def main():
ref_bed = snakemake.input.ref_bed
nonref_bed = snakemake.input.nonref_bed
reference_fasta = snakemake.input.reference_fasta
threads = snakemake.threads
log = snakemake.params.log
sample_name = snakemake.params.sample_name
out_dir = snakemake.params.out_dir
chromosomes = snakemake.params.chromosomes.split(",")
status_log = snakemake.params.status_log
out_bed = snakemake.output[0]
succeeded = mccutils.check_status_file(status_log)
if succeeded:
mccutils.log("ngs_te_mapper2","processing ngs_te_mapper2 results", log=log)
insertions = read_insertions(ref_bed, nonref_bed, chromosomes, sample_name, out_dir)
if len(insertions) > 0:
insertions = output.make_redundant_bed(insertions, sample_name, out_dir, method="ngs_te_mapper2")
intertions = output.make_nonredundant_bed(insertions, sample_name, out_dir, method="ngs_te_mapper2")
output.write_vcf(insertions, reference_fasta, sample_name, "ngs_te_mapper2", out_dir)
else:
mccutils.run_command(["touch", out_dir+"/"+sample_name+"_ngs_te_mapper2_redundant.bed"])
mccutils.run_command(["touch", out_dir+"/"+sample_name+"_ngs_te_mapper2_nonredundant.bed"])
mccutils.log("ngs_te_mapper2","ngs_te_mapper2 postprocessing complete")
else:
mccutils.run_command(["touch", out_dir+"/"+sample_name+"_ngs_te_mapper2_redundant.bed"])
mccutils.run_command(["touch", out_dir+"/"+sample_name+"_ngs_te_mapper2_nonredundant.bed"])
def main():
mccutils.log("retroseq","processing RetroSeq results")
retroseq_out = snakemake.input.retroseq_out
reference_fasta = snakemake.input.reference_fasta
out_dir = snakemake.params.out_dir
ref_name = snakemake.params.ref_name
sample_name = snakemake.params.sample_name
chromosomes = snakemake.params.chromosomes.split(",")
status_log = snakemake.params.status_log
prev_steps_succeeded = mccutils.check_status_file(status_log)
if prev_steps_succeeded:
insertions = read_insertions(retroseq_out, sample_name, chromosomes, support_threshold=config.PARAMS["read_support_threshold"], breakpoint_threshold=config.PARAMS["breakpoint_confidence_threshold"])
if len(insertions) >= 1:
insertions = output.make_redundant_bed(insertions, sample_name, out_dir, method="retroseq")
insertions = output.make_nonredundant_bed(insertions, sample_name, out_dir, method="retroseq")
output.write_vcf(insertions, reference_fasta, sample_name, "retroseq", out_dir)
else:
mccutils.run_command(["touch",out_dir+"/"+sample_name+"_retroseq_redundant.bed"])
mccutils.run_command(["touch",out_dir+"/"+sample_name+"_retroseq_nonredundant.bed"])
else:
mccutils.run_command(["touch",out_dir+"/"+sample_name+"_retroseq_redundant.bed"])
mccutils.run_command(["touch",out_dir+"/"+sample_name+"_retroseq_nonredundant.bed"])
mccutils.log("retroseq","RetroSeq post processing complete")
def main():
mccutils.log("tebreak","running tebreak post processing")
tebreak_out = snakemake.input.tebreak_out
ref_fasta = snakemake.input.ref_fasta
out_dir = snakemake.params.out_dir
ref_name = snakemake.params.ref_name
sample_name = snakemake.params.sample_name
chromosomes = snakemake.params.chromosomes.split(",")
status_log = snakemake.params.status_log
prev_steps_succeeded = mccutils.check_status_file(status_log)
if prev_steps_succeeded:
insertions = read_insertions(tebreak_out, sample_name, chromosomes, config)
if len(insertions) > 0:
insertions = output.make_redundant_bed(insertions, sample_name, out_dir, method="tebreak")
insertions = output.make_nonredundant_bed(insertions, sample_name, out_dir, method="tebreak")
output.write_vcf(insertions, ref_fasta, sample_name, "tebreak", out_dir)
else:
