def test_bs_seeker_filter_02():
"""
Test that it is possible to call the BSseeker filter
"""
resource_path = os.path.join(os.path.dirname(__file__), "data/")
home = os.path.expanduser('~')
input_files = {"fastq": resource_path + "bsSeeker.Mouse.SRR892982_2.fastq"}
output_files = {
"fastq_filtered":
resource_path + "bsSeeker.Mouse.SRR892982_2.filtered.fastq"
}
metadata = {
"fastq":
Metadata("data_wgbs", "fastq", input_files["fastq"], None,
{'assembly': 'test'})
}
config_param = {
"aligner": "bowtie2",
"aligner_path": home + "/lib/bowtie2-2.3.4-linux-x86_64",
"bss_path": home + "/lib/BSseeker2"
}
bsi = bs_seeker_filter.filterReadsTool(config_param)
bsi.run(input_files, metadata, output_files)
assert os.path.isfile(output_files["fastq_filtered"]) is True
assert os.path.getsize(output_files["fastq_filtered"]) > 0
def work(self):
"""
Worker function for aligning single ended FASTQ reads using Bowtie2
Parameters
----------
genome_fa : str
Location of the FASTA file of the genome to align the reads to
genome_idx : str
Location of the index files in .tar.gz file prepared by the BWA
indexer
fastq_file : str
Location of the FASTQ file
output_bam : str
Location of the aligned reads in bam format
"""
frt = filterReadsTool()
frt.bss_seeker_filter(self.fastq_file, self.fastq_filtered,
self.bss_path)
bss_aligner = bssAlignerTool({"no-untar": True})
bss_aligner.bs_seeker_aligner_single(self.fastq_filtered, self.aligner,
self.aligner_path, self.bss_path,
[], self.genome_fa,
self.genome_idx, self.output_bam)
bam_handle = bamUtils()
bam_handle.bam_sort(self.output_bam)
def run(self, input_files, metadata, output_files):
"""
This pipeline processes paired-end FASTQ files to identify
methylated regions within the genome.
Parameters
----------
input_files : dict
List of strings for the locations of files. These should include:
genome_fa : str
Genome assembly in FASTA
fastq1 : str
Location for the first FASTQ file for single or paired end
reads
fastq2 : str
[OPTIONAL]Location for the second FASTQ file if paired end
reads
metadata : dict
Input file meta data associated with their roles
genome_fa : str
fastq1 : str
fastq2 : str
[OPTIONAL]
output_files : dict
index : str
fastq1_filtered : str
fastq2_filtered : str
[OPTIONAL]
bam : str
bai : str
wig_file : str
cgmap_file : str
atcgmap_file : str
Returns
-------
fastq1_filtered|fastq1_filtered : str
Locations of the filtered FASTQ files from which alignments were
made
bam|bai : str
Location of the alignment bam file and the associated index
wig_file : str
Location of the wig file containing the methylation peak calls
cgmap_file : str
Location of the CGmap file generated by BS-Seeker2
atcgmap_file : str
Location of the ATCGmap file generated by BS-Seeker2
"""
output_results_files = {}
output_metadata = {}
logger.info("WGBS - BS-Seeker2 Index")
# Build the matching WGBS genome index
builder = bssIndexerTool(self.configuration)
genome_idx, gidx_meta = builder.run(remap(input_files, "genome"),
remap(metadata, "genome"),
remap(output_files, "index"))
output_results_files["index"] = genome_idx["index"]
output_metadata["index"] = gidx_meta["index"]
# Filter the FASTQ reads to remove duplicates
logger.info("WGBS - Filter")
frt = filterReadsTool(self.configuration)
fastq1f, filter1_meta = frt.run(
{"fastq": input_files["fastq1"]}, {"fastq": metadata["fastq1"]},
