def predict_genes(self,
output_prefix,
annotation_species_prefix,
genome_fasta,
augustus_species,
output_directory="./",
augustus_strand=None,
augustus_gene_model=None,
augustus_config_dir=None,
augustus_use_softmasking=None,
augustus_other_options="",
augustus_hintsfile=None,
augustus_extrinsicCfgFile=None,
augustus_predict_UTR=None,
augustus_min_intron_len=None,
threads=1,
augustus_dir="",
hmmer_dir="",
blast_dir="",
stop_codons_list=("TGA", "TAA", "TAG"),
genetic_code_table=1):
draft_file_prefix = "%s/raw/%s" % (output_directory, output_prefix)
augustus_splited_input_dir = "%s/splited_input/" % output_directory
augustus_splited_output_dir = "%s/splited_output_dir" % output_directory
output_raw_gff = "%s.raw.gff" % draft_file_prefix
output_gff = "%s.renamed.gff" % draft_file_prefix
augustus_pep = "%s.pep" % draft_file_prefix
AUGUSTUS.path = augustus_dir
AUGUSTUS.threads = threads
HMMER3.path = hmmer_dir
HMMER3.threads = threads
BLASTp.path = blast_dir
BLASTp.threads = threads
print("Annotating genes...")
AUGUSTUS.parallel_predict(
augustus_species,
genome_fasta,
output_raw_gff,
strand=augustus_strand,
gene_model=augustus_gene_model,
output_gff3=True,
other_options=augustus_other_options,
config_dir=augustus_config_dir,
use_softmasking=augustus_use_softmasking,
hints_file=augustus_hintsfile,
split_dir=augustus_splited_input_dir,
splited_output_dir=augustus_splited_output_dir,
extrinsicCfgFile=augustus_extrinsicCfgFile,
predict_UTR=augustus_predict_UTR,
combine_output_to_single_file=True,
min_intron_len=augustus_min_intron_len)
#replace_augustus_ids(augustus_gff, output_prefix, species_prefix=None, number_of_digits_in_id=8):
AUGUSTUS.replace_augustus_ids(output_raw_gff,
draft_file_prefix,
species_prefix=annotation_species_prefix,
number_of_digits_in_id=8)
#extract_transcript_sequences(self, input_gff_file, genomic_fasta_file, output_prefix, coding_only=False)
gffread_file_prefix = "%s.gffread" % draft_file_prefix
gffread_transcripts_file, gffread_cds_file, gffread_pep_file = Gffread.extract_transcript_sequences(
output_gff, genome_fasta, gffread_file_prefix)
gffread_trimmed_cds = ".".join(
gffread_cds_file.split(".")[:-1]) + ".trimmed.cds"
gffread_trimmed_pep = ".".join(
gffread_pep_file.split(".")[:-1]) + ".trimmed.pep"
self.trim_cds_and_remove_terminal_stop_codons(
gffread_cds_file,
gffread_trimmed_cds,
stop_codons_list=stop_codons_list
) # using default stop_codons(from universal genetic_code)/ Note that this will affect mtDNA proteins
inframe_stop_codons_file_prefix = "%s.inframe_stop_codon" % draft_file_prefix
self.translate_sequences_from_file(
gffread_trimmed_cds,
gffread_trimmed_pep,
format="fasta",
id_expression=None,
genetic_code_table=genetic_code_table,
translate_to_stop=False,
prefix_of_file_inframe_stop_codons_seqsin=
inframe_stop_codons_file_prefix) # Universal code !!!
AUGUSTUS.extract_gene_ids_from_output(output_gff,
all_annotated_genes_ids)
AUGUSTUS.extract_CDS_annotations_from_output(output_gff, CDS_gff)
print("Extracting peptides...")
AUGUSTUS.extract_proteins_from_output(
output_gff,
output_pep,
id_prefix="",
evidence_stats_file=output_evidence_stats,
supported_by_hints_file=output_supported_stats)
self.compare_sequences_from_files(output_pep,
"%s.trimmed.pep" % args.output,
"comparison_of_peptides",
format="fasta",
verbose=True)
os.system("awk -F'\\t' 'NR==1 {}; NR > 1 {print $2}' %s > %s" %
(output_supported_stats, output_supported_stats_ids))
print("Annotating domains(Pfam database)...")
