def test_align_larger(self):
valid = "data/YAL068C.fasta"
seq1, seq2 = parse_fasta.parse_fasta(valid).values()
actual = align(seq1, seq2, get_scoring_matrix('default'))
expected_score = 118
self.assertEquals(actual[1], expected_score, "Alignment score is not correct")
print_alignment(actual[0])
def test_tenuous(self):
valid = "data/tenuous.fasta"
seq1, seq2 = parse_fasta.parse_fasta(valid).values()
expected_align = [('C', 'C', '|'), ('C', 'D', ':'), ('C', 'E', ':'), ('C', 'C', '|'), ('D', 'C', ':'),
('E', 'C', ':'), ('C', 'C', '|')]
expected_score = 3
actual = align(seq1, seq2, get_scoring_matrix('default'))
self.assertEquals(actual[0], expected_align, "Alignment is not correct")
self.assertEquals(actual[1], expected_score, "Alignment score is not correct")
print_alignment(actual[0])
def test_align(self):
# get some valid data from a test file
valid = "data/small.fasta"
seq1, seq2 = parse_fasta.parse_fasta(valid).values()
expected_align = [('A', 'A', '|'), ('-', 'C', ' '), ('D', 'D', '|'), ('E', 'E', '|')]
expected_score = 1
actual = align(seq1, seq2, get_scoring_matrix('default'))
self.assertEquals(actual[0], expected_align, "Alignment is not correct")
self.assertEquals(actual[1], expected_score, "Alignment score is not correct")
print_alignment(actual[0])
def transform_sequence_input(full_input, transform_function):
output = []
# check whether the input is fasta-formatted or just sequence
# full_input is a list of lines, so convert it to string or this won't work
if str(full_input).count('>')>0: fasta = True
else: fasta = False
if debug: print '\n\t### INPUT:\n%s\t### END_INPUT\n'%full_input
if fasta:
for (header,seq) in parse_fasta.parse_fasta(full_input):
output.append((header,transform_function(seq)))
else:
for line in full_input:
output.append(transform_function(line))
if debug: print '\n\t######### FINAL OUTPUT: #########'%output
return output
for k, v in siteDict.items():
if len(set(v)) == 1:
continue
else:
var.append(k + 1)
return var
if __name__ == "__main__":
if len(sys.argv[1:]) == 0:
sys.argv.append("-h")
parser = argparse.ArgumentParser()
parser.add_argument("alignment", help="FASTA-formatted alignment \
to extract variable sites")
args = parser.parse_args()
seqs = dict([x for x in parse_fasta(args.alignment)])
sites = get_site_dict(seqs)
# print(sites)
variable = get_variable(sites)
print(variable)
for k, v in seqs.items():
print(">" + k)
outSeq = ""
for i, j in enumerate(v):
if i in variable:
outSeq += j
print(outSeq)
if __name__ == "__main__":
if len(sys.argv[1:]) == 0:
sys.argv.append("-h")
parser = argparse.ArgumentParser()
parser.add_argument("sequence", help="Alignment in FASTA format")
parser.add_argument("flag1", help="Flag to recognise sequences \
in group 1. Must be first substring of name.")
parser.add_argument("flag2", help="Flag to recognise sequences \
in group 2. Must be first substring of name.")
