def run(self, input_files, metadata, output_files):
"""
This is the main function that run the tools to create
.baitmap.
Parameters
----------
input_files: dict
genome: str
Indexed Ref genome used used in the experiment.
metadata: dict
input metadata
output_files: dict
Rtree_files: str
Name of the Rtree files
bait_sam: str
whole path of SAM file, generated to locate baits
out_baitmap: str
whole path for the .baitmap file
Returns
-------
output_files_Baitmap : bool
output_metadata_Baitmap : dict
metadata for baitmap
files
"""
try:
baitmap_caller = makeBaitmapTool(self.configuration)
output_files_baitmap, output_metadata_baitmap = baitmap_caller.run(
{
"genome_idx": input_files["genome_idx"],
"probes_fa": input_files["probes_fa"],
"Rtree_file_dat": input_files["Rtree_file_dat"],
"Rtree_file_idx": input_files["Rtree_file_idx"],
"genome_fa": input_files["genome_fa"],
"chr_handler": input_files["chr_handler"]
},
{
"genome_fa": metadata["genome_fa"],
"probes_fa": metadata["probes_fa"],
"Rtree_file_dat": metadata["Rtree_file_dat"],
"Rtree_file_idx": metadata["Rtree_file_idx"],
"genome_idx": metadata["genome_idx"]
},
{
"bait_sam": output_files["bait_sam"],
"out_baitmap": output_files["out_baitmap"],
"out_bam": output_files["out_bam"]
}
)
logger.info(".baitmap file generated succesfully")
except IOError:
logger.fatal("generate_CHiCAGO_baitmap failed to generate .baitmap file")
return output_files_baitmap, output_metadata_baitmap
def test_baitmap():
"""
Function to test the makeBaitmap tool. Tool that
generate .baitmap files
"""
import sys
sys._run_from_cmdl = True # pylint: disable=protected-access
path = os.path.join(os.path.dirname(__file__), "data/")
configuration = {
"execution": path,
"chic_RE_name": "HindIII",
"chic_RE_sequence": "A|AGCTT"
}
input_files = {
"genome_idx": path + "test_baitmap/bwa.tar.gz",
"probes_fa": path + "test_baitmap/baits.fa",
"Rtree_file_dat": path + "test_rmap/rtree_file.dat",
"Rtree_file_idx": path + "test_rmap/rtree_file.idx",
"genome_fa": path + "test_baitmap/chr21_hg19.fa",
"chr_handler": path + "test_baitmap/chr_handler.txt"
}
output_files = {
"bait_sam": path + "test_baitmap/baits.sam",
"out_bam": path + "test_baitmap/baits.bam",
"out_baitmap": path + "test_run_chicago/test.baitmap"
}
metadata = {
"genome_idx":
Metadata("index_bwa", "tar", input_files["genome_idx"],
[input_files["genome_fa"]], {
"assembly": "test",
"tool": "bwa_indexer"
}, 9606),
"genome_fa":
Metadata("hg38", "fasta", input_files["genome_fa"], [], {
"assembly": "test",
"tool": "bwa_indexer"
}, 9606),
"probes_fa":
Metadata("C-HiC probes", "fasta", input_files["probes_fa"], [], {
"assembly": "test",
"tool": "bwa_indexer"
}, 9606),
"Rtree_file_dat":
Metadata("Rtree files", "dat", input_files["Rtree_file_dat"], [], {
"genome": input_files["genome_fa"],
"RE": {
"HindIII": 'A|AGCTT'
}
}, 9606),
"Rtree_file_idx":
Metadata("Rtree files", "idx", input_files["Rtree_file_idx"], [], {
"genome": input_files["genome_fa"],
"RE": {
"HindIII": 'A|AGCTT'
}
}, 9606)
}
baitmap_handler = makeBaitmapTool(configuration)
baitmap_handler.run(input_files, metadata, output_files)
assert os.path.getsize(output_files["out_bam"]) > 0
assert os.path.getsize(output_files["out_baitmap"]) > 0
def run(self, input_files, metadata, output_files):
"""
This is the main function that run the tools to create
.baitmap.
