def calculate_p_distance(self):
from RouToolPa.Routines import SequenceRoutines
if self.parsing_mode == "generator":
raise ValueError(
"ERROR!!! P distance calculation was not implemented for generator mode!"
)
if self.seq_lengths is None:
self.get_stats_and_features(count_gaps=False, sort=False)
seq_len = self.seq_lengths["length"].unique()
if len(seq_len) > 1:
raise ValueError("ERROR!!! Some sequences have different length!")
else:
seq_len = seq_len[0]
distance_df = pd.DataFrame(0,
index=self.scaffolds,
columns=self.scaffolds)
for record_id_a in self.scaffolds:
for record_id_b in self.scaffolds:
if record_id_a == record_id_b:
continue
distance_df.loc[record_id_a, record_id_b] = distance_df.loc[
record_id_b, record_id_a] = SequenceRoutines.p_distance(
self.records[record_id_a], self.records[record_id_b],
seq_len)
return distance_df
def correct_coordinates(self, sequence_dict):
for primer_pair in self.primer_pair_list:
primer_pair.left_primer.start = sequence_dict[self.seq_id].find(
primer_pair.left_primer.seq)
primer_pair.right_primer.start = sequence_dict[self.seq_id].find(
SequenceRoutines.reverse_complement(
primer_pair.right_primer.seq)
) + primer_pair.right_primer.length - 1
def extract_proteins_from_selected_families(
families_id_file,
fam_file,
pep_file,
output_dir="./",
pep_format="fasta",
out_prefix=None,
create_dir_for_each_family=False):
from RouToolPa.Routines import SequenceRoutines
fam_id_list = IdList()
fam_dict = SynDict()
#print(pep_file)
FileRoutines.safe_mkdir(output_dir)
out_dir = FileRoutines.check_path(output_dir)
create_directory_for_each_family = True if out_prefix else create_dir_for_each_family
if families_id_file:
fam_id_list.read(families_id_file)
fam_dict.read(fam_file, split_values=True, values_separator=",")
protein_dict = SeqIO.index_db("tmp.idx", pep_file, format=pep_format)
for fam_id in fam_id_list if families_id_file else fam_dict:
if fam_id in fam_dict:
if create_directory_for_each_family:
fam_dir = "%s%s/" % (out_dir, fam_id)
FileRoutines.safe_mkdir(fam_dir)
out_file = "%s%s.pep" % (fam_dir, out_prefix
if out_prefix else fam_id)
else:
out_file = "%s/%s.pep" % (out_dir, out_prefix
if out_prefix else fam_id)
SeqIO.write(SequenceRoutines.record_by_id_generator(
protein_dict, fam_dict[fam_id], verbose=True),
out_file,
format=pep_format)
else:
print("%s was not found" % fam_id)
os.remove("tmp.idx")
help=
"Format of input and output file. Allowed formats genbank, fasta(default)")
parser.add_argument("-p",
"--parsing_mode",
action="store",
dest="parsing_mode",
default="index_db",
help="Parsing mode for input sequence file. "
"Possible variants: 'index_db'(default), 'index', 'parse'")
args = parser.parse_args()
"""
example of usage
~/Soft/MAVR/scripts/sequence/filter_sequences_by_id_expression.py -i GSS_BOH_BAC_end.fa \
-a GSS_BOH_BAC_end.forward.fa \
-b GSS_BOH_BAC_end.reverse.fa \
-e "\.F$" -p parse
"""
SequenceRoutines.filter_seq_by_reg_expression_from_file(
args.input,
args.regular_expression,
args.filtered_file,
args.filtered_out_file,
parsing_mode=args.parsing_mode,
format=args.format,
index_file="tmp.idx",
retain_index=False,
reg_exp_flags=0)
def extract_proteins_from_output(self,
augustus_output,
protein_output,
evidence_stats_file=None,
supported_by_hints_file=None,
complete_proteins_id_file=None,
id_prefix="p."):
if evidence_stats_file:
ev_fd = open(evidence_stats_file, "w")
ev_fd.write(
"#gene_id\ttranscript_id\tsupported_fraction\tcds_support\tintron_support\t"