mccutils.run_command(["touch", out_dir+"/"+sample_name+"_tebreak_redundant.bed"])
mccutils.run_command(["touch", out_dir+"/"+sample_name+"_tebreak_nonredundant.bed"])
else:
mccutils.run_command(["touch", out_dir+"/"+sample_name+"_tebreak_redundant.bed"])
mccutils.run_command(["touch", out_dir+"/"+sample_name+"_tebreak_nonredundant.bed"])
mccutils.log("tebreak","tebreak postprocessing complete")
def main():
mccutils.log("te-locate", "processing TE-Locate results")
telocate_raw = snakemake.input.telocate_raw
te_gff = snakemake.input.te_gff
reference_fasta = snakemake.input.reference_fasta
out_dir = snakemake.params.out_dir
sample_name = snakemake.params.sample_name
chromosomes = snakemake.params.chromosomes.split(",")
insertions = read_insertions(
telocate_raw,
sample_name,
chromosomes,
rp_threshold=config.READ_PAIR_SUPPORT_THRESHOLD)
insertions = filter_by_reference(insertions, te_gff)
if len(insertions) > 0:
insertions = output.make_redundant_bed(insertions,
sample_name,
out_dir,
method="telocate")
intertions = output.make_nonredundant_bed(insertions,
sample_name,
out_dir,
method="telocate")
output.write_vcf(insertions, reference_fasta, sample_name, "telocate",
out_dir)
else:
mccutils.run_command(
["touch", out_dir + "/" + sample_name + "_telocate_redundant.bed"])
mccutils.run_command([
"touch", out_dir + "/" + sample_name + "_telocate_nonredundant.bed"
])
mccutils.log("te-locate", "TE-Locate post processing complete")
def main():
mccutils.log("te-locate","processing TE-Locate results")
telocate_raw = snakemake.input.telocate_raw
te_gff = snakemake.input.te_gff
reference_fasta = snakemake.input.reference_fasta
out_dir = snakemake.params.out_dir
sample_name = snakemake.params.sample_name
chromosomes = snakemake.params.chromosomes.split(",")
status_log = snakemake.params.status_log
prev_steps_succeeded = mccutils.check_status_file(status_log)
if prev_steps_succeeded:
insertions = read_insertions(telocate_raw, sample_name, chromosomes, rp_threshold=config.PARAMS['read_pair_support_threshold'])
insertions = filter_by_reference(insertions, te_gff)
if len(insertions) > 0:
insertions = output.make_redundant_bed(insertions, sample_name, out_dir, method="telocate")
intertions = output.make_nonredundant_bed(insertions, sample_name, out_dir,method="telocate")
output.write_vcf(insertions, reference_fasta, sample_name, "telocate", out_dir)
else:
mccutils.run_command(["touch", out_dir+"/"+sample_name+"_telocate_redundant.bed"])
mccutils.run_command(["touch", out_dir+"/"+sample_name+"_telocate_nonredundant.bed"])
else:
mccutils.run_command(["touch", out_dir+"/"+sample_name+"_telocate_redundant.bed"])
mccutils.run_command(["touch", out_dir+"/"+sample_name+"_telocate_nonredundant.bed"])
mccutils.log("te-locate", "TE-Locate post processing complete")
def main():
mccutils.log("retroseq", "processing RetroSeq results")
retroseq_out = snakemake.input.retroseq_out
reference_fasta = snakemake.input.reference_fasta
out_dir = snakemake.params.out_dir
ref_name = snakemake.params.ref_name
sample_name = snakemake.params.sample_name
chromosomes = snakemake.params.chromosomes.split(",")
insertions = read_insertions(
retroseq_out,
sample_name,
chromosomes,
support_threshold=config.READ_SUPPORT_THRESHOLD,
breakpoint_threshold=config.BREAKPOINT_CONFIDENCE_THRESHOLD)
if len(insertions) >= 1:
insertions = output.make_redundant_bed(insertions,
sample_name,
out_dir,
method="retroseq")
insertions = output.make_nonredundant_bed(insertions,
sample_name,
out_dir,
method="retroseq")
output.write_vcf(insertions, reference_fasta, sample_name, "retroseq",
out_dir)
else:
mccutils.run_command(
