def hmmer_to_markers(input, temp_dir):
global refpkg
fragments = MutableAlignment()
fragments.read_filepath(input)
reverse = dict([(name + '_rev', reverse_sequence(seq))
for (name, seq) in fragments.items()])
all_frags = MutableAlignment()
all_frags.set_alignment(fragments)
all_frags.set_alignment(reverse)
frag_file = temp_dir + "/frags.fas"
_write_fasta(all_frags, frag_file)
# Now bin the fragments
frag_scores = dict([(name, [-10000, 'NA', 'NA'])
for name in fragments.keys()])
for gene in refpkg["genes"]:
# Now run HMMER search
hmmer_output = temp_dir + '/' + gene + ".out"
hmmer_search(frag_file, refpkg[gene]["hmm"], hmmer_output)
results = read_hmmsearch_results(hmmer_output)
# Now select best direction for each frag
for name, value in results.items():
bitscore = value[1]
direction = 'forward'
true_name = name
if (name.find('_rev') != -1):
true_name = true_name.replace('_rev', '')
direction = 'reverse'
if frag_scores[true_name][0] < bitscore:
frag_scores[true_name] = [bitscore, gene, direction]
# Now bin the fragments
genes = dict([])
for name, val in frag_scores.items():
if (val[1] not in genes):
genes[val[1]] = {}
if (val[2] == 'forward'):
genes[val[1]][name] = fragments[name]
else:
genes[val[1]][name] = reverse_sequence(fragments[name])
genes.pop("NA", None)
for gene, seq in genes.items():
gene_file = temp_dir + '/' + gene + ".frags.fas.fixed"
_write_fasta(seq, gene_file)
binned_fragments = {}
for gene, seq in genes.items():
binned_fragments[gene] = {}
binned_fragments[gene]["file"] = temp_dir + '/' + gene \
+ ".frags.fas.fixed"
binned_fragments[gene]["nfrags"] = len(seq.keys())
return binned_fragments
def hmmer_to_markers(input, temp_dir):
global marker_genes
fragments = MutableAlignment()
fragments.read_filepath(input)
reverse = dict([(name+'_rev', reverse_sequence(seq))
for (name, seq) in fragments.items()])
all_frags = MutableAlignment()
all_frags.set_alignment(fragments)
all_frags.set_alignment(reverse)
frag_file = temp_dir+"/frags.fas"
_write_fasta(all_frags, frag_file)
# Now bin the fragments
frag_scores = dict([(name, [-10000, 'NA', 'NA'])
for name in fragments.keys()])
gene_set = marker_genes
align_name = 'sate'
if (options().genes == 'cogs'):
gene_set = cog_genes
align_name = 'pasta'
for gene in gene_set:
# Now run HMMER search
hmmer_search(
frag_file,
os.path.join(
options().__getattribute__('reference').path,
'refpkg/%s.refpkg/%.profile' % (gene, align_name)),
temp_dir + "/%s.out" % gene)
results = read_hmmsearch_results(temp_dir + "/%s.out" % gene)
# Now select best direction for each frag
for name, value in results.items():
bitscore = value[1]
direction = 'forward'
true_name = name
if (name.find('_rev') != -1):
true_name = true_name.replace('_rev', '')
direction = 'reverse'
if frag_scores[true_name][0] < bitscore:
frag_scores[true_name] = [bitscore, gene, direction]
# Now bin the fragments
genes = dict([])
for name, val in frag_scores.items():
if (val[1] not in genes):
genes[val[1]] = {}
if (val[2] == 'forward'):
genes[val[1]][name] = fragments[name]
else:
genes[val[1]][name] = reverse_sequence(fragments[name])
genes.pop("NA", None)
for gene, seq in genes.items():
gene_file = temp_dir + "/%s.frags.fas" % gene
_write_fasta(seq, gene_file + ".fixed")
return genes
def hmmer_to_markers(input, temp_dir):
global marker_genes
fragments = MutableAlignment()
fragments.read_filepath(input)
reverse = dict([(name + '_rev', reverse_sequence(seq))
for (name, seq) in fragments.items()])
all_frags = MutableAlignment()
all_frags.set_alignment(fragments)
all_frags.set_alignment(reverse)
frag_file = temp_dir + "/frags.fas"
_write_fasta(all_frags, frag_file)
#Now bin the fragments