parser.add_argument("-d", "--distance", help="distance \
metric to use [euc (default)/jsd]",
default="euc")
args = parser.parse_args()
seqs1 = dict([x for x in parse_fasta(args.sequence)
if x[0].startswith(args.flag1)])
seqs2 = dict([x for x in parse_fasta(args.sequence)
if x[0].startswith(args.flag2)])
cols1 = get_columns(seqs1)
cols2 = get_columns(seqs2)
colProps1 = calc_col_prop(cols1)
# print(colProp1)
colProps2 = calc_col_prop(cols2)
# print(colProp2)
if args.distance == "euc":
dist = calc_euclidean(colProps1, colProps2)
elif args.distance == "jsd":
dist = calc_jsd_scipy(colProps1, colProps2)
else:
print("distance argument not recognised")
import numpy as np
import minineedle # https://github.com/scastlara/minineedle
import miniseq # https://github.com/scastlara/miniseq
if __name__ == '__main__':
with open('sets.json', 'r') as f:
sets = json.load(f)
sequences = dict()
for dp, dn, filenames in os.walk('.'):
for f in filenames:
if f == 'sequence.fa':
data = parse_fasta(os.path.join(dp, f))
name = os.path.basename(dp)
sequences[name] = data['sequences'][0]
set_a = sets['training_set']
set_b = sets['benchmark_set_membrane']
homologies = np.empty((len(set_a), len(set_b)), dtype=np.float)
for idx_a, a in enumerate(set_a):
for idx_b, b in enumerate(set_b):
seq_a = miniseq.Protein(a, sequences[a])
seq_b = miniseq.Protein(b, sequences[b])
alignment = minineedle.Needleman(seq_a, seq_b)
alignment.align()
seq_a, seq_b = alignment.alseq1, alignment.alseq2
n = float(len(seq_a))
identity = sum(i == j for i, j in zip(seq_a, seq_b)) / n
import sys
import argparse
from parse_fasta import parse_fasta
if __name__ == "__main__":
if len(sys.argv[1:]) == 0:
sys.argv.append("-h")
ap = argparse.ArgumentParser()
ap.add_argument("-a", "--alignment", help="Empirical alignment, \
in FASTA format.")
ap.add_argument("-s", "--simulated", help="Simulated alignment, \
in FASTA format.")
args = ap.parse_args()
emp_dict = dict([x for x in parse_fasta(args.alignment)])
sim_dict = dict([x for x in parse_fasta(args.simulated)])
for k, v in sim_dict.items():
for n, _ in enumerate(v):
try:
if emp_dict[k][n] == "-":
sim_dict[k] = sim_dict[k][:n]+"-"+sim_dict[k][n+1:]
except KeyError:
sys.stderr.write(k + " not in simulated data, skipping")
for k, v in sim_dict.items():
print(">"+k)
print(v)
def analyze(seq1_filename: str, seq2_filename: str, nucleotides: bool = False):
"""
Performs an alignment-based analysis on the sequences in the provided FASTA files.
`nucleotides` should be `True` if the two filenames refer to nucleotide sequences.
"""
# Read first sequence
seq_name, seq1 = list(parse_fasta(get_data(seq1_filename)))[0]
# Analyze second sequence
print("Analyzing %s..." % seq2_filename)
seq2 = list(parse_fasta(get_data(seq2_filename)))[0][1]
alignment_result = align_sequences(seq2, seq1, nucleotides=nucleotides)
largest_mismatch_pos, largest_mismatch = alignment_result.largest_mismatch(
)
percent_similarity = 1 - (alignment_result.hamming_distance() /
alignment_result.get_alignment_length())
if nucleotides:
trimmed_alignment_1, trimmed_alignment_2 = trim_for_dnds(
alignment_result)
dnds_ratio_data = [
sliding_window_dnds(trimmed_alignment_1,
trimmed_alignment_2,
window_size=i) for i in DNDS_WINDOW_SIZES
]
make_dnds_graph(f"{seq2_filename}_dnds_ratios.png", DNDS_WINDOW_SIZES,
dnds_ratio_data)
for clusters in CLUSTER_COUNTS:
clustered_mismatches = alignment_result.clustered_mismatches(
cluster_count=clusters)
clustered_mismatch_variance = alignment_result.clustered_mismatch_variance(
cluster_count=clusters)
# Output Supplementary Data 4
make_output_dir()
with open(get_output(f"{seq2_filename}_{clusters}.aln.txt"),
"w+") as f:
f.write(alignment_result.format_result(line_length=100))
with open(get_output(f"{seq2_filename}_{clusters}.meta.txt"),
"w+") as f:
f.write(
"Formatted metadata -- not for programmatic use.\n\n" +
f"Information for alignment with {seq_name}:\n\n" +
f"Percent similarity: {percent_similarity}\n" +
f"Largest mismatch location: {largest_mismatch_pos}\n" +
f"Largest mismatch size: {largest_mismatch}bp\n" +
f"Variance between clusters ({clusters} clusters): {clustered_mismatch_variance}\n"
+ f"Clustered mismatches: {clustered_mismatches}\n")
with open(get_output(f"{seq2_filename}_{clusters}.meta.json"),
"w+") as f:
json_output = {
"percent_similarity": percent_similarity,
"largest_mismatch_pos": largest_mismatch_pos,
"largest_mismatch": largest_mismatch,
"clustered_mismatch_variance": clustered_mismatch_variance,
"clustered_mismatches": clustered_mismatches,
}
json.dump(
json_output,
f,
)
make_cluster_graphs(seq2_filename, alignment_result)
if __name__ == "__main__":
if len(sys.argv[1:]) == 0:
sys.argv.append("-h")
parser = argparse.ArgumentParser()
parser.add_argument("alignments",
help="alignments for each group, \
columns matching",
nargs="+")
args = parser.parse_args()
# print(len(args.alignments))
alns = {}
for a in args.alignments:
alns[args.alignments.index(a)] = dict([x for x in parse_fasta(a)])
lens = []
for v in alns.values():
lens.append(len(v))
if len(set(lens)) > 1:
print("alignments are not of the same length!")