["touch", out_dir + "/" + sample_name + "_retroseq_redundant.bed"])
mccutils.run_command([
"touch", out_dir + "/" + sample_name + "_retroseq_nonredundant.bed"
])
mccutils.log("retroseq", "RetroSeq post processing complete")
def main():
mccutils.log("jitterbug", "jitterbug postprocessing")
jitterbug_out = snakemake.input.jitterbug_out
te_taxonomy = snakemake.input.taxonomy
reference_fasta = snakemake.input.reference_fasta
out_dir = snakemake.params.out_dir
log = snakemake.params.log
sample_name = snakemake.params.sample_name
chromosomes = snakemake.params.chromosomes.split(",")
status_log = snakemake.params.status_log
out = snakemake.output.out
prev_steps_succeeded = mccutils.check_status_file(status_log)
if prev_steps_succeeded:
insertions = read_insertions(
jitterbug_out,
te_taxonomy,
chromosomes,
sample_name,
min_fwd_read_support=config.FILTER['MIN_FWD_READ_SUPPORT'],
min_rev_read_support=config.FILTER['MIN_REV_READ_SUPPORT'],
min_sr_support=config.FILTER['MIN_SPLIT_READ_SUPPORT'],
min_zygosity=config.FILTER['MIN_ZYGOSITY'])
if len(insertions) >= 1:
insertions = output.make_redundant_bed(insertions,
sample_name,
out_dir,
method="jitterbug")
insertions = output.make_nonredundant_bed(insertions,
sample_name,
out_dir,
method="jitterbug")
output.write_vcf(insertions, reference_fasta, sample_name,
"jitterbug", out_dir)
else:
mccutils.run_command([
"touch",
out_dir + "/" + sample_name + "_jitterbug_redundant.bed"
])
mccutils.run_command([
"touch",
out_dir + "/" + sample_name + "_jitterbug_nonredundant.bed"
])
else:
mccutils.run_command([
"touch", out_dir + "/" + sample_name + "_jitterbug_redundant.bed"
])
mccutils.run_command([
"touch",
out_dir + "/" + sample_name + "_jitterbug_nonredundant.bed"
])
def main():
mccutils.log("popoolationte2", "processing PopoolationTE2 results")
te_predictions = snakemake.input.popoolationte2_out
te_gff = snakemake.input.te_gff
taxonomy = snakemake.input.taxonomy
reference_fasta = snakemake.input.reference_fasta
out_dir = snakemake.params.out_dir
sample_name = snakemake.params.sample_name
chromosomes = snakemake.params.chromosomes.split(",")
log = snakemake.params.log
status_log = snakemake.params.status_log
prev_step_succeeded = mccutils.check_status_file(status_log)
if prev_step_succeeded:
ref_tes = get_ref_tes(te_gff, taxonomy, chromosomes)
insertions = read_insertions(
te_predictions,
ref_tes,
chromosomes,
sample_name,
both_end_support_needed=config.PARAMS["require_both_end_support"],
support_threshold=config.PARAMS["frequency_threshold"])
if len(insertions) >= 1:
insertions = output.make_redundant_bed(insertions,
sample_name,
out_dir,
method="popoolationte2")
insertions = output.make_nonredundant_bed(insertions,
sample_name,
out_dir,
method="popoolationte2")
output.write_vcf(insertions, reference_fasta, sample_name,
"popoolationte2", out_dir)
else:
mccutils.run_command([
"touch",
out_dir + "/" + sample_name + "_popoolationte2_redundant.bed"
])
mccutils.run_command([
"touch", out_dir + "/" + sample_name +
"_popoolationte2_nonredundant.bed"
])
else:
mccutils.run_command([
"touch",
out_dir + "/" + sample_name + "_popoolationte2_redundant.bed"
])
mccutils.run_command([
"touch",
out_dir + "/" + sample_name + "_popoolationte2_nonredundant.bed"
])
mccutils.log("popoolationte2", "PopoolationTE2 postprocessing complete")
def main():
mccutils.log("teflon", "TEFLoN postprocessing")
teflon_raw = snakemake.input.teflon_out
ref_te_bed = snakemake.input.ref_bed
reference_fasta = snakemake.input.reference_fasta
out_dir = snakemake.params.out_dir
sample_name = snakemake.params.sample_name
