result is already fresh
#==========================================================================
snpma_file_path = options_dict['snpmaFile']
source_files = []
if not options_dict['forceFlag']:
for sample_directory in list_of_sample_directories:
consensus_file_path = os.path.join(sample_directory, options_dict['consFileName'])
source_files.append(consensus_file_path)
if not utils.target_needs_rebuild(source_files, snpma_file_path):
verbose_print("SNP matrix %s has already been freshly built. Use the -f option to force a rebuild." % snpma_file_path)
verbose_print("# %s %s finished" % (timestamp(), program_name()))
return
#==========================================================================
# Create snp matrix. Write results to file.
#==========================================================================
with open(snpma_file_path, "w") as output_file:
for sample_directory in list_of_sample_directories:
consensus_file_path = os.path.join(sample_directory, options_dict['consFileName'])
verbose_print("Merging " + consensus_file_path)
with open(consensus_file_path, "r") as input_file:
for line in input_file:
output_file.write(line)
verbose_print("")
verbose_print("# %s %s finished" % (timestamp(), program_name()))
def call_consensus(options_dict):
"""Call the consensus base for a sample
Call the consensus base for a sample at the positions where SNPs were found
in any of the samples.
This function expects, or creates '(*)', the following
files arranged in the following way:
snplist.txt
samples
sample_name_one/reads.all.pileup
sample_name_one/consensus.fasta (*)
The files are used as follows:
1. The snplist.txt input file contains the list of SNP positions
extracted from all the var.flt.vcf files combined.
2. The reads.all.pileup input file is a pileups at all positions
used to determine the nucleotide base at each SNP position.
3. The consensus.fasta output file contains the SNP calls for each
sequence, arranged as a fasta file with one sequence per sample.
The snplist.txt, and reads.snp.pileup are created outside of this function.
The package documentation provides an example
of creating these files based on the lambda_virus sequence that is used
as one test for this package.
Args:
forceFlag : boolean
flag to force processing even when result file already exists and
is newer than inputs
snpListFile : str
File path (not just file name) of text format list of SNP positions
allPileupFile : str
Relative or absolute path to the genome-wide pileup file for this
sample
consensusFile : str
Output file. Relative or absolute path to the consensus fasta file
for this sample.
minBaseQual : int
Mimimum base quality score to count a read. All other snp filters
take effect after the low-quality reads are discarded.
minConsFreq : float
Consensus frequency. Mimimum fraction of high-quality reads
supporting the consensus to make a call.
minConsStrdDpth : int
Consensus strand depth. Minimum number of high-quality reads
supporting the consensus which must be present on both the
forward and reverse strands to make a call.
minConsStrdBias : float
Strand bias. Minimum fraction of the high-quality
consensus-supporting reads which must be present on both the
forward and reverse strands to make a call. The numerator of this
fraction is the number of high-quality consensus-supporting reads
on one strand. The denominator is the total number of high-quality
consensus-supporting reads on both strands combined.
Raises:
Examples:
options_dict = {'snpListFile':'snplist.txt',
'allPileupFile':'reads.all.pileup',
'consensusFile':'consensus.fasta',
'minBaseQual':15,
'minConsFreq':0.6,
'minConsStrdDpth':4
'minConsStrdBias':0.10
}
call_consensus(options_dict)
"""
print_log_header()
verbose_print("# %s %s" % (timestamp(), command_line_short()))
verbose_print("# %s version %s" % (program_name(), __version__))
print_arguments(options_dict)
snp_list_file_path = options_dict['snpListFile']
all_pileup_file_path = options_dict['allPileupFile']
sample_directory = os.path.dirname(os.path.abspath(all_pileup_file_path))
sample_name = os.path.basename(sample_directory)
consensus_file_path = options_dict['consensusFile']
consensus_file_dir = os.path.dirname(os.path.abspath(consensus_file_path))
vcf_file_name = options_dict['vcfFileName']
vcf_file_path = os.path.join(consensus_file_dir, vcf_file_name) if vcf_file_name else None
# Check if the result is already fresh
source_files = [snp_list_file_path, all_pileup_file_path]
if not options_dict['forceFlag'] and not utils.target_needs_rebuild(source_files, consensus_file_path):
verbose_print("Consensus call file %s has already been freshly built. Use the -f option to force a rebuild." % consensus_file_path)
verbose_print("# %s %s finished" % (timestamp(), program_name()))
return
# Load the list of which positions to called
snp_list = utils.read_snp_position_list(snp_list_file_path)
snplist_length = len(snp_list)
verbose_print("snp position list length = %d" % snplist_length)
# Call consensus. Write results to file.
position_consensus_base_dict = dict()
caller = pileup.ConsensusCaller(options_dict['minConsFreq'],
options_dict['minConsStrdDpth'],
options_dict['minConsStrdBias'])
snp_positions = set(snp_list)
parse_positions = None if options_dict['vcfAllPos'] else snp_positions
pileup_reader = pileup.Reader(all_pileup_file_path,
options_dict['minBaseQual'],
parse_positions)
if vcf_file_name:
writer = vcf_writer.SingleSampleWriter(vcf_file_path)
filters = caller.get_filter_descriptions()
writer.write_header(sample_name, filters, options_dict['vcfRefName'])
for pileup_record in pileup_reader:
chrom = pileup_record.chrom
pos = pileup_record.position
consensus_base, fail_reasons = caller.call_consensus(pileup_record)
if (chrom, pos) in snp_positions:
if fail_reasons:
position_consensus_base_dict[(chrom, pos)] = '-'
else:
position_consensus_base_dict[(chrom, pos)] = consensus_base
if vcf_file_name:
writer.write_from_pileup(pileup_record, fail_reasons)
if vcf_file_name:
writer.close()
verbose_print("called consensus positions = %i" % (len(position_consensus_base_dict)))
consensus_list = [position_consensus_base_dict.get(key, '-') for key in snp_list]
consensus_str = ''.join(consensus_list)
snp_seq_record = SeqRecord(Seq(consensus_str), id=sample_name, description="")
# Write the consensus calls to a fasta file
with open(consensus_file_path, "w") as fasta_file_object:
SeqIO.write([snp_seq_record], fasta_file_object, "fasta")
verbose_print("")
verbose_print("# %s %s finished" % (timestamp(), program_name()))