)
ev_fd.write(
"5'UTR_support\t3'UTR_support\tincompatible_hints_groups\tprotein_length\n"
)
if evidence_stats_file:
sup_fd = open(supported_by_hints_file, "w")
sup_fd.write(
"#gene_id\ttranscript_id\tsupported_fraction\tcds_support\tintron_support\t"
)
sup_fd.write(
"5'UTR_support\t3'UTR_support\tincompatible_hints_groups\tprotein_length\n"
)
if complete_proteins_id_file:
complete_fd = open(complete_proteins_id_file, "w")
with open(protein_output, "w") as out_fd:
with open(augustus_output, "r") as in_fd:
for line in in_fd:
if line[:12] == "# start gene":
gene = line.strip().split()[-1]
elif "\ttranscript\t" in line:
transcript_id = line.split("\t")[8].split(
";")[0].split("=")[1]
start_presence = False
stop_presence = False
#out_fd.write(">%s%s\t gene=%s\n" % (id_prefix, transcript_id, gene))
elif "\tstart_codon\t" in line:
start_presence = True
elif "\tstop_codon\t" in line:
stop_presence = True
elif "# protein sequence" in line:
protein = line.strip().split("[")[-1]
if "]" in protein:
protein = protein.split("]")[0]
else:
while True:
part = in_fd.readline().split()[-1]
if "]" in part:
protein += part.split("]")[0]
break
else:
protein += part
if complete_proteins_id_file:
#print "AAAAA"
#print (start_presence, stop_presence)
if start_presence and stop_presence:
complete_fd.write("%s%s\n" %
(id_prefix, transcript_id))
out_fd.write(
">%s%s\t gene=%s start_presence=%s stop_presence=%s\n"
% (id_prefix, transcript_id, gene,
str(start_presence), str(stop_presence)))
out_fd.write(protein)
protein_len = len(protein)
out_fd.write("\n")
elif evidence_stats_file or supported_by_hints_file:
if line[:17] == "# % of transcript":
supported_fraction = line.strip().split()[-1]
while True:
tmp_line = in_fd.readline()
if tmp_line[:12] == "# CDS exons:":
cds_support = tmp_line.strip().split()[-1]
elif tmp_line[:14] == "# CDS introns:":
introns_support = tmp_line.strip().split(
)[-1]
elif tmp_line[:13] == "# 5'UTR exons":
five_utr_support = tmp_line.strip().split(
)[-1]
elif tmp_line[:13] == "# 3'UTR exons":
three_introns_support = tmp_line.strip(
).split()[-1]
elif tmp_line[:
27] == "# incompatible hint groups:":
incompatible_hint_groups = tmp_line.strip(
).split()[-1]
if evidence_stats_file:
ev_fd.write("%s\t%s\t%s\t" %
(gene, transcript_id,
supported_fraction))
ev_fd.write(
"%s\t%s\t%s\t%s\t%s\t%i\n" %
(cds_support, introns_support,
five_utr_support,
three_introns_support,
incompatible_hint_groups,
protein_len))
if supported_by_hints_file and (
float(supported_fraction) > 0):
sup_fd.write("%s\t%s\t%s\t" %
(gene, transcript_id,
supported_fraction))
sup_fd.write(
"%s\t%s\t%s\t%s\t%s\t%i\n" %
(cds_support, introns_support,
five_utr_support,
three_introns_support,
incompatible_hint_groups,
protein_len))
break
if evidence_stats_file:
ev_fd.close()
self.extract_longest_isoforms(evidence_stats_file,
"%s.longest_pep" % evidence_stats_file,
minimum_supported_fraction=0)
SequenceRoutines.extract_sequence_by_ids(
protein_output, "%s.longest_pep.ids" % evidence_stats_file,
"%s.longest_pep.pep" % evidence_stats_file)
if supported_by_hints_file:
supported_by_hints_longest_pep_evidence = "%s.longest_pep" % supported_by_hints_file
supported_by_hints_longest_pep = "%s.longest_pep.pep" % supported_by_hints_file
supported_by_hints_longest_pep_ids = "%s.longest_pep.ids" % supported_by_hints_file
self.extract_longest_isoforms(
evidence_stats_file,
supported_by_hints_longest_pep_evidence,