chromosomes = snakemake.params.chromosomes.split(",")
status_log = snakemake.params.status_log
out = snakemake.output.out
prev_steps_succeeded = mccutils.check_status_file(status_log)
if prev_steps_succeeded:
ref_tes = get_ref_tes(ref_te_bed)
insertions = read_insertions(
teflon_raw,
chromosomes,
sample_name,
ref_tes,
min_presence=config.PARAMS['min_presence_reads'],
max_absence=config.PARAMS['max_absence_reads'],
min_presence_fraction=config.PARAMS['min_presence_fraction'],
require_tsd=config.PARAMS['require_tsd'],
require_both_breakpoints=config.PARAMS['require_both_breakpoints'])
if len(insertions) >= 1:
insertions = output.make_redundant_bed(insertions,
sample_name,
out_dir,
method="teflon")
insertions = output.make_nonredundant_bed(insertions,
sample_name,
out_dir,
method="teflon")
output.write_vcf(insertions, reference_fasta, sample_name,
"teflon", out_dir)
else:
mccutils.run_command([
"touch", out_dir + "/" + sample_name + "_teflon_redundant.bed"
])
mccutils.run_command([
"touch",
out_dir + "/" + sample_name + "_teflon_nonredundant.bed"
])
else:
mccutils.run_command(
["touch", out_dir + "/" + sample_name + "_teflon_redundant.bed"])
mccutils.run_command([
"touch", out_dir + "/" + sample_name + "_teflon_nonredundant.bed"
])
def main():
mccutils.log("popoolationte", "processing PopoolationTE results")
popoolationte_out = snakemake.input.popoolationte_out
genome_fasta = snakemake.input.ref
out_dir = snakemake.params.out_dir
sample_name = snakemake.params.sample_name
log = snakemake.params.log
chromosomes = snakemake.params.chromosomes.split(",")
status_log = snakemake.params.status_log
succeeded = mccutils.check_status_file(status_log)
if succeeded:
insertions = read_insertions(
popoolationte_out,
sample_name,
chromosomes,
require_both_end_support=config.PARAMS["require_both_end_support"],
percent_read_support_threshold=config.
PARAMS["percent_read_support_threshold"])
if len(insertions) >= 1:
insertions = output.make_redundant_bed(insertions,
sample_name,
out_dir,
method="popoolationte")
insertions = output.make_nonredundant_bed(insertions,
sample_name,
out_dir,
method="popoolationte")
output.write_vcf(insertions, genome_fasta, sample_name,
"popoolationte", out_dir)
else:
mccutils.run_command([
"touch",
out_dir + "/" + sample_name + "_popoolationte_redundant.bed"
])
mccutils.run_command([
"touch",
out_dir + "/" + sample_name + "_popoolationte_nonredundant.bed"
])
else:
mccutils.run_command([
"touch",
out_dir + "/" + sample_name + "_popoolationte_redundant.bed"
])
mccutils.run_command([
"touch",
out_dir + "/" + sample_name + "_popoolationte_nonredundant.bed"
])
mccutils.log("popoolationte", "PopoolationTE postprocessing complete")
def main():
mccutils.log("temp", "running TEMP post processing")
insert_summary = snakemake.input.insert_summary
absence_summary = snakemake.input.absence_summary
te_gff = snakemake.input.te_gff
reference_fasta = snakemake.input.reference_fasta
log = snakemake.params.log
sample_name = snakemake.params.sample_name
chromosomes = snakemake.params.chromosomes.split(",")
out_dir = snakemake.params.out_dir
status_log = snakemake.params.status_log
prev_steps_succeeded = mccutils.check_status_file(status_log)
if prev_steps_succeeded:
insertions = read_insertion_summary(insert_summary, sample_name)
absence_bed = make_absence_bed(absence_summary, sample_name, out_dir)
non_absent_ref_insertions = get_non_absent_ref_tes(
te_gff, absence_bed, sample_name, out_dir, log)
insertions += non_absent_ref_insertions
insertions = filter_insertions(
insertions,
chromosomes,
acceptable_classes=config.