sys.exit()
# print(alns)
alnsCols = {}
for k, v in alns.items():
alnsCols[k] = get_columns(v)
# print(alnsCols)
colsProps = {}
for k, v in alnsCols.items():
if len(sys.argv[1:]) == 0:
sys.argv.append("-h")
parser = argparse.ArgumentParser()
parser.add_argument("aln1", help="first group alignment")
parser.add_argument("aln2",
help="second group alignment, \
columns matching")
parser.add_argument("-d",
"--distance",
help="distance \
metric to use [euc (default)/jsd]",
default="euc")
args = parser.parse_args()
seqs1 = dict([x for x in parse_fasta(args.aln1)])
seqs2 = dict([x for x in parse_fasta(args.aln2)])
cols1 = get_columns(seqs1)
cols2 = get_columns(seqs2)
colProps1 = calc_col_prop(cols1)
# print(colProps1) # debug
colProps2 = calc_col_prop(cols2)
# print(colProps2) # debug
if args.distance == "euc":
dist = calc_euclidean(colProps1, colProps2)
elif args.distance == "jsd":
dist = calc_jsd_scipy(colProps1, colProps2)
else:
print("distance argument not recognised")
sys.exit()
print("pos,dist")
if __name__ == "__main__":
# Parse arguments
parser = argparse.ArgumentParser(
description=
"Run a Monte-Carlo simulation for CsTSI and CsGSI alignment.")
parser.add_argument("--id", dest="simulation_id", type=int)
parser.add_argument("--trials", dest="n_trials", type=int)
args = parser.parse_args()
simulation_id = args.simulation_id
n_trials = args.n_trials
# Read CsTSI sequence
cstsi_seq = list(parse_fasta(get_data(CSTSI_PROTEIN)))[0][1]
# Analyze CsGSI sequence
print("Analyzing %s..." % CSGSI_PROTEIN)
csgsi_seq = list(parse_fasta(get_data(CSGSI_PROTEIN)))[0][1]
alignment_result = align_sequences(csgsi_seq, cstsi_seq, nucleotides=False)
for clusters in CLUSTER_COUNTS:
print(
f"Variance between clusters ({clusters} clusters): {str(alignment_result.clustered_mismatch_variance(cluster_count=clusters))}"
)
# Simulate random sequences
simulation_result = monte_carlo(
get_clustering_simulation_fn(cstsi_seq, csgsi_seq),
#! /usr/bin/python3
import os
import sys
from parse_fasta import parse_fasta
# extracts alignment columns given in args.
if __name__ == "__main__":
if len(sys.argv) < 3:
print("Usage: python " + sys.argv[0] + " aln col1 col2 col3 ...")