minimum_supported_fraction=0.00001)
SequenceRoutines.extract_sequence_by_ids(
protein_output, supported_by_hints_longest_pep_ids,
supported_by_hints_longest_pep)
evidence_files = (evidence_stats_file,
"%s.longest_pep" % evidence_stats_file,
"%s.longest_pep" % supported_by_hints_file) if supported_by_hints_file else \
(evidence_stats_file,)
for evidence_file in evidence_files:
print("Drawing transcript support distribution for %s" %
evidence_file)
MatplotlibRoutines.percent_histogram_from_file(
evidence_file,
evidence_file,
column_list=(2, ),
separator=None,
comments="#",
n_bins=20,
title="Transcript support by hints",
xlabel="%%",
ylabel="Number",
extensions=["svg", "png"],
legend_location="upper center",
stats_as_legend=True)
parser = argparse.ArgumentParser()
parser.add_argument("-i",
"--input",
action="store",
dest="input",
required=True,
help="Input fasta with raw cDS")
parser.add_argument(
"-s",
"--stop_codons",
action="store",
dest="stop_codons_list",
default=["TGA", "TAA", "TAG"],
type=lambda s: s.split(","),
help=
"Comma-separated list of stop codons. Can be set using any case and both RNA and DNA alphabet."
"Default: TGA, TAA, TAG")
parser.add_argument("-o",
"--output",
action="store",
dest="output",
required=True,
help="Output file to write trimmed CDS")
args = parser.parse_args()
print("Using %s as stop codons" % ",".join(args.stop_codons_list))
SequenceRoutines.trim_cds_and_remove_terminal_stop_codons(
args.input, args.output, args.stop_codons_list)
import argparse
from RouToolPa.Routines import SequenceRoutines
parser = argparse.ArgumentParser()
parser.add_argument("-r",
"--reference",
action="store",
dest="reference",
required=True,
help="File with reference genome")
parser.add_argument("-s",
"--samtools_directory",
action="store",
dest="samtools_dir",
default="",
help="Directory with samtools binaries")
parser.add_argument("-p",
"--picard_directory",
action="store",
dest="picard_dir",
default="",
help="Directory with PICARD jar")
args = parser.parse_args()
SequenceRoutines.prepare_reference_for_GATK(args.reference,
picard_dir=args.picard_dir,
samtools_dir=args.samtools_dir)
syn_dict = SynDict()
syn_dict.read(pep_uniq_description_no_isoform_versions,
header=False,
separator="\t",
allow_repeats_of_key=True,
split_values=True,
values_separator=",",
key_index=1,
value_index=0,
comments_prefix="#")
syn_dict.write(pep_description_collapsed_isoforms,
splited_values=True,
values_separator=",")
length_dict = SequenceRoutines.get_lengths_from_seq_file(args.input,
format="fasta",
out_file=len_file)
descr_with_len_fd = open(pep_description_collapsed_isoforms_with_len, "w")
descr_longest_isoform_fd = open(pep_description_longest_isoform, "w")
descr_longest_isoform_ids_fd = open(pep_description_longest_isoform_ids, "w")
for gene in syn_dict:
len_list = []
longest_isoform = None
max_len = 0
for isoform_id in syn_dict[gene]:
length = length_dict[isoform_id]
len_list.append(length)
if length > max_len:
max_len = length
in_fd = open(args.in_file, "r")
max_length_list = []
number_poly_list = []
number_of_UTRs = 0
with open(args.out_file, "w") as out_fd:
out_fd.write(
"#main_id\tUTR_length\tmax_homopolymer_length\tnumber_homopolymers\tCoordinates_list\tOther_ids\n"
)
for line in in_fd:
name_line = line.strip()
sequence = in_fd.readline().strip()
number_of_UTRs += 1
coords_list, length_list = SequenceRoutines.find_homopolymers(
sequence,
args.nucleotide,
min_size=args.min_size,