Parameters
----------
input_files: dict
fastq1: str
fastq2: str
genome_fa: str
genome in fasta format
input_metadata: dict
input metadata
output_files: dict
Returns
-------
output_files
output_metadata
"""
#call hicup
try:
hicup_caller = hicup(self.configuration)
output_files_hicup, output_metadata_hicup = hicup_caller.run(
{
"genome_fa": input_files["genome_fa"],
"fastq1": input_files["fastq1"],
"fastq2" : input_files["fastq2"],
"bowtie_gen_idx": input_files["bowtie_gen_idx"]
},
{
"genome_fa": metadata["genome_fa"],
"fastq1": metadata["fastq1"],
"fastq2": metadata["fastq2"]
},
{
"hicup_outdir_tar" : output_files["hicup_outdir_tar"]
}
)
logger.info("hicup runned succesfully =)")
except IOError:
logger.fatal("hicup failed to run succesfully =(")
#call ramp
try:
rmap_caller = makeRmapFile(self.configuration)
output_files_rmap, output_metadata_rmap = rmap_caller.run(
{
"genome_fa" : input_files["genome_fa"]
},
{
"genome_fa" : metadata["genome_fa"]
},
{
"RMAP" : output_files["RMAP"],
"Rtree_file_dat" : output_files["Rtree_file_dat"],
"Rtree_file_idx" : output_files["Rtree_file_idx"],
"chr_handler" : output_files["chr_handler"]
}
)
logger.info(".rmap file generated succesfully")
except IOError:
logger.fatal("rmap_tool failed to generate .rmap file")
#produce Baitmap file
try:
baitmap_caller = makeBaitmapTool(self.configuration)
output_files_baitmap, output_metadata_baitmap = baitmap_caller.run(
{
"genome_idx" : input_files["genome_idx"],
"probes_fa": input_files["probes_fa"],
"Rtree_file_dat": input_files["Rtree_file_dat"],
"Rtree_file_idx": input_files["Rtree_file_idx"],
"genome_fa" : input_files["genome_fa"],
"chr_handler" : input_files["chr_handler"]
},
{
"genome_fa" : metadata["genome_fa"],
"probes_fa" : metadata["probes_fa"],
"Rtree_file_dat": metadata["Rtree_file_dat"],
"Rtree_file_idx": metadata["Rtree_file_idx"],
"genome_idx": metadata["genome_idx"]
},
{
"bait_sam" : output_files["bait_sam"],
"out_baitmap" : output_files["out_baitmap"],
"out_bam" : output_files["out_bam"]
}
)
logger.info(".baitmap file generated succesfully")
except IOError:
logger.fatal("generate_CHiCAGO_baitmap failed to generate .baitmap file")
try:
design_caller = makeDesignFilesTool(self.configuration)
design_out, design_meta = design_caller.run(
{
"RMAP" : input_files["RMAP"],
"BAITMAP": input_files["BAITMAP"]
},
{
"RMAP" : metadata["RMAP"],
"BAITMAP" : metadata["BAITMAP"]
},
{
"nbpb" : output_files["nbpb"],
"npb" : output_files["npb"],
"poe" : output_files["poe"]
}
)
logger.info("design files succesfully generated =)")
except IOError:
logger.fatal("process_makeDesign failed to" +
"generate design files")
try:
bam2chicago_caller = bam2chicagoTool(self.configuration)
output_files_bam2chicago, output_metadata_bam2chicago = bam2chicago_caller.run(
{
"hicup_outdir_tar" : input_files["hicup_outdir_tar"],
"RMAP" : input_files["RMAP"],
"BAITMAP" : input_files["BAITMAP"]
},
{
"hicup_outdir_tar" : metadata["hicup_outdir_tar"],
"RMAP" : metadata["RMAP"],
"BAITMAP" : metadata["BAITMAP"]
},
{
"chinput": output_files["chinput"]
}
)
logger.info("bam2chicago_tool succesfully generate chinput files =)")
except IOError:
logger.fatal("process_bam2chicago failed to generate .chinput files")
try:
chicago_caller = ChicagoTool(self.configuration)
output_files_chicago, output_metadata_chicago = chicago_caller.run(
input_files, metadata, output_files)
except IOError:
logger.info("chicago failed to generate output files =(")
output_files = {}
output_metadata = {}
output_files.update(output_files_rmap)
output_files.update(output_files_baitmap)
output_files.update(design_out)
output_files.update(output_files_hicup)
output_files.update(output_files_bam2chicago)
output_files.update(output_files_chicago)
output_metadata.update(output_metadata_rmap)
output_metadata.update(output_metadata_baitmap)
output_metadata.update(design_meta)
output_metadata.update(output_metadata_hicup)
output_metadata.update(output_metadata_bam2chicago)
output_metadata.update(output_metadata_chicago)
return output_files, output_metadata
def run(self, input_files, metadata, output_files):
"""
This is the main function that run the tools to create
.baitmap.
