def Run_Uverskey(Fasta1, Fasta2, OutFile):
amyload_seq = load_fasta_file(Fasta1)
disprot_seq = load_fasta_file(Fasta2)
net_abs_charge = Feature(get_aa2charge(default=0)).then(average_absolute)
mean_hydropathy = Feature(get_aa2hydropathy(default=0)).then(average)
uversky_fs = FeatureSet("uversky")
uversky_fs.add(mean_hydropathy, name="mean_hydropathy")
uversky_fs.add(net_abs_charge, name="net_abs_charge")
amyload_uversky_seq = uversky_fs(amyload_seq)
disprot_uversky_seq = uversky_fs(disprot_seq)
amyload_data_x = amyload_uversky_seq.columns(feature="mean_hydropathy")[0]
amyload_data_y = amyload_uversky_seq.columns(feature="net_abs_charge")[0]
plt.plot(amyload_data_x, amyload_data_y,'.', label="Amyload")
disprot_data = compact(disprot_uversky_seq).columns()
plt.plot(disprot_data[0], disprot_data[1],'.', label="Disprot")
plt.plot([-0.78, 0.835], [0.0, 0.5],'k')
plt.xlabel("mean hydrophobicity")
plt.ylabel("net abs charge")
plt.legend()
plt.savefig(OutFile)
def get_df_from_file(fname):
""" Loads data from a file to a dataframe.
The identifiers are set as a primary
key of the dataframe.
The sequence entries are a1, a2,... and so on.
"""
# Load the file
f = load_fasta_file(fname)
# Get the identifiers and the sequences
names, dataset = [], []
for i in range(len(f)):
dataset.append(f[i].data)
names.append(f[i].identifier)
# Generate a header for the dataframe
headers = ['a' + str(i + 1) for i in range(np.shape(dataset)[1])]
# Generate dataframe
df = pd.DataFrame(dataset, columns=headers)
df['names'] = names
df = df.set_index('names')
return df
def run(Fasta1, Fasta2, windows_per_frame, overlap_factor, xlabel, ylabel,
pop1_label, pop2_label, htmlOutDir, htmlFname, Workdirpath):
if not os.path.exists(htmlOutDir):
os.makedirs(htmlOutDir)
amyload_pos_seq = load_fasta_file(Fasta1)
amyload_neg_seq = load_fasta_file(Fasta2)
# Calculate quantitive features: volume and hydropathy
mean_volume = Feature(get_aa2volume()).then(average)
mean_hydropathy = Feature(get_aa2hydropathy()).then(average)
fs = FeatureSet("volume'n'hydropathy")
fs.add(mean_volume)
fs.add(mean_hydropathy)
amyload_pos_conv_seq = fs(amyload_pos_seq)
amyload_neg_conv_seq = fs(amyload_neg_seq)
# Do local Fisher:
result = local_fisher_2d(amyload_pos_conv_seq,
amyload_neg_conv_seq,
windows_per_frame=int(windows_per_frame),
overlap_factor=int(overlap_factor))
# Plot local Fisher:
_plot_local_fisher_2d(result,
xlabel=xlabel,
ylabel=ylabel,
pop1_label=pop1_label,
pop2_label=pop2_label,
out_file_path=os.path.join(os.getcwd(), "out.png"))
# plt.savefig(os.path.join(Workdirpath, htmlOutDir, "1.png"))
HTML_Gen(os.path.join(Workdirpath, htmlOutDir, htmlFname))
def Run_ngrams(fasta1, fasta2, OutFile ):
alphasyn_seq = load_fasta_file(fasta1)
amyload_pos_seq = load_fasta_file(fasta2)
fs_aa = FeatureSet("aa patterns")
fs_aa.add(identity)
fs_aa.add(pattern_match, pattern='VT', padded=True)
fs_aa.add(pattern_count, pattern='VT')
result_seq = fs_aa(alphasyn_seq)
fs_hp = FeatureSet("hydropathy patterns")
fs_hp.add(Feature(get_aa2hydropathy()))
fs_hp.add(Feature(get_aa2hydropathy()).then(pattern_match, pattern=[0.0, 2.0],
metric='taxi', radius=1.0))
result_seq2 = fs_hp(alphasyn_seq)
result_freq = ngram_count(alphasyn_seq, n=2)
result_fit = zipf_law_fit(amyload_pos_seq, n=3, verbose=True)
counts = sorted(result_fit["ngram_counts"], reverse=True)
ranks = range(1, len(counts)+1)
slope = result_fit["slope"]
harmonic_num = sum([rank**-slope for rank in ranks])
fitted_counts = [(rank**-slope) / harmonic_num * sum(counts) for rank in ranks]
plt.plot(ranks, counts, 'k', label="empirical")
plt.plot(ranks, fitted_counts, 'k--',
label="Zipf's law\nslope: {:.2f}".format((slope)))
plt.xlabel('rank')
plt.ylabel('count')
plt.xscale('log')
plt.yscale('log')
plt.legend()
plt.savefig(OutFile)
def encoded_seq_from_file(fname, dirname, particle, index):
""" Function to encode the sequences from
a file using AAindex. The encoded sequences
are then padded to maximum length.