search_type=args.search_type,
max_single_insert_size=args.max_single_insert_size,
max_total_insert_length=args.max_total_insert_length,
max_number_of_insertions=args.max_number_of_insertions)
if not coords_list:
continue
id_list = name_line.split("|")[1].split(",")
max_length = max(length_list)
number_of_homopolymers = len(length_list)
max_length_list.append(max_length)
number_poly_list.append(number_of_homopolymers)
coords_str_list = map(lambda x: "(%i,%i)" % (x[0], x[1]), coords_list)
out_fd.write(
"%s\t%i\t%i\t%i\t%s\t%s\n" %
(id_list[0], len(sequence), max_length, number_of_homopolymers,
",".join(coords_str_list), ",".join(id_list)))
import argparse
from RouToolPa.Routines import SequenceRoutines
parser = argparse.ArgumentParser()
parser.add_argument("-i",
"--input",
action="store",
dest="input",
required=True,
help="Input genbank file")
parser.add_argument("-o",
"--output",
action="store",
dest="output",
required=True,
help="Output file with species_counts")
parser.add_argument("-f",
"--format",
action="store",
dest="format",
default="genbank",
help="Format of input file. Default - genbank ")
args = parser.parse_args()
SequenceRoutines.get_id_to_species_accordance_from_file(args.input,
format=args.format,
output=args.output)
dest="prefix",
help="Prefix of output files")
parser.add_argument("-o",
"--output_directory",
action="store",
dest="output_dir",
help="Directory to write output files")
parser.add_argument("-n",
"--num_of_records_per_file",
action="store",
dest="num_of_records_per_file",
type=int,
help="Number of sequences per output file")
parser.add_argument("-f",
"--num_of_out_files",
action="store",
dest="num_of_out_files",
type=int,
help="Number of output files")
args = parser.parse_args()
if args.num_of_records_per_file and args.num_of_out_files:
raise ValueError("Options -n and -f can't be set simultaneously")
SequenceRoutines.split_fasta(args.input,
args.output_dir,
num_of_recs_per_file=args.num_of_records_per_file,
num_of_files=args.num_of_out_files,
output_prefix=args.prefix)
"--black_list",
action="store",
dest="black_list",
help="File with record ids from black list")
parser.add_argument("-w",
"--white_list",
action="store",
dest="white_list",
help="File with record ids from white list")
parser.add_argument("-m",
"--masking",
action="store",
dest="masking",
help="0-based BED file with regions to mask")
parser.add_argument("-t",
"--trimming",
action="store",
dest="trimming",
help="0-based BED file with regions to trim")
args = parser.parse_args()
SequenceRoutines.correct_sequences_from_file(
args.input,
args.output,
black_list_file=args.black_list,
white_list_file=args.white_list,
regions_to_trim_file=args.trimming,
regions_to_mask_file=args.masking,
parsing_mode="parse",
format=args.format)
"-i",
"--input",
action="store",
dest="input",
required=True,
type=lambda s: FileRoutines.make_list_of_path_to_files(s.split(",")),
help=
"Comma-separated list of genbank files/directories with transcript annotations"
)
parser.add_argument("-o",
"--output",
action="store",
dest="output",
required=True,
help="Output file")
parser.add_argument("-d",
"--id_file",
action="store",
dest="id_file",
help="File with id of transcripts to deal with")
args = parser.parse_args()
if args.id_file:
id_list = IdList()
id_list.read(args.id_file)
else:
id_list = None
SequenceRoutines.extract_introns_from_transcripts_from_genbank_files(
args.input, args.output, transcript_id_white_list=id_list)