{"fastq_filtered": output_files["fastq1_filtered"]})
try:
output_results_files["fastq1_filtered"] = fastq1f["fastq_filtered"]
output_metadata["fastq1_filtered"] = filter1_meta["fastq_filtered"]
tool_name = output_metadata["fastq1_filtered"].meta_data["tool"]
output_metadata["fastq1_filtered"].meta_data[
"tool_description"] = tool_name
output_metadata["fastq1_filtered"].meta_data[
"tool"] = "process_wgbs"
except KeyError:
logger.fatal("WGBS - FILTER: Error while filtering")
return {}, {}
if "fastq2" in input_files:
logger.info("WGBS - Filter background")
fastq2f, filter2_meta = frt.run(
{"fastq": input_files["fastq2"]},
{"fastq": metadata["fastq2"]},
{"fastq_filtered": output_files["fastq2_filtered"]})
try:
output_results_files["fastq2_filtered"] = fastq2f[
"fastq_filtered"]
output_metadata["fastq2_filtered"] = filter2_meta[
"fastq_filtered"]
tool_name = output_metadata["fastq2_filtered"].meta_data[
"tool"]
output_metadata["fastq2_filtered"].meta_data[
"tool_description"] = tool_name
output_metadata["fastq2_filtered"].meta_data[
"tool"] = "process_wgbs"
except KeyError:
logger.fatal(
"WGBS - FILTER (background): Error while filtering")
return {}, {}
logger.info("WGBS - BS-Seeker2 Aligner")
# Handles the alignment of all of the split packets then merges them
# back together.
bss_aligner = bssAlignerTool(self.configuration)
aligner_input_files = {
"genome": input_files["genome"],
"fastq1": fastq1f["fastq_filtered"]
}
aligner_input_files["index"] = genome_idx["index"]
aligner_meta = {
"genome": metadata["genome"],
"fastq1": filter1_meta["fastq_filtered"],
"index": output_metadata["index"]
}
if "fastq2" in input_files:
aligner_input_files["fastq2"] = fastq2f["fastq_filtered"]
aligner_meta["fastq2"] = filter2_meta["fastq_filtered"]
bam, bam_meta = bss_aligner.run(aligner_input_files, aligner_meta,
remap(output_files, "bam", "bai"))
try:
output_results_files["bam"] = bam["bam"]
output_results_files["bai"] = bam["bai"]
output_metadata["bam"] = bam_meta["bam"]
output_metadata["bai"] = bam_meta["bai"]
tool_name = output_metadata["bam"].meta_data["tool"]
output_metadata["bam"].meta_data["tool_description"] = tool_name
output_metadata["bam"].meta_data["tool"] = "process_wgbs"
tool_name = output_metadata["bai"].meta_data["tool"]
output_metadata["bai"].meta_data["tool_description"] = tool_name
output_metadata["bai"].meta_data["tool"] = "process_wgbs"
except KeyError:
logger.fatal("WGBS - Aligner failed")
return {}, {}
# Methylation peak caller
peak_caller_handle = bssMethylationCallerTool(self.configuration)
mct_input_files = {
"genome": input_files["genome"],
"index": genome_idx["index"],
"fastq1": fastq1f["fastq_filtered"],
"bam": bam["bam"],
"bai": bam["bai"]
}
mct_meta = {
"genome": metadata["genome"],
"index": gidx_meta["index"],
"fastq1": filter1_meta["fastq_filtered"],
"bam": output_metadata["bam"],
"bai": bam_meta["bai"]
}
if "fastq2" in input_files:
mct_input_files["fastq2"] = fastq2f["fastq_filtered"]
mct_meta["fastq2"] = filter2_meta["fastq_filtered"]
peak_files, peak_meta = peak_caller_handle.run(
mct_input_files, mct_meta,
remap(output_files, "wig_file", "cgmap_file", "atcgmap_file"))
# output_metadata["peak_calling"] = peak_meta
try:
output_results_files["wig_file"] = peak_files["wig_file"]
output_results_files["cgmap_file"] = peak_files["cgmap_file"]
output_results_files["atcgmap_file"] = peak_files["atcgmap_file"]
