def intersect_ids(list_of_group_a, list_of_group_b, mode="common"):
# possible modes: common, only_a, only_b, not_common, combine, count
a = IdSet()
b = IdSet()
if mode == "common":
expression = lambda a, b: a & b
elif mode == "only_a":
expression = lambda a, b: a - b
elif mode == "only_b":
expression = lambda a, b: b - a
elif mode == "not_common":
expression = lambda a, b: a ^ b
elif mode == "combine":
expression = lambda a, b: a | b
for id_list in list_of_group_a:
a = a | IdSet(id_list)
for id_list in list_of_group_b:
b = b | IdSet(id_list)
if mode != "count":
return IdSet(expression(a, b))
else:
return len(a), len(b), len(a & b), len(a - b), len(b - a), len(a ^ b), len(a | b)
def extract_monocluster_ids_from_file(self,
dir_with_cluster_files,
out_file,
file_with_white_list_ids=None):
# filenames are counted as species names
white_list_ids = None
if file_with_white_list_ids:
white_list_ids = IdSet()
white_list_ids.read(file_with_white_list_ids)
clusters_dict = self.read_cluster_files_from_dir(
dir_with_cluster_files)
monoclusters = self.extract_monocluster_ids(
clusters_dict, out_file=out_file, white_list_ids=white_list_ids)
return monoclusters
def get_sequence_names(clusters_dict,
write_ids=False,
out_prefix=None,
white_list_ids=None):
sequence_names_dict = SynDict()
for species in clusters_dict:
sequence_names_dict[species] = IdSet()
for species in clusters_dict:
for cluster_id in clusters_dict[species]:
if white_list_ids:
if cluster_id not in white_list_ids:
continue
sequence_names_dict[species] = sequence_names_dict[
species] | IdSet(clusters_dict[species][cluster_id])
if write_ids:
for species in clusters_dict:
out_file = "%s_%s.ids" % (
out_prefix, species) if out_prefix else "%s.ids" % species
sequence_names_dict[species].write(out_file)
return sequence_names_dict
def extract_monocluster_ids(self,
clusters_dict,
white_list_ids=None,
out_file=None):
"""
Extracts clusters with only one sequence in all species.
"""
monocluster_ids = IdSet()
cluster_names = self.get_cluster_names(clusters_dict)
for cluster_name in cluster_names:
for species in clusters_dict:
if white_list_ids:
if cluster_name not in white_list_ids:
break
if cluster_name not in clusters_dict[species]:
break
if len(clusters_dict[species][cluster_name]) > 1:
break
else:
monocluster_ids.add(cluster_name)
if out_file:
monocluster_ids.write(out_file)
return monocluster_ids
def rename_scaffolds_in_gff(self, input_gff, syn_file, output_prefix, verbose=True):
syn_dict = SynDict(filename=syn_file)
skipped_id_list = IdSet()
output_gff = "%s.renamed.gff" % output_prefix
skipped_gff = "%s.skipped.gff" % output_prefix
skipped_id_file = "%s.skipped_scaffolds.ids" % output_prefix
with self.metaopen(input_gff, "r") as in_fd, \
self.metaopen(output_gff, "w") as out_fd, \
self.metaopen(skipped_gff, "w") as skipped_fd:
for line in in_fd:
if line[0] == "#":
out_fd.write(line)
gff_list = line.split("\t")
if gff_list[0] in syn_dict:
gff_list[0] = syn_dict[gff_list[0]]
out_fd.write("\t".join(gff_list))
else:
skipped_fd.write(line)
skipped_id_list.add(gff_list[0])
if verbose:
print("Not renamed scaffolds: %i" % len(skipped_id_list))
skipped_id_list.write(skipped_id_file)
def get_column_value_set_from_file(self,
input_file,
column_number,
output_file=None,
separator="\t",
comments_prefix="#",
verbose=False):
column_value_set = IdSet([
line_list[column_number] for line_list in
self.file_line_as_list_generator(input_file,
separator=separator,
comments_prefix=comments_prefix)
])
if output_file:
column_value_set.write(output_file)
if verbose:
print("#Column %i (0-based) contains %i different values" %