frag_scores = dict([(name, [-10000, 'NA', 'NA'])
for name in fragments.keys()])
gene_set = marker_genes
align_name = 'sate'
if (options().genes == 'cogs'):
gene_set = cog_genes
align_name = 'pasta'
for gene in gene_set:
#Now run HMMER search
hmmer_search(
frag_file,
os.path.join(options().__getattribute__('reference').path,
'refpkg/%s.refpkg/%.profile' % (gene, align_name)),
temp_dir + "/%s.out" % gene)
results = read_hmmsearch_results(temp_dir + "/%s.out" % gene)
#Now select best direction for each frag
for name in results.keys():
bitscore = results[name][1]
direction = 'forward'
true_name = name
if (name.find('_rev') != -1):
true_name = true_name.replace('_rev', '')
direction = 'reverse'
if frag_scores[true_name][0] < bitscore:
frag_scores[true_name] = [bitscore, gene, direction]
#Now bin the fragments
genes = dict([])
for name in frag_scores.keys():
if (frag_scores[name][1] not in genes):
genes[frag_scores[name][1]] = {}
if (frag_scores[name][2] == 'forward'):
genes[frag_scores[name][1]][name] = fragments[name]
else:
genes[frag_scores[name][1]][name] = reverse_sequence(
fragments[name])
genes.pop("NA", None)
for gene in genes.keys():
gene_file = temp_dir + "/%s.frags.fas" % gene
_write_fasta(genes[gene], gene_file + ".fixed")
return genes
def hmmer_to_markers(input, temp_dir):
global marker_genes
fragments = MutableAlignment()
fragments.read_filepath(input)
reverse = dict([(name + "_rev", reverse_sequence(seq)) for (name, seq) in fragments.items()])
all_frags = MutableAlignment()
all_frags.set_alignment(fragments)
all_frags.set_alignment(reverse)
frag_file = temp_dir + "/frags.fas"
_write_fasta(all_frags, frag_file)
# Now bin the fragments
frag_scores = dict([(name, [-10000, "NA", "NA"]) for name in fragments.keys()])
gene_set = marker_genes
align_name = "sate"
if options().genes == "cogs":
gene_set = cog_genes
align_name = "pasta"
for gene in gene_set:
# Now run HMMER search
hmmer_search(
frag_file,
os.path.join(
options().__getattribute__("reference").path, "refpkg/%s.refpkg/%.profile" % (gene, align_name)
),
temp_dir + "/%s.out" % gene,
)
results = read_hmmsearch_results(temp_dir + "/%s.out" % gene)
# Now select best direction for each frag
for name in results.keys():
bitscore = results[name][1]
direction = "forward"
true_name = name
if name.find("_rev") != -1:
true_name = true_name.replace("_rev", "")
direction = "reverse"
if frag_scores[true_name][0] < bitscore:
frag_scores[true_name] = [bitscore, gene, direction]
# Now bin the fragments
genes = dict([])
for name in frag_scores.keys():
if frag_scores[name][1] not in genes:
genes[frag_scores[name][1]] = {}
if frag_scores[name][2] == "forward":
genes[frag_scores[name][1]][name] = fragments[name]
else:
genes[frag_scores[name][1]][name] = reverse_sequence(fragments[name])
genes.pop("NA", None)
for gene in genes.keys():
gene_file = temp_dir + "/%s.frags.fas" % gene
_write_fasta(genes[gene], gene_file + ".fixed")
return genes
def main():
args = parse_args()
sequences = MutableAlignment()
assert os.path.isfile(args.input) and os.access(args.input, os.R_OK), "Input file %s does not exist\n" % args.input
sequences.read_file_object(args.input)
frag = MutableAlignment()
full = MutableAlignment()
for (key,seq) in sequences.items():
if (len(seq) <= args.threshold):
frag[key]=seq
else:
full[key]=seq
frag.write_to_path("%s.frag.fas" % args.output)
full.write_to_path("%s.full.fas" % args.output)
def main():
args = parse_args()
sequences = MutableAlignment()
assert os.path.isfile(args.input) and os.access(
args.input, os.R_OK), "Input file %s does not exist\n" % args.input
sequences.read_file_object(args.input)
frag = MutableAlignment()
full = MutableAlignment()