"""
# Load the fasta file
f = load_fasta_file(dirname + '/' + fname)
feat_map = _get_feature_map(index)
# Get the sequences in a dataset
dataset = []
for i in range(len(f)):
dataset.append(f[i])
# Create a dictionary with keys as identifiers
# and their values as the data.
enc = {}
if particle == 'virus':
for seq in dataset:
seq_id = _change_format_virus(seq.identifier)
enc[seq_id] = feat_map(seq).data
elif particle == 'mouse':
for seq in dataset:
seq_id = _change_format_mouse(seq.identifier)
if seq_id not in ids_set_mouse:
print seq.identifier, seq_id
enc[seq_id] = feat_map(seq).data
# Pad all sequences to maximum value in the
# dataset.
maxlen = max([len(val) for val in enc.values()])
enc = _pad_encoding(enc, maxlen)
# Check if all values have lengths
# equal to maxlen.
for val in enc.values():
assert len(val) == maxlen
return enc
import os
import sys
sys.path.insert(0, os.path.abspath('..'))
from quantiprot.utils.io import load_fasta_file
from quantiprot.utils.feature import Feature, FeatureSet
from quantiprot.metrics.aaindex import get_aaindex_file
from quantiprot.metrics.basic import average
# Load data:
seq = load_fasta_file("data/Alphasyn.fasta")
# Build a feature: average polarity (Graham, 1974), AAindex entry: GRAR740102:
feat = Feature(get_aaindex_file("GRAR740102")).then(average)
# Add the feature to new feature set:
fs = FeatureSet("my set")
fs.add(feat)
# Process sequences:
res_seq = fs(seq)
# Export average polarities
res = res_seq.columns()
print res
sys.path.insert(0, os.path.abspath('..'))
from quantiprot.utils.io import load_fasta_file
from quantiprot.utils.feature import Feature, FeatureSet
from quantiprot.metrics.aaindex import get_aa2hydropathy
from quantiprot.metrics.basic import identity
# Ngram-related imports
from quantiprot.metrics.ngram import pattern_match, pattern_count
from quantiprot.analysis.ngram import ngram_count
from quantiprot.analysis.ngram import zipf_law_fit
from matplotlib import pyplot as plt
# Load some data
alphasyn_seq = load_fasta_file("data/Alphasyn.fasta")
amyload_pos_seq = load_fasta_file("data/Amyload_positive.fasta")
# Find and count matches to a pattern 'VT'
fs_aa = FeatureSet("aa patterns")
fs_aa.add(identity)
fs_aa.add(pattern_match, pattern='VT', padded=True)
fs_aa.add(pattern_count, pattern='VT')
result_seq = fs_aa(alphasyn_seq)
for seq in result_seq[:3]:
print seq
# ...and something much more subtle:
# Map a sequence to the hydrophaty scale, and search for the pattern 0.0 - 2.0
# feature2
if args.quantify2 in ['rec', 'det', 'pal', 'ratio_det', 'ratio_pal']:
feat2 = feat2.then(quantify_method[args.quantify2],
metric=args.metric2, radius=float(args.radius2),
dim=int(args.dim2), tau=int(args.tau2),
det_len=int(args.diaglen2), pal_len=int(args.diaglen2))
else:
feat2 = feat2.then(quantify_method[args.quantify2])
# Add the features to a FeatureSet
fs = FeatureSet("fs")
fs.add(feat1)
fs.add(feat2)
# Convert and plot input1 sequences in the 2d space
input_seq1 = load_fasta_file(args.input1)
conv_seq1 = fs(input_seq1)
conv_data1_x = conv_seq1.columns(feature=feat1.name)[0]
conv_data1_y = conv_seq1.columns(feature=feat2.name)[0]
plt.plot(conv_data1_x, conv_data1_y, '.', label="input1")
# Convert and plot input1 sequences in the 2d space
if args.input2 is not None:
input_seq2 = load_fasta_file(args.input2)
conv_seq2 = fs(input_seq2)
conv_data2_x = conv_seq2.columns(feature=feat1.name)[0]
conv_data2_y = conv_seq2.columns(feature=feat2.name)[0]
plt.plot(conv_data2_x, conv_data2_y, '.', label="input2")
# Show legend and labels
plt.xlabel(feat1.name)
def getLabelIndex(fromFile):
print(fromFile)
splitArray = fromFile.split(' ', 1)
# Remove last element from split
splitArray.pop(0)
y = splitArray[0].split(' ')
y = sorted([int(i) for i in y[:-1]])
return y
# Load the 'xxxxx.fasta' sequence set
alphasyn_seq = load_fasta_file("./Benchmark/benchmark3.fasta")
alphasyn_seq1 = load_fasta_file("./Benchmark/benchmark3.fasta")
# Get array of lengths
fastaLength, fastaID, count = [],[], 0
for seq in alphasyn_seq1:
fastaLength.append(len(seq.data))
fastaID.append(seq.identifier)
for leng in fastaLength:
count += leng
print(fastaLength)
help='num. of classes (default: 3)')
group_simplify.add_argument('-t', '--iterations', default=0,
help='num. of iterations for kmeans (default: 0)')
group_ngrams = parser.add_argument_group('N-grams')
group_ngrams.add_argument('-n', '--n', default='1', help='n-gram size (default: 1)')
group_ngrams.add_argument('-m', '--metric', default='identity',
choices=['identity', 'taxi', 'euclid', 'sup', 'inf'],
help='metric for matching n-grams (default: identity)')
group_ngrams.add_argument('-r', '--radius', default=0.0,
help='similarity radius (default: 0.0)')
args = parser.parse_args()
# Load the 'input' sequence set
input_seq = load_fasta_file(args.input, unique=False)
# Retrieve AAindex mapping for the 'property'
if args.property is not None:
try:
aa_mapping = get_aaindex_file(args.property)
except ValueError:
aa_mapping = get_aaindex_www(args.property)
# Simplify if and as requested
if args.simplify is not None:
aa_mapping = simplify(aa_mapping, aa_mapping.__name__+"/"+args.classes,
method=args.simplify, k=int(args.classes),
iters=int(args.iterations))
# Assign 'default' value for the Mapping
import os
import sys
sys.path.insert(0, os.path.abspath('..'))