import argparse
from RouToolPa.Routines import SequenceRoutines
parser = argparse.ArgumentParser()
parser.add_argument("-i",
"--input",
action="store",
dest="input",
required=True,
help="Input genbank file")
parser.add_argument("-o",
"--output",
action="store",
dest="output",
required=True,
help="Output file with species counts")
parser.add_argument("-f",
"--format",
action="store",
dest="format",
default="genbank",
help="Format of input file. Default - genbank ")
args = parser.parse_args()
SequenceRoutines.count_species_from_file(args.input,
format=args.format,
output_filename="count_species.count")
from RouToolPa.Routines import SequenceRoutines
parser = argparse.ArgumentParser()
parser.add_argument("-i", "--input_file_list", action="store", dest="input", required=True,
type=lambda s: make_list_of_path_to_files(s.split(",")),
help="Comma-separated list of input files/directories with sequences")
parser.add_argument("-o", "--output_file", action="store", dest="output", default="stdout",
help="Output file with renamed 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("-s", "--syn_file", action="store", dest="syn_file", required=True,
help="File to write correspondences between new and old ids")
parser.add_argument("-n", "--numerical_part_of_id_length", action="store", dest="numerical_part_of_id_length",
default=8, type=int,
help="Length of numerical part of id. Default: 8")
parser.add_argument("-d", "--id_prefix", action="store", dest="id_prefix", required=True,
help="Prefix of new sequence ids")
parser.add_argument("-l", "--clear_description", action="store_true", dest="clear_description", default=False,
help="Clear description. Default - False")
args = parser.parse_args()
SequenceRoutines.rename_records_by_sequential_ids_from_files(args.input, args.output, args.syn_file, format=args.format,
clear_description=args.clear_description,
record_id_prefix=args.id_prefix,
length_of_numerical_part=args.numerical_part_of_id_length,
parse_mode="parse", index_file="temp.idx")
import argparse
from RouToolPa.Routines import SequenceRoutines
parser = argparse.ArgumentParser()
parser.add_argument("-a",
"--seq_file_a",
action="store",
dest="seq_file_a",
required=True,
help="Sequence file A")
parser.add_argument("-b",
"--seq_file_b",
action="store",
dest="seq_file_b",
required=True,
help="Sequence file B")
parser.add_argument("-o",
"--output_prefix",
action="store",
dest="output_prefix",
required=True,
help="Prefix of output files")
args = parser.parse_args()
SequenceRoutines.compare_sequences_by_length_from_file(args.seq_file_a,
args.seq_file_b,
args.output_prefix)
#!/usr/bin/env python
__author__ = 'Sergei F. Kliver'
import argparse
from RouToolPa.Routines import SequenceRoutines
parser = argparse.ArgumentParser()
parser.add_argument("-i", "--input_file", action="store", dest="input", required=True,
help="Input file with protein sequences")
parser.add_argument("-o", "--output_file_prefix", action="store", dest="output_prefix", required=True,
help="Prefix of output files")
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("-s", "--stop_codons", action="store", dest="stop_codons",
default=("*", "."),
type=lambda s: set(s.split(",")),
help="Comma-separated list of stop codon symbols. Default - '.', '*'")
args = parser.parse_args()
SequenceRoutines.check_proteins_for_stop_codons_from_file(args.input, args.output_prefix,
stop_codon_symbol_set=args.stop_codons,
format=args.format)