(column_number, len(column_value_set)))
return column_value_set
def get_cluster_names(clusters_dict, out_file=None, white_list_ids=None):
cluster_names = IdSet()
for species in clusters_dict:
species_clusters = IdSet(clusters_dict[species].keys())
cluster_names |= species_clusters
if out_file:
cluster_names.write(out_file)
return cluster_names & IdSet(
white_list_ids) if white_list_ids else cluster_names
def get_scaffold_ids_from_gff(gff_file, out_file=None):
scaffold_id_set = IdSet()
with open(gff_file, "r") as gff_fd:
for line in gff_fd:
if line[0] == "#":
continue
scaffold_id = line.split("\t")[0]
scaffold_id_set.add(scaffold_id)
if out_file:
scaffold_id_set.write(out_file)
return scaffold_id_set
help="Input fam file")
parser.add_argument("-d", "--id_file", action="store", dest="id_file", required=True,
help="File with ids of families to extract")
parser.add_argument("-o", "--output", action="store", dest="output", default="stdout",
help="File to write extracted families. Default - stdout")
parser.add_argument("-v", "--verbose", action="store_true", dest="verbose",
help="Print not found ids. Default - no")
args = parser.parse_args()
out_file = sys.stdout if args.output == "stdout" else open(args.output, "w")
fam_dict = SynDict()
fam_dict.read(args.input)
id_set = IdSet()
id_set.read(args.id_file)
extracted_dict = SynDict()
for id_entry in id_set:
if id_entry in fam_dict:
extracted_dict[id_entry] = fam_dict[id_entry]
else:
if args.verbose:
print("%s was not found" % id_entry)
extracted_dict.write(out_file, close_after_if_file_object=True)
def intersect_ids_from_files(files_with_ids_from_group_a, files_with_ids_from_group_b,
result_file=None, mode="common"):
a = IdSet()
b = IdSet()
if mode == "common":
expression = lambda a, b: a & b
elif mode == "only_a":
expression = lambda a, b: a - b
elif mode == "only_b":
expression = lambda a, b: b - a
elif mode == "not_common":
expression = lambda a, b: a ^ b
elif mode == "combine":
expression = lambda a, b: a | b
#print(files_with_ids_from_group_a)
for filename in [files_with_ids_from_group_a] if isinstance(files_with_ids_from_group_a, str) else files_with_ids_from_group_a:
id_set = IdSet()
id_set.read(filename, comments_prefix="#")
a = a | id_set
for filename in [files_with_ids_from_group_b] if isinstance(files_with_ids_from_group_b, str) else files_with_ids_from_group_b:
id_set = IdSet()
id_set.read(filename, comments_prefix="#")
b = b | id_set
result_fd = open(result_file, "w") if result_file else sys.stdout
if mode != "count":
final_set = IdSet(expression(a, b))
final_set.write(result_fd)
else:
result_fd.write("Group_A\t%i\nGroup_B\t%i\nCommon\t%i\nOnly_group_A\t%i\nOnly_group_B\t%i\nNot_common\t%i\nAll\t%i\n" %
(len(a), len(b), len(a & b), len(a - b), len(b - a), len(a ^ b), len(a | b)))
def extract_transcripts_by_ids(self, input_gff, transcript_id_file, output_gff):
transcript_ids = IdSet()
transcript_ids.read(transcript_id_file, header=False)
GFF.write(self.record_with_extracted_transcripts_generator(input_gff, transcript_ids),
open(output_gff, "w"))
for species in args.species_list:
species_syn_dict[species] = read_synonyms_dict("%s%s/all.t" % (args.species_dir, species))
species_syn_dict.write("families_all_species.t", absent_symbol=".")
nonassembled = species_syn_dict.filter_by_line(filter_nonassembled)
species_syn_dict.write("correctly_assembled_families_species.t", absent_symbol=".")
nonassembled.write("not_assembled_families_in_all_species.t", absent_symbol=".")
complicated_families_dict = nonassembled.filter_by_line(filter_splited_to_several_fam)
complicated_families_dict.write("complicated_families.t", absent_symbol=".")