PARAMS["acceptable_insertion_support_classes"],
frequency_theshold=config.PARAMS["frequency_threshold"])
if len(insertions) > 0:
insertions = output.make_redundant_bed(insertions,
sample_name,
out_dir,
method="temp")
insertions = output.make_nonredundant_bed(insertions,
sample_name,
out_dir,
method="temp")
output.write_vcf(insertions, reference_fasta, sample_name, "temp",
out_dir)
else:
mccutils.run_command(
["touch", out_dir + "/" + sample_name + "_temp_redundant.bed"])
mccutils.run_command([
"touch", out_dir + "/" + sample_name + "_temp_nonredundant.bed"
])
else:
mccutils.run_command(
["touch", out_dir + "/" + sample_name + "_temp_redundant.bed"])
mccutils.run_command(
["touch", out_dir + "/" + sample_name + "_temp_nonredundant.bed"])
mccutils.log("temp", "TEMP postprocessing complete")
def main():
mccutils.log("temp2", "running TEMP2 post processing")
insert_bed = snakemake.input.insert_bed
absence_summary = snakemake.input.absence_summary
te_gff = snakemake.input.te_gff
reference_fasta = snakemake.input.reference_fasta
log = snakemake.params.log
sample_name = snakemake.params.sample_name
chromosomes = snakemake.params.chromosomes.split(",")
out_dir = snakemake.params.out_dir
status_log = snakemake.params.status_log
prev_steps_succeeded = mccutils.check_status_file(status_log)
if prev_steps_succeeded:
insertions = read_insertions(insert_bed, sample_name, chromosomes,
config)
absence_bed = make_absence_bed(absence_summary, sample_name, out_dir)
non_absent_ref_insertions = get_non_absent_ref_tes(
te_gff, absence_bed, sample_name, chromosomes, out_dir, log)
insertions += non_absent_ref_insertions
if len(insertions) > 0:
insertions = output.make_redundant_bed(insertions,
sample_name,
out_dir,
method="temp2")
insertions = output.make_nonredundant_bed(insertions,
sample_name,
out_dir,
method="temp2")
output.write_vcf(insertions, reference_fasta, sample_name, "temp2",
out_dir)
else:
mccutils.run_command([
"touch", out_dir + "/" + sample_name + "_temp2_redundant.bed"
])
mccutils.run_command([
"touch",
out_dir + "/" + sample_name + "_temp2_nonredundant.bed"
])
else:
mccutils.run_command(
["touch", out_dir + "/" + sample_name + "_temp2_redundant.bed"])
mccutils.run_command(
["touch", out_dir + "/" + sample_name + "_temp2_nonredundant.bed"])
mccutils.log("temp2", "TEMP2 postprocessing complete")
def main():
raw_bed = snakemake.input.raw_bed
reference_fasta = snakemake.input.reference_fasta
threads = snakemake.threads
log = snakemake.params.log
sample_name = snakemake.params.sample_name
out_dir = snakemake.params.out_dir
chromosomes = snakemake.params.chromosomes.split(",")
out_bed = snakemake.output[0]
mccutils.log("ngs_te_mapper", "processing ngs_te_mapper results", log=log)
insertions = read_insertions(raw_bed,
chromosomes,
sample_name,
out_dir,
min_read_cutoff=config.MIN_READ_SUPPORT)
if len(insertions) > 0:
insertions = output.make_redundant_bed(insertions,
sample_name,
out_dir,
method="ngs_te_mapper")
intertions = output.make_nonredundant_bed(insertions,
sample_name,
out_dir,
method="ngs_te_mapper")
output.write_vcf(insertions, reference_fasta, sample_name,
"ngs_te_mapper", out_dir)
else:
mccutils.run_command([
"touch",
out_dir + "/" + sample_name + "_ngs_te_mapper_redundant.bed"
])
mccutils.run_command([
"touch",
out_dir + "/" + sample_name + "_ngs_te_mapper_nonredundant.bed"
])
mccutils.log("ngs_te_mapper", "ngs_te_mapper postprocessing complete")
def main():
mccutils.log("popoolationte2", "processing PopoolationTE2 results")
