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
chromosomes = snakemake.params.chromosomes.split(",")
sample_name = snakemake.params.sample_name
out_dir = snakemake.params.out_dir
mccutils.log("tepid", "running TEPID post processing")
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:
mccutils.make_redundant_bed(insertions,
sample_name,
out_dir,
method="tepid")
mccutils.make_nonredundant_bed(insertions,
sample_name,
out_dir,
method="tepid")
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():
mccutils.log("popoolationte", "processing PopoolationTE results")
popoolationte_out = snakemake.input.popoolationte_out
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 = mccutils.make_redundant_bed(insertions,
sample_name,
out_dir,
method="popoolationte")
mccutils.make_nonredundant_bed(insertions,
sample_name,
out_dir,
method="popoolationte")
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("retroseq", "processing RetroSeq results")
retroseq_out = snakemake.input.retroseq_out
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 = mccutils.make_redundant_bed(insertions,
sample_name,
out_dir,
method="retroseq")
mccutils.make_nonredundant_bed(insertions,
sample_name,
out_dir,
method="retroseq")
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():
nonref_gff = snakemake.input.nonref_gff
ref_gff = snakemake.input.ref_gff
rm_out = snakemake.input.rm_out
log = snakemake.params.log
out_dir = snakemake.params.out_dir
sample_name = snakemake.params.sample_name
chromosomes = snakemake.params.chromosomes.split(",")
mccutils.log("relocate2", "processing RelocaTE2 results")
ref_insertions = get_insertions(
ref_gff,
sample_name,
chromosomes,
insert_type="ref",
l_support_threshold=config.REF_LEFT_SUPPORT_THRESHOLD,
r_support_threshold=config.REF_RIGHT_SUPPORT_THRESHOLD,
l_junction_threshold=config.REF_LEFT_JUNCTION_THRESHOLD,
r_junction_threshold=config.REF_RIGHT_JUNCTION_THRESHOLD)
nonref_insertions = get_insertions(
nonref_gff,
sample_name,
chromosomes,
insert_type="nonref",
l_support_threshold=config.NONREF_LEFT_SUPPORT_THRESHOLD,
r_support_threshold=config.NONREF_RIGHT_SUPPORT_THRESHOLD,
l_junction_threshold=config.NONREF_LEFT_JUNCTION_THRESHOLD,
r_junction_threshold=config.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 = mccutils.make_redundant_bed(all_insertions,
sample_name,
out_dir,
method="relocate2")
mccutils.make_nonredundant_bed(all_insertions,
sample_name,
out_dir,
method="relocate2")
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")
def main():
mccutils.log("te-locate","processing TE-Locate results")
telocate_raw = snakemake.input.telocate_raw
te_gff = snakemake.input.te_gff
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 = mccutils.make_redundant_bed(insertions, sample_name, out_dir, method="telocate")
mccutils.make_nonredundant_bed(insertions, sample_name, out_dir,method="telocate")
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("jitterbug", "jitterbug postprocessing")
jitterbug_out = snakemake.input.jitterbug_out
te_taxonomy = snakemake.input.taxonomy
out_dir = snakemake.params.out_dir
log = snakemake.params.log
sample_name = snakemake.params.sample_name
chromosomes = snakemake.params.chromosomes.split(",")
out = snakemake.output.out
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 = mccutils.make_redundant_bed(insertions,
sample_name,
out_dir,
method="jitterbug")
mccutils.make_nonredundant_bed(insertions,
sample_name,
out_dir,
method="jitterbug")
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():
raw_bed = snakemake.input.raw_bed
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 = mccutils.make_redundant_bed(insertions,
sample_name,
out_dir,
method="ngs_te_mapper")
mccutils.make_nonredundant_bed(insertions,
sample_name,
out_dir,
method="ngs_te_mapper")
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("temp","running TEMP post processing")
insert_summary = snakemake.input.insert_summary
absence_summary = snakemake.input.absence_summary
te_gff = snakemake.input.te_gff
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 = mccutils.make_redundant_bed(insertions, sample_name, out_dir, method="temp")
mccutils.make_nonredundant_bed(insertions, sample_name, out_dir, method="temp")
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("popoolationte2", "processing PopoolationTE2 results")
te_predictions = snakemake.input.popoolationte2_out
te_gff = snakemake.input.te_gff
taxonomy = snakemake.input.taxonomy
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 = mccutils.make_redundant_bed(insertions,
sample_name,
out_dir,
method="popoolationte2")
mccutils.make_nonredundant_bed(insertions,
sample_name,
out_dir,
method="popoolationte2")
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
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 = mccutils.make_redundant_bed(insertions, sample_name, out_dir, method="relocate")
mccutils.make_nonredundant_bed(insertions, sample_name, out_dir, method="relocate")
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")
