def simple_count_main(args):
import simple_count
output_dir = os.path.dirname(args.output_file)
if output_dir != "" and not os.path.exists(output_dir):
os.makedirs(output_dir)
# intron_db.generate_edge_bed(args.ref_gene_file, output_prefix + ".refGene.edge.bed", args.chr_name_list)
intron_db.generate_intron_retention_list(
args.ref_gene_file, args.output_file + ".refGene.edge.bed", "1,0", "0,1", args.chr_name_list
)
intron_db.broaden_edge(
args.output_file + ".refGene.edge.bed",
args.output_file + ".refGene.edge_broaden.bed",
args.intron_retention_check_size,
)
simple_count.filterImproper(args.bam_file, args.output_file + ".filt.bam", args.mapping_qual_thres)
hout = open(args.output_file + ".filt.bed12", "w")
s_ret = subprocess.call(["bedtools", "bamtobed", "-bed12", "-i", args.output_file + ".filt.bam"], stdout=hout)
hout.close()
if s_ret != 0:
print >>sys.stderr, "error in generating filt.bed12"
sys.exit(1)
hout = open(args.output_file + ".edge.bed", "w")
s_ret = subprocess.call(
[
"bedtools",
"intersect",
"-a",
args.output_file + ".filt.bed12",
"-b",
args.output_file + ".refGene.edge.bed",
"-split",
"-wo",
],
stdout=hout,
)
hout.close()
if s_ret != 0:
print >>sys.stderr, "error in generating edge.bed"
sys.exit(1)
hout = open(args.output_file + ".edge_broaden.bed", "w")
s_ret = subprocess.call(
[
"bedtools",
"intersect",
"-a",
args.output_file + ".filt.bed12",
"-b",
args.output_file + ".refGene.edge_broaden.bed",
"-split",
"-wo",
],
stdout=hout,
)
hout.close()
if s_ret != 0:
print >>sys.stderr, "error in generating edge_broaden.bed"
sys.exit(1)
simple_count.summarize_edge(
args.output_file + ".edge.bed",
args.output_file + ".edge_broaden.bed",
args.output_file + ".unsorted",
args.intron_retention_check_size,
)
# print header
hout = open(args.output_file, "w")
print >> hout, "\t".join(
[
"Chr",
"Boundary_Pos",
"Gene_Symbol",
"Motif_Type",
"Strand",
"Junction_List",
"Gene_ID_List",
"Exon_Num_List",
"Edge_Read_Count",
"Intron_Retention_Read_Count",
]
)
hout.close()
# sort the result
hout = open(args.output_file, "a")
subprocess.call(["sort", "-k1,1", "-k2,2n", "-k3,3n", args.output_file + ".unsorted"], stdout=hout)
hout.close()
if not args.debug:
subprocess.call(["rm", "-rf", args.output_file + ".filt.bam"])
subprocess.call(["rm", "-rf", args.output_file + ".filt.bed12"])
subprocess.call(["rm", "-rf", args.output_file + ".refGene.edge.bed"])
subprocess.call(["rm", "-rf", args.output_file + ".refGene.edge_broaden.bed"])
subprocess.call(["rm", "-rf", args.output_file + ".edge.bed"])
subprocess.call(["rm", "-rf", args.output_file + ".edge_broaden.bed"])
subprocess.call(["rm", "-rf", args.output_file + ".unsorted"])
def allele_count_main(args):
import mutation, allele_count, pyssw
output_dir = os.path.dirname(args.output_file)
if output_dir != "" and not os.path.exists(output_dir):
os.makedirs(output_dir)
intron_db.generate_intron_retention_list(
args.ref_gene_file,
args.output_file + ".intron_retention_list.bed",
args.donor_size,
args.acceptor_size,
args.chr_name_list,
)
mutation.anno2bed(args.mutation_file, args.output_file + ".mutation_list.bed")
hout = open(args.output_file + ".mutation_list.overlap.bed", "w")
subprocess.call(
[
"bedtools",
"intersect",
"-a",
args.output_file + ".mutation_list.bed",
"-b",
args.output_file + ".intron_retention_list.bed",
"-wa",
"-wb",
],
stdout=hout,
)
hout.close()
cnum = 0
hout = open(args.output_file, "w")
# print header
print >> hout, "\t".join(
[
"Gene_Symbol",
"Chr_Mut",
"Start_Mut",
"End_Mut",
"Ref_Mut",
"Alt_Mut",
"Chr_Motif",
"Start_Motif",
"End_Motif",
"Type_Motif",
"Strand_Motif",
"Splice_Junction_Negative",
"Splice_Junction_Positive",
"Intron_Retention_Negative",
"Intron_Retention_Positive",
]
)
with open(args.output_file + ".mutation_list.overlap.bed", "r") as hin:
for line in hin:
F = line.rstrip("\n").split("\t")
mut_chr, mut_start, mut_end, mut_ref, mut_alt = F[0], int(F[1]) + 1, int(F[2]), F[3], F[4]
motif_chr, motif_start, motif_end, motif_type, motif_strand, junc_list = (
F[5],
int(F[6]) + 1,
int(F[7]) + 1,
F[9],
F[10],
F[11],
)
motif_gene = F[8]
# generate template sequence (splicing junction with and/or without mutation, intron retention with and/or withoug mutation)
allele_count.generate_template_seq(
args.output_file + ".tmp.template_seq.fa" + str(cnum),
args.reference,
mut_chr,
mut_start,
mut_end,
mut_ref,
mut_alt,
motif_chr,
motif_start,
motif_end,
motif_type,
motif_strand,
junc_list,
args.donor_size,
args.acceptor_size,
args.template_size,
)
# extract short reads from bam files around the exon-intron boundary
allele_count.extract_read_around_boundary(
args.bam_file,
args.output_file + ".tmp.read_seq.fa" + str(cnum),
args.reference,
motif_chr,
motif_start,
motif_end,
args.read_search_margin,
)
# perform smith-waterman alignment check
type2count = pyssw.main2(
args.output_file + ".tmp.read_seq.fa" + str(cnum),
args.output_file + ".tmp.template_seq.fa" + str(cnum),
4 * args.template_size - args.template_score_margin,
)
print >> hout, "\t".join(
[
motif_gene,
mut_chr,
str(mut_start),
str(mut_end),
mut_ref,
mut_alt,
motif_chr,
str(motif_start),
str(motif_end),
motif_type,
motif_strand,
str(type2count["splice_junction_negative"]),
str(type2count["splice_junction_positive"]),
str(type2count["intron_retention_negative"]),
str(type2count["intron_retention_positive"]),
]
)
if not args.debug:
subprocess.call(["rm", "-rf", args.output_file + ".tmp.template_seq.fa" + str(cnum)])
subprocess.call(["rm", "-rf", args.output_file + ".tmp.read_seq.fa" + str(cnum)])
cnum = cnum + 1
hout.close()
if not args.debug:
subprocess.call(["rm", "-rf", args.output_file + ".intron_retention_list.bed"])
subprocess.call(["rm", "-rf", args.output_file + ".mutation_list.bed"])
subprocess.call(["rm", "-rf", args.output_file + ".mutation_list.overlap.bed"])