output_metadata["wig_file"] = peak_meta["wig_file"]
output_metadata["cgmap_file"] = peak_meta["cgmap_file"]
output_metadata["atcgmap_file"] = peak_meta["atcgmap_file"]
output_metadata["wig_file"].meta_data["tool_description"] = output_metadata["wig_file"].meta_data["tool"] # pylint: disable=line-too-long
output_metadata["wig_file"].meta_data["tool"] = "process_wgbs"
output_metadata["cgmap_file"].meta_data["tool_description"] = output_metadata["cgmap_file"].meta_data["tool"] # pylint: disable=line-too-long
output_metadata["cgmap_file"].meta_data["tool"] = "process_wgbs"
output_metadata["atcgmap_file"].meta_data["tool_description"] = output_metadata["atcgmap_file"].meta_data["tool"] # pylint: disable=line-too-long
output_metadata["atcgmap_file"].meta_data["tool"] = "process_wgbs"
except KeyError:
logger.fatal("WGBS - Peak caller failed")
return {}, {}
return (output_results_files, output_metadata)
def run(self, input_files, metadata, output_files):
"""
This pipeline processes FASTQ files to filter duplicate entries
Parameters
----------
input_files : dict
List of strings for the locations of files. These should include:
fastq1 : str
Location for the first FASTQ file for single or paired end reads
fastq2 : str
Location for the second FASTQ file if paired end reads [OPTIONAL]
metadata : dict
Input file meta data associated with their roles
fastq1 : str
fastq2 : str
[OPTIONAL]
output_files : dict
fastq1_filtered : str
fastq2_filtered : str
[OPTIONAL]
Returns
-------
fastq1_filtered|fastq1_filtered : str
Locations of the filtered FASTQ files from which alignments were made
fastq2_filtered|fastq2_filtered : str
Locations of the filtered FASTQ files from which alignments were made
"""
output_results_files = {}
output_metadata = {}
logger.info("BS-Filter")
frt = filterReadsTool(self.configuration)
fastq1f, filter1_meta = frt.run(
{"fastq": input_files["fastq1"]}, {"fastq": metadata["fastq1"]},
{"fastq_filtered": output_files["fastq1_filtered"]})
try:
output_results_files["fastq1_filtered"] = fastq1f["fastq_filtered"]
output_metadata["fastq1_filtered"] = filter1_meta["fastq_filtered"]
tool_name = output_metadata["fastq1_filtered"].meta_data["tool"]
output_metadata["fastq1_filtered"].meta_data[
"tool_description"] = tool_name
output_metadata["fastq1_filtered"].meta_data[
"tool"] = "process_wgbs"
except KeyError:
logger.fatal("WGBS - FILTER: Error while filtering")
return {}, {}
if "fastq2" in input_files:
logger.info("WGBS - Filter background")
fastq2f, filter2_meta = frt.run(
{"fastq": input_files["fastq2"]},
{"fastq": metadata["fastq2"]},
{"fastq_filtered": output_files["fastq2_filtered"]})
try:
output_results_files["fastq2_filtered"] = fastq2f[
"fastq_filtered"]
output_metadata["fastq2_filtered"] = filter2_meta[
"fastq_filtered"]
tool_name = output_metadata["fastq2_filtered"].meta_data[
"tool"]
output_metadata["fastq2_filtered"].meta_data[
"tool_description"] = tool_name
output_metadata["fastq2_filtered"].meta_data[
"tool"] = "process_wgbs"
except KeyError:
logger.fatal(
"WGBS - FILTER (background): Error while filtering")
return {}, {}
return (output_results_files, output_metadata)
def _filter_reads_mp(self, fastq_in, fastq_out, filter_path):
frt = filterReadsTool()
frt.bss_seeker_filter(fastq_in, fastq_out, filter_path)
fq_handle = fastqUtils()
fq_handle.fastq_sort_file(fastq_out)