complicated_families_syn_dict = SynDict()
complicated_families_syn_ids = IdSet()
sl_keys = list(complicated_families_dict.sl_keys())
for sl_key in sl_keys:
sp_set = set()
for species in complicated_families_dict:
if sl_key not in complicated_families_dict[species]:
continue
tmp = complicated_families_dict[species][sl_key].split(";")
for i in range(0, len(tmp)):
if "_" in tmp[i]:
tmp[i] = tmp[i][2:]
tmp[i] = tmp[i].split(",")
for syn_id in tmp[i]:
complicated_families_syn_ids.add(syn_id)
sp_set.add(syn_id)
complicated_families_syn_dict[sl_key] = sp_set
def extract_sequences_by_clusters(self,
dir_with_cluster_files,
dir_with_sequence_files,
output_dir,
file_with_white_list_cluster_ids=None,
mode="families",
sequence_file_extension="fasta",
sequence_file_format="fasta",
label_species=False,
separator_for_labeling="@",
species_label_first=True):
"""
basenames of cluster and sequence files must be same
mode:
clusters - extract sequences from clusters in separate files,
species - extract sequences from species to separate files
"""
white_list_ids = None
if file_with_white_list_cluster_ids:
white_list_ids = IdSet()
white_list_ids.read(file_with_white_list_cluster_ids)
clusters_dict = self.read_cluster_files_from_dir(
dir_with_cluster_files)
cluster_names = self.get_cluster_names(clusters_dict,
white_list_ids=white_list_ids)
sequence_super_dict = OrderedDict()
out_dir = FileRoutines.check_path(output_dir)
for species in clusters_dict:
idx_file = "%s_tmp.idx" % species
sequence_file = "%s%s.%s" % (FileRoutines.check_path(
dir_with_sequence_files), species, sequence_file_extension)
sequence_super_dict[species] = SeqIO.index_db(
idx_file, sequence_file, format=sequence_file_format)
if mode == "species":
seqeuence_names = self.get_sequence_names(
clusters_dict,
write_ids=False,
out_prefix=None,
white_list_ids=white_list_ids)
for species in seqeuence_names:
out_file = "%s%s.%s" % (out_dir, species,
sequence_file_extension)
SeqIO.write(SequenceRoutines.record_by_id_generator(
sequence_super_dict[species], seqeuence_names[species]),
out_file,
format=sequence_file_format)
elif mode == "families":
def per_family_record_generator(seq_super_dict, clust_dict,
cluster_id):
if species_label_first:
label_sequence = lambda label, name: "%s%s%s" % (
label, separator_for_labeling, name)
else:
label_sequence = lambda label, name: "%s%s%s" % (
name, separator_for_labeling, label)
for species in seq_super_dict:
#print species, cluster_id
for record_id in clust_dict[species][cluster_id]:
if label_species:
record = deepcopy(
seq_super_dict[species][record_id])
record.id = label_sequence(species, record_id)
yield record
else:
yield seq_super_dict[species][record_id]
for cluster_name in cluster_names:
out_file = "%s%s.%s" % (out_dir, cluster_name,
sequence_file_extension)
SeqIO.write(per_family_record_generator(
sequence_super_dict, clusters_dict, cluster_name),
out_file,
format=sequence_file_format)
for species in clusters_dict:
os.remove("%s_tmp.idx" % species)
"""
parser.add_argument("-o", "--output_file", action="store", dest="output", default="stdout",
help="Output file. Default: stdout")
"""
args = parser.parse_args()
# run after scripts/expansion/compare_cluster.py
# out_fd = sys.stdout if args.output == "stdout" else open(args.output, "w")
species_syn_dict = TwoLvlDict()
for species in args.species_list:
species_syn_dict[species] = read_synonyms_dict("%s%s/all.t" %
(args.species_dir, species))
species_syn_dict.write("families_all_species.t", absent_symbol=".")
not_assembled = species_syn_dict.filter_by_line(is_assembled)
species_syn_dict.write("correctly_assembled_families_species.t",
absent_symbol=".")
assembled_ids = IdSet(species_syn_dict.sl_keys())
assembled_ids.write("assembled_families.ids")
not_assembled_ids = IdSet(not_assembled.sl_keys())
not_assembled_ids.write("non_assembled_families.ids")
"""
if args.output != "stdout":
out_fd.close()
"""
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)
"""
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)
if args.swissprot_db:
print("Annotating peptides(Swissprot database)...")