Parameters
----------
input_files: dict
fastq1: str
fastq2: str
genome_fa: str
genome in fasta format
input_metadata: dict
input metadata
output_files: dict
Returns
-------
output_files
output_metadata
"""
if not os.path.exists("tests/data/test_bam2chicago_tool"):
os.makedirs("tests/data/test_bam2chicago_tool")
if not os.path.exists("tests/data/test_hicup"):
os.makedirs("tests/data/test_hicup")
if not os.path.exists("tests/data/test_rmap"):
os.makedirs("tests/data/test_rmap")
self.configuration["bowtie2_fasta_input"] = "True"
if "genome_fa_public" in input_files:
input_files["genome_fa"] = input_files.pop("genome_fa_public")
metadata["genome_fa"] = metadata.pop("genome_fa_public")
input_files["bowtie_gen_idx"] = input_files.pop(
"bowtie_gen_idx_public")
metadata["bowtie_gen_idx"] = metadata.pop("bowtie_gen_idx_public")
#call hicup
try:
hicup_caller = hicup(self.configuration)
output_files_hicup, output_metadata_hicup = hicup_caller.run(
{
"genome_fa": input_files["genome_fa"],
"fastq1": input_files["fastq1"],
"fastq2": input_files["fastq2"],
"bowtie_gen_idx": input_files["bowtie_gen_idx"]
}, {
"genome_fa": metadata["genome_fa"],
"fastq1": metadata["fastq1"],
"fastq2": metadata["fastq2"]
}, {"hicup_outdir_tar": output_files["hicup_outdir_tar"]})
logger.info("hicup runned succesfully =)")
except IOError:
logger.fatal("hicup failed to run succesfully =(")
#call ramp
try:
rmap_caller = makeRmapFile(self.configuration)
output_files_rmap, output_metadata_rmap = rmap_caller.run(
{"genome_fa": input_files["genome_fa"]},
{"genome_fa": metadata["genome_fa"]}, {})
logger.info(".rmap file generated succesfully")
except IOError:
logger.fatal("rmap_tool failed to generate .rmap file")
#produce Baitmap file
try:
baitmap_caller = makeBaitmapTool(self.configuration)
output_files_baitmap, output_metadata_baitmap = baitmap_caller.run(
{
"bowtie_gen_idx": input_files["bowtie_gen_idx"],
"probes_fa": input_files["probes_fa"],
"genome_fa": input_files["genome_fa"],
}, {
"genome_fa": metadata["genome_fa"],
"probes_fa": metadata["probes_fa"],
"bowtie_gen_idx": metadata["bowtie_gen_idx"]
}, {})
logger.info(".baitmap file generated succesfully")
except IOError:
logger.fatal(
"generate_CHiCAGO_baitmap failed to generate .baitmap file")
try:
design_caller = makeDesignFilesTool(self.configuration)
design_out, design_meta = design_caller.run({}, {}, {})
logger.info("design files succesfully generated =)")
except IOError:
logger.fatal("process_makeDesign failed to" +
"generate design files")
try:
bam2chicago_caller = bam2chicagoTool(self.configuration)
output_files_bam2chicago, output_metadata_bam2chicago = bam2chicago_caller.run(
input_files, metadata, output_files)
logger.info(
"bam2chicago_tool succesfully generate chinput files =)")
except IOError:
logger.fatal(
"process_bam2chicago failed to generate .chinput files")
try:
pychic_caller = run_pyCHiC(self.configuration)
output_files_pychic, output_metadata_pychic = pychic_caller.run(
input_files, metadata, output_files)
except IOError:
logger.info("chicago failed to generate output files =(")
output_files = {}
output_metadata = {}
output_files.update(output_files_rmap)
output_files.update(output_files_baitmap)
output_files.update(design_out)
output_files.update(output_files_hicup)
output_files.update(output_files_bam2chicago)
output_files.update(output_files_pychic)
output_metadata.update(output_metadata_rmap)
output_metadata.update(output_metadata_baitmap)
output_metadata.update(design_meta)
output_metadata.update(output_metadata_hicup)
output_metadata.update(output_metadata_bam2chicago)
output_metadata.update(output_metadata_pychic)
return output_files, output_metadata