output_swissprot_pfam_supported_transcripts_ids,
mode="combine")
HMMER3.intersect_ids_from_files(
output_swissprot_pfam_supported_transcripts_ids,
output_supported_stats_ids,
output_swissprot_pfam_or_hints_supported_transcripts_ids,
mode="combine")
HMMER3.intersect_ids_from_files(
output_swissprot_pfam_supported_transcripts_ids,
output_supported_stats_ids,
output_swissprot_pfam_and_hints_supported_transcripts_ids,
mode="common")
print("Extracting sequences...")
SequenceRoutines.extract_sequence_by_ids(
output_pep, output_swissprot_pfam_or_hints_supported_transcripts_ids,
output_swissprot_pfam_or_hints_supported_transcripts_pep)
SequenceRoutines.extract_sequence_by_ids(
output_pep, output_swissprot_pfam_and_hints_supported_transcripts_ids,
output_swissprot_pfam_and_hints_supported_transcripts_pep)
print("Extracting evidence...")
AUGUSTUS.extract_evidence_by_ids(
output_evidence_stats,
output_swissprot_pfam_or_hints_supported_transcripts_ids,
output_swissprot_pfam_or_hints_supported_transcripts_evidence)
AUGUSTUS.extract_evidence_by_ids(
output_evidence_stats,
output_swissprot_pfam_and_hints_supported_transcripts_ids,
output_swissprot_pfam_and_hints_supported_transcripts_evidence)
print("Extracting longest isoforms...")
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)
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
longest_isoform = isoform_id
descr_with_len_fd.write(
"%s\t%s\t%s\n" %
(gene, ",".join(syn_dict[gene]), ",".join(map(str, len_list))))
descr_longest_isoform_fd.write("%s\t%s\t%i\n" %
(gene, longest_isoform, max_len))
descr_longest_isoform_ids_fd.write(longest_isoform)
descr_longest_isoform_ids_fd.write("\n")
for file_descriptor in descr_with_len_fd, descr_longest_isoform_fd, descr_longest_isoform_ids_fd:
file_descriptor.close()
SequenceRoutines.extract_sequence_by_ids(args.input,
pep_description_longest_isoform_ids,
pep_description_longest_isoform_pep,
format="fasta",
verbose=True)
help=
"Allow multiple coincidence report of sequences for partial coincidence mode."
"By default an error is raised")
parser.add_argument("-s",
"--syn_file",
action="store",
dest="syn_file",
help="File with synonyms of ids to use. Default - not set")
parser.add_argument(
"-r",
"--invert_match",
action="store_true",
dest="invert_match",
help="Invert match, i. e. remove sequences. Default - not set")
args = parser.parse_args()
SequenceRoutines.extract_sequence_by_ids(
args.input,
args.id_file,
args.output,
format=args.format,
verbose=True,
id_column_number=args.id_column,
coincidence_mode=args.coincidence_mode,
allow_multiple_coincidence_report=args.allow_multiple_coincidence_report,
syn_file=args.syn_file,
parsing_mode="parse",
index_file="tmp.idx",
invert_match=args.invert_match)