def make_gff(fasta_file, tabular_file, gff_file, cut_method):
cut_col, score_col = {
"NN_Cmax": (2, 1),
"NN_Ymax": (5, 4),
"NN_Smax": (8, 7),
"HMM_Cmax": (16, 15),
}[cut_method]
source = "SignalP"
strand = "." #not stranded
phase = "." #not phased
tags = "Note=%s" % cut_method
tab_handle = open(tabular_file)
line = tab_handle.readline()
assert line.startswith("#ID\t"), line
gff_handle = open(gff_file, "w")
gff_handle.write("##gff-version 3\n")
for (title, seq), line in zip(fasta_iterator(fasta_file), tab_handle):
parts = line.rstrip("\n").split("\t")
seqid = parts[0]
assert title.startswith(seqid), "%s vs %s" % (seqid, title)
if len(seq) == 0:
#Is it possible to have a zero length reference in GFF3?
continue
cut = int(parts[cut_col])
if cut == 0:
assert cut_method == "HMM_Cmax", cut_method
#TODO - Why does it do this?
cut = 1
assert 1 <= cut <= len(seq), "%i for %s len %i" % (cut, seqid,
len(seq))
score = parts[score_col]
gff_handle.write("##sequence-region %s %i %i\n" \
% (seqid, 1, len(seq)))
#If the cut is at the very begining, there is no signal peptide!
if cut > 1:
#signal_peptide = SO:0000418
gff_handle.write("%s\t%s\t%s\t%i\t%i\t%s\t%s\t%s\t%s\n" \
% (seqid, source,
"signal_peptide", 1, cut-1,
score, strand, phase, tags))
#mature_protein_region = SO:0000419
gff_handle.write("%s\t%s\t%s\t%i\t%i\t%s\t%s\t%s\t%s\n" \
% (seqid, source,
"mature_protein_region", cut, len(seq),
score, strand, phase, tags))
tab_handle.close()
gff_handle.close()
def make_gff(fasta_file, tabular_file, gff_file, cut_method):
cut_col, score_col = {"NN_Cmax": (2, 1),
"NN_Ymax": (5, 4),
"NN_Smax": (8, 7),
"HMM_Cmax": (16, 15),
}[cut_method]
source = "SignalP"
strand = "." # not stranded
phase = "." # not phased
tags = "Note=%s" % cut_method
tab_handle = open(tabular_file)
line = tab_handle.readline()
assert line.startswith("#ID\t"), line
gff_handle = open(gff_file, "w")
gff_handle.write("##gff-version 3\n")
for (title, seq), line in zip(fasta_iterator(fasta_file), tab_handle):
parts = line.rstrip("\n").split("\t")
seqid = parts[0]
assert title.startswith(seqid), "%s vs %s" % (seqid, title)
if len(seq) == 0:
# Is it possible to have a zero length reference in GFF3?
continue
cut = int(parts[cut_col])
if cut == 0:
assert cut_method == "HMM_Cmax", cut_method
# TODO - Why does it do this?
cut = 1
assert 1 <= cut <= len(seq), "%i for %s len %i" % (cut, seqid, len(seq))
score = parts[score_col]
gff_handle.write("##sequence-region %s %i %i\n"
% (seqid, 1, len(seq)))
# If the cut is at the very begining, there is no signal peptide!
if cut > 1:
# signal_peptide = SO:0000418
gff_handle.write("%s\t%s\t%s\t%i\t%i\t%s\t%s\t%s\t%s\n"
% (seqid, source,
"signal_peptide", 1, cut - 1,
score, strand, phase, tags))
# mature_protein_region = SO:0000419
gff_handle.write("%s\t%s\t%s\t%i\t%i\t%s\t%s\t%s\t%s\n"
% (seqid, source,
"mature_protein_region", cut, len(seq),
score, strand, phase, tags))
tab_handle.close()
gff_handle.close()
raise ValueError("Could not determine version of %s" % exe)
# Run hmmsearch for Whisson et al. (2007)
if model == "Whisson2007":
hmm_file = os.path.join(
os.path.split(sys.argv[0])[0], "whisson_et_al_rxlr_eer_cropped.hmm"
)
if not os.path.isfile(hmm_file):
sys.exit("Missing HMM file for Whisson et al. (2007)")
if not get_hmmer_version(hmmer_search, "HMMER 2.3.2 (Oct 2003)"):
sys.exit("Missing HMMER 2.3.2 (Oct 2003) binary, %s" % hmmer_search)
hmm_hits = set()
valid_ids = set()
for title, seq in fasta_iterator(fasta_file):
name = title.split(None, 1)[0]
if name in valid_ids:
sys.exit("Duplicated identifier %r" % name)
else:
valid_ids.add(name)
if not valid_ids:
# Special case, don't need to run HMMER if there are no sequences
pass
else:
# I've left the code to handle HMMER 3 in situ, in case
# we revisit the choice to insist on HMMER 2.
hmmer3 = 3 == get_hmmer_version(hmmer_search)
# Using zero (or 5.6?) for bitscore threshold
if hmmer3:
# The HMMER3 table output is easy to parse
else:
raise ValueError("Could not determine version of %s" % exe)
# Run hmmsearch for Whisson et al. (2007)
if model == "Whisson2007":
hmm_file = os.path.join(os.path.split(sys.argv[0])[0],
"whisson_et_al_rxlr_eer_cropped.hmm")
if not os.path.isfile(hmm_file):
sys.exit("Missing HMM file for Whisson et al. (2007)")
if not get_hmmer_version(hmmer_search, "HMMER 2.3.2 (Oct 2003)"):
sys.exit("Missing HMMER 2.3.2 (Oct 2003) binary, %s" % hmmer_search)
hmm_hits = set()
valid_ids = set()
for title, seq in fasta_iterator(fasta_file):
name = title.split(None, 1)[0]
if name in valid_ids:
sys.exit("Duplicated identifier %r" % name)
else:
valid_ids.add(name)
if not valid_ids:
# Special case, don't need to run HMMER if there are no sequences
pass
else:
# I've left the code to handle HMMER 3 in situ, in case
# we revisit the choice to insist on HMMER 2.
hmmer3 = (3 == get_hmmer_version(hmmer_search))
# Using zero (or 5.6?) for bitscore threshold
if hmmer3:
# The HMMER3 table output is easy to parse