parser.add_argument("-i", "--input", action="store", dest="input", required=True,
type=lambda s: FileRoutines.make_list_of_path_to_files(s.split(",")),
help="Comma-separated list of files/directories with sequences")
parser.add_argument("-o", "--output_bed_file", action="store", dest="output", required=True,
help="Output bed file")
parser.add_argument("-f", "--format", action="store", dest="format", default="fasta",
help="Format of input files. Allowed formats genbank, fasta(default)")
parser.add_argument("-w", "--white_list_ids", action="store", dest="white_list_ids",
help="File with ids of regions from white list")
parser.add_argument("-b", "--black_list_ids", action="store", dest="black_list_ids",
help="File with ids of regions from black list")
parser.add_argument("-e", "--bed_format", action="store", dest="bed_format", default="0-based",
help="Format of output bed format. Allowed: 0-based(default), 1-based")
parser.add_argument("-m", "--min_len", action="store", dest="min_len",
help="Minimum length of sequence to count. Default: not set")
parser.add_argument("-x", "--max_len", action="store", dest="max_len",
help="Maximum length of sequence to count. Default: not set")
parser.add_argument("-p", "--parsing_mode", action="store", dest="parsing_mode", default="index_db",
help="Parsing mode for input sequence file. "
"Possible variants: 'index_db'(default), 'index', 'parse'")
args = parser.parse_args()
SequenceRoutines.make_region_bed_file_from_file(args.input, args.output, white_id_file=args.white_list_ids,
black_id_file=args.black_list_ids,
output_format=args.bed_format, input_format=args.format,
min_len=args.min_len, max_len=args.max_len,
parsing_mode=args.parsing_mode,
index_file="tmp.idx", retain_index=False)
"-e",
"--end_column_id",
action="store",
dest="end_column_id",
type=int,
default=2,
help="0-based index of column with feature end. Default: 2")
parser.add_argument(
"-n",
"--coordinates_type",
action="store",
dest="coordinates_type",
default="1-based",
help="Type of coordinates. Allowed: 0-based, 1-based(default)")
args = parser.parse_args()
SequenceRoutines.split_sequence_by_regions_from_file(
args.input,
args.regions,
args.output_prefix,
retain_description=False,
min_length=args.min_length,
parsing_mode="parse",
scaffold_column_index=args.scaffold_column_id,
start_column_index=args.start_column_id,
end_column_index=args.end_column_id,
coordinates_type=args.coordinates_type,
input_separator="\t",
sequence_format="fasta")
try:
os.mkdir(args.output_directory)
except OSError:
pass
split_index = 1
records_written = 0
record_ids_list = list(sequence_dict.keys())
number_of_records = len(record_ids_list)
while (records_written + args.number_of_sequences) <= number_of_records:
SeqIO.write(SequenceRoutines.record_by_id_generator(
sequence_dict,
record_ids_list[records_written:records_written +
args.number_of_sequences],
verbose=True),
"%s/%s_%i.fasta" %
(args.splited_directory, args.output_prefix, split_index),
format="fasta")
split_index += 1
records_written += args.number_of_sequences
if records_written != number_of_records:
SeqIO.write(SequenceRoutines.record_by_id_generator(
sequence_dict, record_ids_list[records_written:], verbose=True),
"%s/%s_%i.fasta" %
(args.splited_directory, args.output_prefix, split_index),
format="fasta")
"--parsing_mode",
action="store",
dest="parsing_mode",
default="parse",
help="Parsing mode of sequence files. Allowed: parse, index, index_db."