HMMER3.parallel_hmmscan(
args.pfam_db,
output_pep,
output_hmmscan,
num_of_seqs_per_scan=None,
split_dir="splited_hmmscan_fasta/",
splited_output_dir="splited_hmmscan_output_dir",
tblout_outfile=None,
domtblout_outfile=output_domtblout,
pfamtblout_outfile=None,
splited_tblout_dir=None,
splited_domtblout_dir="hmmscan_domtblout/")
HMMER3.extract_dom_ids_hits_from_domtblout(
output_domtblout, output_pfam_annotated_dom_ids)
hits_dict = HMMER3.extract_dom_names_hits_from_domtblout(
output_domtblout, output_pfam_annotated_dom_names)
supported_ids = IdSet(hits_dict.keys())
supported_ids.write(output_pfam_supported_transcripts_ids)
remove_transcript_ids_str = "sed -re 's/\.t[0123456789]+//' %s | sort -k 1 | uniq > %s" % (
output_pfam_supported_transcripts_ids,
output_pfam_supported_genes_ids)
os.system(remove_transcript_ids_str)
print("Annotating peptides(Swissprot database)...")
BLASTp.parallel_blastp(output_pep,
args.swissprot_db,
evalue=0.0000001,
output_format=6,
outfile=output_swissprot_blastp_hits,
split_dir="splited_blastp_fasta",
splited_output_dir="splited_blastp_output_dir")
hits_dict = BLASTp.extract_hits_from_tbl_output(
output_swissprot_blastp_hits, output_swissprot_blastp_hits_names)
supported_ids = IdSet(hits_dict.keys())
supported_ids.write(output_swissprot_supported_transcripts_ids)
remove_transcript_ids_str = "sed -re 's/\.t[0123456789]+//' %s | sort -k 1 | uniq > %s" % (
output_swissprot_supported_transcripts_ids,
output_swissprot_supported_genes_ids)
os.system(remove_transcript_ids_str)
"""
AUGUSTUS.parallel_predict(args.species,
args.input,
output_raw_gff,
strand=args.strand,
gene_model=args.gene_model,
output_gff3=True,
other_options=args.other_options,
config_dir=args.config_dir,
use_softmasking=args.softmasking,
hints_file=args.hintsfile,
extrinsicCfgFile=args.extrinsicCfgFile,
predict_UTR=args.predict_UTR,
parsing_mode="parse")
AUGUSTUS.replace_augustus_ids(output_raw_gff,
args.output,
species_prefix=args.species_prefix,
number_of_digits_in_id=8)
Gffread.extract_transcript_sequences(output_gff, args.input, args.output)
SequenceRoutines.trim_cds_and_remove_terminal_stop_codons(
"%s.cds" % args.output,
"%s.trimmed.cds" % args.output,
stop_codons_list=("TGA", "TAA", "TAG")
) # using default stop_codons(from universal genetic_code)/ Note that this will affect mtDNA proteins
SequenceRoutines.translate_sequences_from_file(
"%s.trimmed.cds" % args.output,
"%s.trimmed.pep" % args.output,
format="fasta",
id_expression=None,
#!/usr/bin/env python
__author__ = 'Sergei F. Kliver'
import argparse
from RouToolPa.Tools.Annotation import AUGUSTUS
parser = argparse.ArgumentParser()
parser.add_argument("-i", "--input_gff", action="store", dest="input_gff", required=True,
help="Input gff from AUGUSTUS")
parser.add_argument("-o", "--output_prefix", action="store", dest="output_prefix", required=True,
help="Prefix of output files")
parser.add_argument("-s", "--species_prefix", action="store", dest="species_prefix", required=True,
help="Species prefix for ids")
parser.add_argument("-d", "--number_of_digits_in_id", action="store", dest="number_of_digits_in_id", type=int,
default=8, help="Number of digits in ids. Default - 8")
args = parser.parse_args()
AUGUSTUS.replace_augustus_ids(args.input_gff, args.output_prefix, species_prefix=args.species_prefix,
number_of_digits_in_id=args.number_of_digits_in_id)