BLASTp.threads = args.threads
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")
def convert_rm_out_to_gff(input_file, output_file,
annotated_repeat_classes_file,
annotated_repeat_families_file):
repeat_classes_set = IdSet()
repeat_families_set = IdSet()
with open(input_file, "r") as in_fd:
for i in range(0, 3):
in_fd.readline()
with open(output_file, "w") as out_fd:
for line in in_fd:
tmp = line.strip().split()
strand = "+" if tmp[8] == "+" else "-"
repeat_class_family = tmp[10].split("/")
if len(repeat_class_family) == 1:
repeat_class_family.append(".")
repeat_classes_set.add(repeat_class_family[0])
repeat_families_set.add("/".join(repeat_class_family))
parameters = "Class=%s;Family=%s;Matching_repeat=%s;SW_score=%s;Perc_div=%s;Perc_del=%s;Pers_ins=%s" \
% (repeat_class_family[0], repeat_class_family[1],
tmp[9], tmp[0], tmp[1], tmp[2], tmp[3])
out_fd.write(
"%s\tRepeatMasker\trepeat\t%s\t%s\t.\t%s\t.\t%s\n" %
(tmp[4], tmp[5], tmp[6], strand, parameters))
repeat_classes_set.write(annotated_repeat_classes_file)
repeat_families_set.write(annotated_repeat_families_file)
type=FileRoutines.make_list_of_path_to_files_from_string,
help="Comma-separated list of input files/directories with sequences")
parser.add_argument("-o", "--output_directory", action="store", dest="output", type=FileRoutines.check_path,
help="Directory to output groups_of sequences")
parser.add_argument("-f", "--format", action="store", dest="format", default="fasta",
help="Format of input and output files. Allowed formats genbank, fasta(default)")
parser.add_argument("-e", "--extension", action="store", dest="extension",
help="Extension of output files. Default: equal to -f")
parser.add_argument("-d", "--id_file", action="store", dest="id_file",
help="File with groups of sequences to extract(.fam file).")
args = parser.parse_args()
FileRoutines.safe_mkdir(args.output)
args.extension = args.extension if args.extension else args.format
tmp_index_file = "temp.idx"
#id_list = read_ids(args.id_file)
id_list = IdSet(filename=args.id_file)
sequence_groups_id = SynDict()
sequence_groups_id.read(args.id_file, split_values=True)
#print("Parsing %s..." % args.input_file)
sequence_dict = SeqIO.index_db(tmp_index_file, args.input, format=args.format)
for group in sequence_groups_id:
SeqIO.write(SequenceRoutines.record_by_id_generator(sequence_dict, sequence_groups_id[group],
verbose=True),
"%s%s.%s" % (args.output, group, args.extension), format=args.format)
os.remove(tmp_index_file)
accordance_file = "%s/%s.accordance" % (args.accordance_dir, species)
accordance_dict[species] = SynDict()
accordance_dict[species].read(accordance_file, key_index=1, value_index=0)
if args.name_first:
def split_name(pep_name):
gene_list = pep_name.split(args.name_separator)
return gene_list[0], args.name_separator.join(gene_list[1:])
else:
def split_name(pep_name):
gene_list = pep_name.split(args.name_separator)
return gene_list[-1], args.name_separator.join(gene_list[:-1])
families_with_errors = IdSet()
for family in pep_fam_dict:
cds_fam_dict[family] = []
for pep in pep_fam_dict[family]:
species, pep_name = split_name(pep)
if pep_name in accordance_dict[species]:
cds_name = "%s%s%s" % (species, args.name_separator, accordance_dict[species][pep_name]) if args.name_first else \
"%s%s%s" % (accordance_dict[species][pep_name], args.name_separator, species)
cds_fam_dict[family].append(cds_name)
else:
print("%s %s %s doesn't have associated cds in accordance file" % (family, species, pep_name))
families_with_errors.add(family)
for family in families_with_errors:
cds_fam_dict.pop(family, None)