te_predictions = snakemake.input.popoolationte2_out
te_gff = snakemake.input.te_gff
taxonomy = snakemake.input.taxonomy
reference_fasta = snakemake.input.reference_fasta
out_dir = snakemake.params.out_dir
sample_name = snakemake.params.sample_name
chromosomes = snakemake.params.chromosomes.split(",")
log = snakemake.params.log
ref_tes = get_ref_tes(te_gff, taxonomy, chromosomes)
insertions = read_insertions(
te_predictions,
ref_tes,
chromosomes,
sample_name,
both_end_support_needed=config.REQUIRE_BOTH_END_SUPPORT,
support_threshold=config.FREQUENCY_THRESHOLD)
if len(insertions) >= 1:
insertions = output.make_redundant_bed(insertions,
sample_name,
out_dir,
method="popoolationte2")
insertions = output.make_nonredundant_bed(insertions,
sample_name,
out_dir,
method="popoolationte2")
output.write_vcf(insertions, reference_fasta, sample_name,
"popoolationte2", out_dir)
else:
mccutils.run_command([
"touch",
out_dir + "/" + sample_name + "_popoolationte2_redundant.bed"
])
mccutils.run_command([
"touch",
out_dir + "/" + sample_name + "_popoolationte2_nonredundant.bed"
])
mccutils.log("popoolationte2", "PopoolationTE2 postprocessing complete")
def main():
relocate_gff = snakemake.input.relocate_gff
te_gff = snakemake.input.te_gff
reference_fasta = snakemake.input.reference_fasta
out_dir = snakemake.params.out_dir
log = snakemake.params.log
sample_name = snakemake.params.sample_name
chromosomes = snakemake.params.chromosomes.split(",")
mccutils.log("relocate", "processing RelocaTE results")
insertions = get_insertions(
relocate_gff,
sample_name,
chromosomes,
ref_l_threshold=config.REF_LEFT_THRESHOLD,
ref_r_threshold=config.REF_RIGHT_THRESHOLD,
nonref_l_threshold=config.NONREF_LEFT_THRESHOLD,
nonref_r_threshold=config.NONREF_RIGHT_THRESHOLD)
insertions = set_ref_orientations(insertions, te_gff)
if len(insertions) >= 1:
insertions = output.make_redundant_bed(insertions,
sample_name,
out_dir,
method="relocate")
insertions = output.make_nonredundant_bed(insertions,
sample_name,
out_dir,
method="relocate")
output.write_vcf(insertions, reference_fasta, sample_name, "relocate",
out_dir)
else:
mccutils.run_command(
["touch", out_dir + "/" + sample_name + "_relocate_redundant.bed"])
mccutils.run_command([
"touch", out_dir + "/" + sample_name + "_relocate_nonredundant.bed"
])
mccutils.log("relocate", "RelocaTE postprocessing complete")
def main():
relocate_gff = snakemake.input.relocate_gff
te_gff = snakemake.input.te_gff
reference_fasta = snakemake.input.reference_fasta
out_dir = snakemake.params.out_dir
log = snakemake.params.log
sample_name = snakemake.params.sample_name
chromosomes = snakemake.params.chromosomes.split(",")
status_log = snakemake.params.status_log
mccutils.log("relocate","processing RelocaTE results")
prev_step_succeeded = mccutils.check_status_file(status_log)
if prev_step_succeeded:
insertions = get_insertions(
relocate_gff,
sample_name,
chromosomes,
ref_l_threshold=config.PARAMS["ref_left_threshold"],
ref_r_threshold=config.PARAMS["ref_right_threshold"],
nonref_l_threshold=config.PARAMS["nonref_left_threshold"],
nonref_r_threshold=config.PARAMS["nonref_right_threshold"]
)
insertions = set_ref_orientations(insertions, te_gff)
if len(insertions) >= 1:
insertions = output.make_redundant_bed(insertions, sample_name, out_dir, method="relocate")
insertions = output.make_nonredundant_bed(insertions, sample_name, out_dir, method="relocate")
output.write_vcf(insertions, reference_fasta, sample_name, "relocate", out_dir)
else:
mccutils.run_command(["touch",out_dir+"/"+sample_name+"_relocate_redundant.bed"])
mccutils.run_command(["touch",out_dir+"/"+sample_name+"_relocate_nonredundant.bed"])
else:
mccutils.run_command(["touch",out_dir+"/"+sample_name+"_relocate_redundant.bed"])
mccutils.run_command(["touch",out_dir+"/"+sample_name+"_relocate_nonredundant.bed"])
mccutils.log("relocate","RelocaTE postprocessing complete")
def main():
mccutils.log("temp", "running TEMP post processing")
insert_summary = snakemake.input.insert_summary
absence_summary = snakemake.input.absence_summary
te_gff = snakemake.input.te_gff
reference_fasta = snakemake.input.reference_fasta
log = snakemake.params.log
sample_name = snakemake.params.sample_name
chromosomes = snakemake.params.chromosomes.split(",")
out_dir = snakemake.params.out_dir
insertions = read_insertion_summary(insert_summary, sample_name)
absence_bed = make_absence_bed(absence_summary, sample_name, out_dir)
non_absent_ref_insertions = get_non_absent_ref_tes(te_gff, absence_bed,
sample_name, out_dir,
log)
insertions += non_absent_ref_insertions
insertions = filter_insertions(
insertions,
chromosomes,
acceptable_classes=config.ACCEPTABLE_INSERTION_SUPPORT_CLASSES,
frequency_theshold=config.FREQUENCY_THRESHOLD)
if len(insertions) > 0:
insertions = output.make_redundant_bed(insertions,
sample_name,
out_dir,
method="temp")
insertions = output.make_nonredundant_bed(insertions,
sample_name,
out_dir,
method="temp")
output.write_vcf(insertions, reference_fasta, sample_name, "temp",
out_dir)
else:
mccutils.run_command(
["touch", out_dir + "/" + sample_name + "_temp_redundant.bed"])
mccutils.run_command(
["touch", out_dir + "/" + sample_name + "_temp_nonredundant.bed"])
mccutils.log("temp", "TEMP postprocessing complete")
def main():
mccutils.log("popoolationte", "processing PopoolationTE results")
popoolationte_out = snakemake.input.popoolationte_out
genome_fasta = snakemake.input.ref
out_dir = snakemake.params.out_dir
sample_name = snakemake.params.sample_name
log = snakemake.params.log
chromosomes = snakemake.params.chromosomes.split(",")
insertions = read_insertions(
popoolationte_out,
sample_name,
chromosomes,
require_both_end_support=config.REQUIRE_BOTH_END_SUPPORT,
percent_read_support_threshold=config.PERCENT_READ_SUPPORT_THRESHOLD)
if len(insertions) >= 1:
insertions = output.make_redundant_bed(insertions,
sample_name,
out_dir,
method="popoolationte")
insertions = output.make_nonredundant_bed(insertions,
sample_name,
out_dir,
method="popoolationte")
output.write_vcf(insertions, genome_fasta, sample_name,
"popoolationte", out_dir)
else:
mccutils.run_command([
"touch",
out_dir + "/" + sample_name + "_popoolationte_redundant.bed"
])
mccutils.run_command([
"touch",
out_dir + "/" + sample_name + "_popoolationte_nonredundant.bed"
])
mccutils.log("popoolationte", "PopoolationTE postprocessing complete")
def main():
insertions_bed = snakemake.input.insertions_bed
deletions_bed = snakemake.input.deletions_bed
insertions_support = snakemake.input.insertions_support
deletions_support = snakemake.input.deletions_support
te_gff = snakemake.input.te_gff
te_taxonomy = snakemake.input.te_taxonomy
reference_fasta = snakemake.input.reference_fasta
chromosomes = snakemake.params.chromosomes.split(",")
status_log = snakemake.params.status_log
sample_name = snakemake.params.sample_name
out_dir = snakemake.params.out_dir
prev_steps_succeeded = mccutils.check_status_file(status_log)
mccutils.log("tepid", "running TEPID post processing")
if prev_steps_succeeded:
te_to_family = get_te_family_map(te_taxonomy)
te_pos_to_family = get_te_pos_family_map(te_gff, te_to_family)
insertions = read_insertions(insertions_bed,
te_to_family,
sample_name,
te_pos_to_family,
chromosomes,
reference=False)
insertions = add_support(insertions,
insertions_support,
threshold=config.READ_SUPPORT_THRESHOLD)
deletions = read_insertions(deletions_bed,
te_to_family,
sample_name,
te_pos_to_family,
chromosomes,
reference=True)
deletions = add_support(deletions,
deletions_support,
threshold=config.READ_SUPPORT_THRESHOLD)
non_abs_ref_insertions = get_non_absent_ref_tes(
deletions, te_gff, te_to_family, sample_name)
insertions += non_abs_ref_insertions
if len(insertions) > 0:
insertions = output.make_redundant_bed(insertions,
sample_name,
out_dir,
method="tepid")
insertions = output.make_nonredundant_bed(insertions,
sample_name,
out_dir,
method="tepid")
output.write_vcf(insertions, reference_fasta, sample_name, "tepid",
out_dir)
else:
mccutils.run_command([
"touch", out_dir + "/" + sample_name + "_tepid_redundant.bed"
])
mccutils.run_command([
"touch",
out_dir + "/" + sample_name + "_tepid_nonredundant.bed"
])
else:
mccutils.run_command(
["touch", out_dir + "/" + sample_name + "_tepid_redundant.bed"])
mccutils.run_command(
["touch", out_dir + "/" + sample_name + "_tepid_nonredundant.bed"])
mccutils.log("tepid", "TEPID post processing complete")
def main():
nonref_gff = snakemake.input.nonref_gff
ref_gff = snakemake.input.ref_gff
rm_out = snakemake.input.rm_out
reference_fasta = snakemake.input.reference_fasta
log = snakemake.params.log
out_dir = snakemake.params.out_dir
sample_name = snakemake.params.sample_name
chromosomes = snakemake.params.chromosomes.split(",")
status_log = snakemake.params.status_log
prev_steps_succeeded = mccutils.check_status_file(status_log)
mccutils.log("relocate2", "processing RelocaTE2 results")
if prev_steps_succeeded:
ref_insertions = get_insertions(
ref_gff,
sample_name,
chromosomes,
insert_type="ref",
l_support_threshold=config.PARAMS["ref_left_support_threshold"],
r_support_threshold=config.PARAMS["ref_right_support_threshold"],
l_junction_threshold=config.PARAMS["ref_left_junction_threshold"],
r_junction_threshold=config.PARAMS["ref_right_junction_threshold"])
nonref_insertions = get_insertions(
nonref_gff,
sample_name,
chromosomes,
insert_type="nonref",
l_support_threshold=config.PARAMS["nonref_left_support_threshold"],
r_support_threshold=config.
PARAMS["nonref_right_support_threshold"],
l_junction_threshold=config.
PARAMS["nonref_left_junction_threshold"],
r_junction_threshold=config.
PARAMS["nonref_right_junction_threshold"])
ref_insertions = fix_ref_te_names(ref_insertions, rm_out, sample_name)
all_insertions = ref_insertions + nonref_insertions
if len(all_insertions) >= 1:
all_insertions = output.make_redundant_bed(all_insertions,
sample_name,
out_dir,
method="relocate2")
insertions = output.make_nonredundant_bed(all_insertions,
sample_name,
out_dir,
method="relocate2")
output.write_vcf(insertions, reference_fasta, sample_name,
"relocate2", out_dir)
else:
mccutils.run_command([
"touch",
out_dir + "/" + sample_name + "_relocate2_redundant.bed"
])
mccutils.run_command([
"touch",
out_dir + "/" + sample_name + "_relocate2_nonredundant.bed"
])
else:
mccutils.run_command([
"touch", out_dir + "/" + sample_name + "_relocate2_redundant.bed"
])
mccutils.run_command([
"touch",
out_dir + "/" + sample_name + "_relocate2_nonredundant.bed"
])
mccutils.log("relocate2", "RelocaTE2 postprocessing complete")