for (key, seq) in sequences.items():
if (len(seq) <= args.threshold):
frag[key] = seq
else:
full[key] = seq
frag.write_to_path("%s.frag.fas" % args.output)
full.write_to_path("%s.full.fas" % args.output)
def testExtendedAlignment(self):
print "======= starting testExtendedAlignment ========="
subset = [
"SFIF", "SFII", "SCFC", "SGHD", "SDCC", "SBGE", "SFBB", "SDI",
"SCGB", "SJGF", "SGBI", "SCJA", "SGAD", "SHEB", "SFHB", "SDJI",
"SHED", "SJJJ", "SBBE", "SCCH", "SDJB", "SDAC", "SHEH", "SFDC",
"SFEI", "SHHB", "SC", "SIAB", "SDDI", "SBCB", "SJB", "SEBD",
"SFGD", "SHA", "SIDA", "SGHI", "SGIB", "SBFJ", "SFIE", "SCJF",
"SJHJ", "SJBG", "SEJI", "SFFF", "SJ", "SIII", "SJHH", "SEIH",
"SBDC", "SHDJ", "SJDD", "SGDB", "SIHA", "SIBB", "SECC", "SCAD",
"SGBB", "SGIF", "SJHC", "SFCD", "SEAA", "SEFF", "SDFG", "SDJE",
"SCFG", "SFH", "SCJ", "SDDD", "SEGD", "SCIH", "SDAG", "SCJE",
"SFAJ", "SIDJ", "SE", "SHBC", "SJFF", "SCHD", "SBHA", "SEDF",
"SFAF", "SEDD", "SDHD", "SGJD", "SIBH", "SGDF", "SIFA", "SJGA",
"SIJB", "SFI", "SGA", "SBFC", "SBJA", "SFFC", "SFDH", "SFEE",
"SBDF", "SGBJ", "SDHE", "SJIB", "SHHI", "SIDE", "SJII"
]
alg = MutableAlignment()
alg.read_filepath("data/simulated/test.fasta")
alg.delete_all_gap()
tlen = alg.get_length()
frg = MutableAlignment()
frg.read_filepath("data/simulated/test.fas")
#print frg.get_num_taxa()
pp = SeppProblem(alg.keys())
pp.fragments = frg
pp.subalignment = alg
cp1 = SeppProblem(subset, pp)
cp2 = SeppProblem(list(set(alg.keys()) - set(subset)), pp)
cp1.fragments = ReadonlySubalignment(
[k for k in frg.keys() if int(k[-1]) >= 9], frg)
cp2.fragments = ReadonlySubalignment(
[k for k in frg.keys() if int(k[-1]) <= 1], frg)
cp1labels = cp1.write_subalignment_without_allgap_columns(
"data/tmp/cp1.fasta")
cp2labels = cp2.write_subalignment_without_allgap_columns(
"data/tmp/cp2.fasta")
tmp = MutableAlignment().read_filepath("data/tmp/cp1.fasta")
assert all(
[not tmp.is_all_gap(pos) for pos in xrange(0, tmp.get_length())])
tmp = MutableAlignment().read_filepath("data/tmp/cp2.fasta")
assert all(
[not tmp.is_all_gap(pos) for pos in xrange(0, tmp.get_length())])
cp1.fragments.write_to_path("data/tmp/cp1.frags.fas")
cp2.fragments.write_to_path("data/tmp/cp2.frags.fas")
'''We have done the hmmalign before. don't worry about that right now'''
ext1 = ExtendedAlignment(cp1.fragments)
ext1.build_extended_alignment("data/tmp/cp1.fasta",
"data/tmp/cp1.extended.sto")
ext1.relabel_original_columns(cp1labels)
ext2 = ExtendedAlignment(cp2.fragments)
ext2.build_extended_alignment("data/tmp/cp2.fasta",
"data/tmp/cp2.extended.sto")
ext2.relabel_original_columns(cp2labels)
extmerger = ExtendedAlignment([])
extmerger.merge_in(ext1)
mixed = extmerger.merge_in(ext2)
extmerger.write_to_path("data/tmp/extended.merged.fasta")
assert extmerger.is_aligned(), "Merged alignment is not aligned"
in1 = len([x for x in ext1._col_labels if x < 0])
in2 = len([x for x in ext2._col_labels if x < 0])
print "Merged:%d. Insertion1:%d Insertion2:%d BaseLen:%d" % (
extmerger.get_length(), in1, in2, tlen)
assert (in1 + in2 + tlen - mixed) == extmerger.get_length(
), "Lengths don't match up after merging. Merged:%d. Insertion1:%d Insertion2:%d BaseLen:%d Mixed-insertion: %d" % (
extmerger.get_length(), in1, in2, tlen, mixed)
assert (in1 + in2 - mixed) == len(
list(extmerger.iter_insertion_columns())
), "Columns are not correctly labeled after merging. Merged insertion count:%d. Insertion1:%d Insertion2:%d Mixed-insertion: %d" % (
len(list(extmerger.iter_insertion_columns())), in1, in1, mixed)
tmp = extmerger.get_base_readonly_alignment().get_mutable_alignment()
tmp.delete_all_gap()
assert tmp.is_aligned(), "merged alignment should be aligned!"