sys.exit(0)
seqDict = dict([x for x in parse_fasta(sys.argv[1])])
collist = [int(i) - 1 for i in sys.argv[2:]]
# print collist
for k in seqDict.keys():
print(">" + k)
print("".join([seqDict[k][i] for i in collist]))
def main():
parser = argparse.ArgumentParser(description='CBioVikings Global Sequence Alignment Example')
parser.add_argument('-f', '--fasta',
required=True,
dest='fasta',
help='Fasta file to read sequences from')
parser.add_argument('-m', '--scoring_matrix',
dest='scoring_matrix',
help='Similarity matrix to use for scoring. Default=identity')
parser.add_argument('--debug',
action='store_true',
help='Print debug output')
parser.add_argument('-v', '--verbose',
action='store_true',
dest='verbose',
help='Print verbose output')
args = parser.parse_args()
if args.verbose:
sys.stderr.write("# CBioVikings Global Sequence Alignment\n")
sys.stderr.write("# fasta file: " + str(args.fasta) + "\n")
sys.stderr.write("# scoring matrix: " + str(args.scoring_matrix) + "\n")
if args.debug:
sys.stderr.write("# debug is on\n")
sequences = None
scoring_matrix = None
seq1 = None
seq2 = None
# read sequences from the fasta file provided
if args.fasta:
try:
# sequences is a dictionary of the fasta entries
sequences = parse_fasta.parse_fasta(args.fasta)
except Exceptions.EmptyFasta:
report_error("There are no sequences in the fasta file " + args.fasta)
# our algorithm will only align two sequences
if len(sequences.keys()) != 2:
report_error("Fasta file does not contain 2 sequences")
else:
seq1, seq2 = sequences.values()
# get the similarity scoring matrix to use
if args.scoring_matrix:
try:
scoring_matrix = global_align.get_scoring_matrix(args.matrix)
except Exceptions.MissingMatrixType:
report_error("That matrix type is not available")
else:
try:
scoring_matrix = global_align.get_scoring_matrix('default')
except Exceptions.MissingMatrixType:
report_error("Default matrix is not available")
# now actually do the alignment
if sequences and scoring_matrix:
try:
alignment, score = global_align.align(seq1, seq2, scoring_matrix)
except:
raise
print("Alignment Score is: "+str(score))
# print the alignment
if alignment:
global_align.print_alignment(alignment)
the gap reconstruction as fixed, i.e. preferring the \
gap state if PP >= 0.5")
args = parser.parse_args()
fastmlDir = args.fastml_dir
if fastmlDir[-1] != "/":
fastmlDir += "/"
nodeFile = args.nodefile
nodes = read_node_file(nodeFile)
probFile = fastmlDir + "prob.marginal.csv"
gapFile = fastmlDir + "Ancestral_MaxMarginalProb_Char_Indel.txt"
indelProb = fastmlDir + "IndelsMarginalProb.txt"
seqFile = fastmlDir + "seq.marginal_IndelAndChars.txt"
if args.gapmode is None:
gapMode = "prob"
else:
gapMode = args.gapmode
seqs = dict([x for x in parse_fasta(seqFile)])
for k, v in nodes.items():
mapSeq = seqs[k]
altAllDict = main(probFile, gapFile, indelProb, k, gapMode)
altAllSeq = [x for x in altAllDict.values()][0]
with open(v + ".pep.fa", "w") as outf:
outf.write(">" + v + "_MAP\n")
outf.write(mapSeq + "\n")
outf.write(">" + v + "_AltAll\n")
outf.write(altAllSeq + "\n")
if len(sys.argv[1:]) == 0:
sys.argv.append("-h")
parser = argparse.ArgumentParser()
parser.add_argument("-s", "--sequence", help="Alignment in FASTA format")
parser.add_argument("-f1",
"--flag1",
help="Flag to recognise sequences \
in group 1. Must be first substring of name.")
parser.add_argument("-f2",
"--flag2",
help="Flag to recognise sequences \
in group 2. Must be first substring of name.")