"Default: parse")
parser.add_argument(
"-g",
"--genetic_code_table",
action="store",
dest="genetic_code_table",
default=1,
type=int,
help="Genetic code to use for translation of transcript. "
"Allowed: table number from http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi"
"Default: 1(The standard code)")
args = parser.parse_args()
SequenceRoutines.find_cds_coordinates_in_transcript_by_pep_from_file(
args.transcript_file,
args.pep_file,
args.correspondence_file,
args.output_prefix,
parsing_mode=args.parsing_mode,
verbose=args.verbose,
format=args.format,
transcript_index_file=None,
protein_index_file=None,
genetic_code_table=args.genetic_code_table)
default="selenocystein_proteins",
help="Prefix of output files")
parser.add_argument(
"-f",
"--format",
action="store",
dest="format",
default="fasta",
help=
"Format of input and output files. Allowed formats genbank, fasta(default)"
)
args = parser.parse_args()
SequenceRoutines.check_selenocystein_presence_from_file(args.input,
args.output_prefix,
format="fasta")
"""
tmp_index_file = "temp.idx"
print("Parsing %s..." % args.input_file)
sequence_dict = SeqIO.index_db(tmp_index_file, args.input_file, format=args.format)
selenocystein_ids = []
with open(args.out_prefix + ".ids", "w") as out_fd:
for record_id in sequence_dict:
if "U" in sequence_dict[record_id].seq:
selenocystein_ids.append(record_id)
out_fd.write(record_id + "\n")
SeqIO.write(SequenceRoutines.record_by_id_generator(sequence_dict,
selenocystein_ids), "%s_seq.fasta" % args.out_prefix, args.format)
os.remove(tmp_index_file)
"-w",
"-transcript_with_no_pep_idfile",
action="store",
dest="transcript_with_no_pep_idfile",
help=
"File to write ids of transcripts with no protein hit. Default: not set")
parser.add_argument(
"-s",
"-transcript_with_several_pep_idfile",
action="store",
dest="transcript_with_several_pep_idfile",
help=
"File to write ids of transcripts with several protein. Default: not set")
args = parser.parse_args()
SequenceRoutines.get_transcript_to_pep_accordance_from_files(
args.transcript_file,
args.pep_file,
args.out,
verbose=args.verbose,
parsing_mode=args.parsing_mode,
genetic_code_table=args.genetic_code_table,
include_id_check=args.id_check,
transcript_with_no_pep_idfile=args.transcript_with_no_pep_idfile,
transcript_with_several_proteins_idfile=args.
transcript_with_several_pep_idfile)
if args.parsing_mode == "index_db":
os.remove("transcript_tmp.idx")
os.remove("pep_tmp.idx")
import argparse
from RouToolPa.Routines import SequenceRoutines
parser = argparse.ArgumentParser()
parser.add_argument("-i",
"--input_file",
action="store",
dest="input",
required=True,
help="Comma separated list of genbank files/directories")
parser.add_argument("-o",
"--output_file_prefix",
action="store",
dest="output_prefix",
required=True,
help="Prefix of output files")
parser.add_argument(
"-f",
"--format",
action="store",
dest="format",
default="genbank",
help=
"Format of input and output file. Allowed formats genbank(default), fasta")
args = parser.parse_args()
SequenceRoutines.get_random_species_genomes_from_genbank_file(
args.input, args.output_prefix, output_type=args.format)
parser.add_argument("-i",
"--input",
action="store",
dest="input",
help="Genbank file with annotations")
parser.add_argument(
"--fast_parsing",
action="store_true",
dest="fast_parsing",
help="Fast parsing mode - high memory consumption. Default: false")
parser.add_argument("-o",
"--output_prefix",
action="store",
dest="output_prefix",
default="output",
help="Prefix of output files")
args = parser.parse_args()
record_dict = SeqIO.to_dict(SeqIO.parse(
args.input, format="genbank")) if args.fast_parsing else SeqIO.index_db(
"temp_index.idx", [args.input], format="genbank")
SequenceRoutines.get_protein_marking_by_exons_from_genbank(
record_dict,
args.output_prefix,