assert tmp.get_length() == tlen, "merged alignment has wrong length"
assert all([alg[k] == s for (k, s) in tmp.items()
]), "merged alignment should match original alignment"
print "======= finished testExtendedAlignment ========="
def testExtendedAlignment(self):
print "======= starting testExtendedAlignment ========="
subset = ["SFIF","SFII","SCFC","SGHD","SDCC","SBGE","SFBB","SDI","SCGB","SJGF","SGBI","SCJA","SGAD","SHEB","SFHB","SDJI","SHED","SJJJ","SBBE","SCCH","SDJB","SDAC","SHEH","SFDC","SFEI","SHHB","SC","SIAB","SDDI","SBCB","SJB","SEBD","SFGD","SHA","SIDA","SGHI","SGIB","SBFJ","SFIE","SCJF","SJHJ","SJBG","SEJI","SFFF","SJ","SIII","SJHH","SEIH","SBDC","SHDJ","SJDD","SGDB","SIHA","SIBB","SECC","SCAD","SGBB","SGIF","SJHC","SFCD","SEAA","SEFF","SDFG","SDJE","SCFG","SFH","SCJ","SDDD","SEGD","SCIH","SDAG","SCJE","SFAJ","SIDJ","SE","SHBC","SJFF","SCHD","SBHA","SEDF","SFAF","SEDD","SDHD","SGJD","SIBH","SGDF","SIFA","SJGA","SIJB","SFI","SGA","SBFC","SBJA","SFFC","SFDH","SFEE","SBDF","SGBJ","SDHE","SJIB","SHHI","SIDE","SJII"]
alg = MutableAlignment()
alg.read_filepath("data/simulated/test.fasta")
alg.delete_all_gap()
tlen = alg.get_length()
frg = MutableAlignment()
frg.read_filepath("data/simulated/test.fas")
#print frg.get_num_taxa()
pp = SeppProblem(alg.keys())
pp.fragments = frg
pp.subalignment = alg
cp1 = SeppProblem(subset, pp)
cp2 = SeppProblem(list(set(alg.keys()) -set(subset)), pp)
cp1.fragments = ReadonlySubalignment([k for k in frg.keys() if int(k[-1]) >= 9], frg)
cp2.fragments = ReadonlySubalignment([k for k in frg.keys() if int(k[-1]) <= 1], frg)
cp1labels = cp1.write_subalignment_without_allgap_columns("data/tmp/cp1.fasta")
cp2labels = cp2.write_subalignment_without_allgap_columns("data/tmp/cp2.fasta")
tmp = MutableAlignment().read_filepath("data/tmp/cp1.fasta")
assert all([not tmp.is_all_gap(pos) for pos in xrange(0,tmp.get_length())])
tmp = MutableAlignment().read_filepath("data/tmp/cp2.fasta")
assert all([not tmp.is_all_gap(pos) for pos in xrange(0,tmp.get_length())])
cp1.fragments.write_to_path("data/tmp/cp1.frags.fas")
cp2.fragments.write_to_path("data/tmp/cp2.frags.fas")
'''We have done the hmmalign before. don't worry about that right now'''
ext1 = ExtendedAlignment(cp1.fragments)
ext1.build_extended_alignment("data/tmp/cp1.fasta", "data/tmp/cp1.extended.sto")
ext1.relabel_original_columns(cp1labels)
ext2 = ExtendedAlignment(cp2.fragments)
ext2.build_extended_alignment("data/tmp/cp2.fasta", "data/tmp/cp2.extended.sto")
ext2.relabel_original_columns(cp2labels)
extmerger = ExtendedAlignment([])
extmerger.merge_in(ext1)
mixed = extmerger.merge_in(ext2)
extmerger.write_to_path("data/tmp/extended.merged.fasta")
assert extmerger.is_aligned(), "Merged alignment is not aligned"
in1 = len([x for x in ext1._col_labels if x<0])
in2 = len([x for x in ext2._col_labels if x<0])
print "Merged:%d. Insertion1:%d Insertion2:%d BaseLen:%d" %(extmerger.get_length(),in1 , in2 , tlen)
assert ( in1 + in2 + tlen - mixed) == extmerger.get_length(), "Lengths don't match up after merging. Merged:%d. Insertion1:%d Insertion2:%d BaseLen:%d Mixed-insertion: %d" %(extmerger.get_length(),in1, in2 , tlen, mixed)