args = parser.parse_args()
seqs1 = dict(
[x for x in parse_fasta(args.sequence) if x[0].startswith(args.flag1)])
seqs2 = dict(
[x for x in parse_fasta(args.sequence) if x[0].startswith(args.flag2)])
cols1 = get_columns(seqs1)
cols2 = get_columns(seqs2)
colProp1 = calc_col_prop(cols1)
# print(colProp1)
colProp2 = calc_col_prop(cols2)
# print(colProp2)
dist = calc_euclidean(colProp1, colProp2)
print("pos,dist")
tmp = [(a + 1, b) for a, b in zip(sorted(dist, key=dist.get, reverse=True),
sorted(dist.values(), reverse=True))]
for i in tmp:
print(str(i[0]) + "," + str(i[1]))
return siteDict
if __name__ == "__main__":
if len(sys.argv[1:]) == 0:
sys.argv.append("-h")
parser = argparse.ArgumentParser()
parser.add_argument("a1", help="master alignment, in FASTA")
parser.add_argument("a2", help="alignment to compare, in FASTA")
parser.add_argument("pa",
help="profile alignment of a1 and a2, \
in FASTA")
args = parser.parse_args()
aln1 = dict([x for x in parse_fasta(args.a1)])
aln2 = dict([x for x in parse_fasta(args.a2)])
proAln1 = dict([x for x in parse_fasta(args.pa)][:len(aln1)])
proAln2 = dict([x for x in parse_fasta(args.pa)][len(aln1):])
proAln1Sites = get_site_dict(proAln1)
proAln2Sites = get_site_dict(proAln2)
corres = []
posAln1 = 1
posAln2 = 1
for i in range(len(proAln1Sites)):
if all([x == "-" for x in proAln1Sites[i]]): # gap in aln1
corres.append((0, posAln2))
posAln2 += 1
else: # char in aln1
if all([x == "-" for x in proAln2Sites[i]]): # gap in aln2
def main():
parser = argparse.ArgumentParser(
description='CBioVikings Global Sequence Alignment Example')
parser.add_argument('-f',
'--fasta',
required=True,
dest='fasta',
help='Fasta file to read sequences from')
parser.add_argument(
'-m',
'--matrix',
dest='matrix',
help='Similarity matrix to use for scoring. Default=identity')
parser.add_argument('--debug',
action='store_true',
help='Print debug output')
parser.add_argument('-v',
'--verbose',
action='store_true',
dest='verbose',
help='Print verbose output')
args = parser.parse_args()
if args.verbose:
sys.stderr.write("# CBioVikings Global Sequence Alignment\n")
sys.stderr.write("# fasta file: " + str(args.fasta) + "\n")
sys.stderr.write("# matrix: " + str(args.matrix) + "\n")
if args.debug:
sys.stderr.write("# debug is on\n")
# read sequences from the fasta file provided
if args.fasta:
try:
# sequences is a dictionary of the fasta entries
sequences = parse_fasta.parse_fasta(args.fasta)
except:
report_error("There are no sequences in the fasta file " +
args.fasta)
# our algorithm will only align two sequences
if len(sequences.keys()) != 2:
report_error("Fasta file does not contain 2 sequences")
else:
seq1, seq2 = sequences.values()
# TODO check if we have a nucleotide or protein fasta file
# get the similarity matrix to use
if args.matrix:
try:
matrix = global_align.get_matrix(args.matrix)
except:
report_error("That matrix type is not available")
else:
try:
matrix = global_align.get_matrix('default')
except:
report_error("Default matrix is not available")
# now actually do the alignment
if sequences and matrix:
try:
alignment = global_align.align(seq1, seq2, matrix)
except:
raise # TODO nice errors
# print the alignment
if alignment:
global_align.print_alignment(alignment)
of site, node, state, and probability, in the style \
of FastML's Ancestral_MaxMarginalProb_Char_Indel.txt")
args = parser.parse_args()
if args.robust and args.probs is None:
sys.stderr.write("must specify probability file (-p) to calculate " +
"robust substitutions\n")
sys.exit()
with open(args.tree, "r") as t:
for s in t:
s = s.strip()
nwkString = s
curroot = tree_reader.read_tree_string(nwkString)
branches = get_anc_desc(curroot)
seqs = dict([x for x in parse_fasta(args.sequences)])
# print(seqs)
if args.robust:
probs = parse_probs(args.probs)
add_subs_robust(branches, seqs, probs, args.gaps)
else:
add_subs(branches, seqs, args.gaps)
print("parent\tchild\tsubs")
print(curroot.label)
for k, v in branches.items():
print(k[0] + "\t" + k[1] + "\t" + ",".join(v))
def main():
all_peptides = parse_fasta("bigger.fasta") # is a dictionary in the form of ... mass -> [(string,suffixMasses),...]
sorted_masses_peptides = sorted(all_peptides.keys())
parse_mgf("test.mgf",all_peptides,sorted_masses_peptides)