protein_id_field_in_cds_feature="protein_id")
#os.remove("temp_index.idx")
parser.add_argument("-o",
"--output_file_prefix",
action="store",
dest="output_prefix",
required=True,
help="Prefix of output files")
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("-p",
"--print_stats",
action="store_true",
dest="print_stats",
help="Print stats. Default: False")
args = parser.parse_args()
SequenceRoutines.count_softmasked_nucleotides_from_file(
args.input,
args.output_prefix,
verbose=args.print_stats,
parsing_mode="parse",
format=args.format,
index_file=None)
args = parser.parse_args()
if args.labels_list is not None:
if len(args.labels_list) != len(args.input_file_list):
raise ValueError(
"Length of labels list is not equal to number of files with assemblies"
)
assemblies_dict = OrderedDict()
for i in range(0, len(args.input_file_list)):
assembly_label = args.labels_list[i] if args.labels_list else "A%i" % (i +
1)
tmp_index = "%s.tmp.idx" % assembly_label
assemblies_dict[assembly_label] = SequenceRoutines.parse_seq_file(
args.input_file_list[i],
args.parsing_mode,
format=args.format,
index_file=tmp_index)
#SeqIO.index_db(tmp_index, args.input_file_list[i],format=args.format)
assembly_N50_dict = TwoLvlDict()
assembly_L50 = TwoLvlDict()
assembly_bins = []
assembly_contig_cumulative_length = OrderedDict()
assembly_contig_number_values = OrderedDict()
assembly_general_stats = TwoLvlDict()
assembly_length_array = OrderedDict()
assembly_lengths = TwoLvlDict()
for assembly in assemblies_dict:
lengths_array, N50_dict, L50_dict, length_dict, total_length, longest_contig, Ns_number, bins, contig_cumulative_length_values, \
contig_number_values = SequenceRoutines.calculate_assembly_stats(assemblies_dict[assembly],
default=1,
help="Maximum number of sequences per region. Default: 1")
parser.add_argument("-b",
"--scaffold_black_list_file",
action="store",
dest="scaffold_black_list_file",
type=lambda s: IdList(filename=s),
help="File with scaffolds from black list")
parser.add_argument(
"-x",
"--min_scaffold_len",
action="store",
dest="min_scaffold_len",
type=int,
default=None,
help=
"Minimum length of scaffold to be included in regions. Default: not set")
args = parser.parse_args()
SequenceRoutines.prepare_region_list_by_length(
max_length=args.max_length,
max_seq_number=args.max_seq_number,
length_dict=None,
reference=args.reference,
parsing_mode="parse",
output_dir=args.output_dir,
split_scaffolds=args.split_scaffolds,
min_scaffold_length=args.min_scaffold_len,
black_list_scaffolds=None)
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,
genetic_code_table=1,
translate_to_stop=False,
prefix_of_file_inframe_stop_codons_seqs=
prefix_of_file_inframe_stop_codons_seqs) # Universal code !!!
AUGUSTUS.extract_gene_ids_from_output(output_gff, all_annotated_genes_ids)
AUGUSTUS.extract_CDS_annotations_from_output(output_gff, CDS_gff)
help="File to write ids of extracted sequences. Default - don't write")
parser.add_argument(
"-p",
"--parsing_mode",
action="store",
dest="parsing_mode",
default='parse',
help="Parsing mode. Allowed: parse(default), index, index_db")
args = parser.parse_args()
SequenceRoutines.extract_sequences_by_length_from_file(
args.input_file,
args.output_file,
min_len=args.min_length,
max_len=args.max_length,
format=args.format,
tmp_index_file="tmp.idx",
id_file=args.id_file,
parsing_mode=args.parsing_mode)
"""
if (args.min_length is None) and (args.max_length is None):
raise ValueError("Both minimum and maximum lengths were not set")
elif (args.min_length is not None) and (args.max_length is not None) and (args.min_length > args.max_length):
raise ValueError("Minimum length is greater then maximum lengths")
tmp_index_file = "temp.idx"
print("Parsing %s..." % args.input_file)
sequence_dict = SeqIO.index_db(tmp_index_file, args.input_file, format=args.format)