assert ( in1 + in2 - mixed) == len(list(extmerger.iter_insertion_columns())), "Columns are not correctly labeled after merging. Merged insertion count:%d. Insertion1:%d Insertion2:%d Mixed-insertion: %d" %(len(list(extmerger.iter_insertion_columns())),in1 , in1, mixed)
tmp = extmerger.get_base_readonly_alignment().get_mutable_alignment()
tmp.delete_all_gap()
assert tmp.is_aligned(), "merged alignment should be aligned!"
assert tmp.get_length() == tlen, "merged alignment has wrong length"
assert all([alg[k] == s for (k,s) in tmp.items()]), "merged alignment should match original alignment"
print "======= finished testExtendedAlignment ========="
base_alignment.get_sequence_names())
print("Orig alignment sequences: ", original_backbone.get_sequence_names())
print("Base alignment sequences: ", base_alignment.get_sequence_names())
print("num base alignment seqs: ",
len(base_alignment.get_sequence_names()))
frags = MutableAlignment()
sequence_names = []
for file in sequence_files:
seq = MutableAlignment()
done = seq.read_filepath(file)
print('query sequence names:', seq.get_sequence_names())
print("query sequence length:", seq.get_length())
done = sequence_names.extend(seq.get_sequence_names())
for name, seq in seq.items():
frags[name] = seq.upper()
problem = SeppProblem(sequence_names)
problem.set_subalignment(subbackbone)
# constructs sub-base-alignment from the full alignment, delete all gaps
mut_subalg = problem.subalignment.get_mutable_alignment()
remaining_cols = mut_subalg.delete_all_gap()
problem.annotations["ref.alignment.columns"] = remaining_cols
print("num remaining_cols: ", len(remaining_cols))
problem.fragments = frags
ap_alg = problem.read_extendend_alignment_and_relabel_columns(
base_alignment_file, aligned_files)
extendedAlignment.merge_in(ap_alg, convert_to_string=True)
for dir in dirs:
print("Working on %s\n" % dir)
aligned_files = glob.glob('%sFC_*/hmmalign.results.*' % dir)
sequence_files = glob.glob('%sFC_*/hmmalign.frag.*' % dir)
base_alignment_file = glob.glob('%s/*.fasta' % dir)
base_alignment = MutableAlignment()
done = base_alignment.read_filepath(base_alignment_file[0])
subbackbone = original_backbone.get_soft_sub_alignment(
base_alignment.get_sequence_names())
frags = MutableAlignment()
sequence_names = []
for file in sequence_files:
seq = MutableAlignment()
done = seq.read_filepath(file)
done = sequence_names.extend(seq.get_sequence_names())
for name, seq in seq.items():
frags[name] = seq.upper()
problem = SeppProblem(sequence_names)
problem.set_subalignment(subbackbone)
mut_subalg = problem.subalignment.get_mutable_alignment()
remaining_cols = mut_subalg.delete_all_gap()
problem.annotations["ref.alignment.columns"] = remaining_cols
problem.fragments = frags
ap_alg = problem.read_extendend_alignment_and_relabel_columns(
base_alignment_file, aligned_files)
extendedAlignment.merge_in(ap_alg, convert_to_string=False)
extendedAlignment.write_to_path("/projects/sate8/namphuon/ultra_large/1000000/"
"upp_100_10_new/upp.unmasked.fasta")
extendedAlignment.remove_insertion_columns()