from quantiprot.utils.io import load_fasta_file
from quantiprot.utils.sequence import SequenceSet
from quantiprot.utils.sequence import merge
# Load protein sequences from 'data/Amyload_positive.fasta':
amyload_pos_seq = load_fasta_file("data/Amyload_positive.fasta")
# Display first three sequences:
print amyload_pos_seq
for seq in amyload_pos_seq[:3]:
print seq
# Find a sequence 'AMY438|7-13|Sup35' in 'amyload_pos_seq':
my_seq_index = amyload_pos_seq.ids().index("AMY438|7-13|Sup35")
my_seq = amyload_pos_seq[my_seq_index]
print my_seq
# And copy the sequence to a new sequence set:
my_seq_set = SequenceSet("my seq set")
my_seq_set.add(my_seq)
print my_seq_set
# Try again to add the same sequence to 'my_seq_set' with 'unique' = True:
my_seq_set.add(my_seq)
print my_seq_set
from quantiprot.metrics.basic import average
from quantiprot.metrics.ngram import pattern_match, pattern_count
from quantiprot.utils.sequence import compact, subset
from quantiprot.metrics.ngram import NgramFeatureSet
from quantiprot.metrics.alphabet import PROTEIN
from Bio import SeqIO
#Load sequence
length_seqs = []
for record in SeqIO.parse("sequence_2.fasta", "fasta"):
length_seqs.append(len(record))
#print((record))
#load the sequence from the file
seq = load_fasta_file("sequence_2.fasta")
SequenceIds = []
SequenceIds2_list = []
for i in SequenceSet.ids(seq):
SequenceIds.append(i)
for i in SequenceIds:
SequenceIds2 = i[i.find("[") + 1:i.find("]")]
SequenceIds2_list.append(SequenceIds2)
#gather important protein features
polarity = Feature(get_aaindex_file("GRAR740102")).then(average)
hydropathy = Feature(get_aaindex_file("KYTJ820101")).then(average)
iso_point = Feature(get_aaindex_file("ZIMJ680104")).then(average)
pk_COOH = Feature(get_aaindex_file("JOND750102")).then(average)
entropy_form = Feature(get_aaindex_file("HUTJ700103")).then(average)
melting_point = Feature(get_aaindex_file("FASG760102")).then(average)
###quantiprot analysis, it will write out tables with AMK properties for segregating sites
# in order to see what are the physiochemical differences between the haplotypes
from quantiprot.utils.io import load_fasta_file
from quantiprot.utils.sequence import SequenceSet
from quantiprot.utils.sequence import subset, columns
from quantiprot.utils.feature import Feature, FeatureSet
# Conversions-related imports:
from quantiprot.utils.mapping import simplify
from quantiprot.metrics.aaindex import get_aa2charge, get_aa2hydropathy, get_aa2volume, get_aa2mj
from quantiprot.metrics.aaindex import get_aaindex_file
from quantiprot.metrics.basic import identity
import numpy as np
fapr = load_fasta_file('prot_segregating.fasta') #load fasta
fs = FeatureSet("myTLRset")
fs.add(get_aa2charge())
fs.add(get_aa2volume())
fs.add(get_aa2mj())
fs.add(get_aa2hydropathy())
convfapr = fs(fapr)
metrics = ["formal_charge", "volume", "miyazawa-jernigan",
"hydropathy"] # which metrics of AMK to generate
#print convfapr
for m in metrics:
outf = open(m + ".tsv", "w")
with outf as f:
h = np.matrix(columns(convfapr, feature=m, transpose=True))
import os
import sys
sys.path.insert(0, os.path.abspath('..'))
from quantiprot.utils.io import load_fasta_file
from quantiprot.utils.feature import FeatureSet
from quantiprot.metrics.aaindex import get_aa2mj
from quantiprot.metrics.rqa import RQAFeatureSet
from quantiprot.metrics.basic import average
from matplotlib import pyplot as plt
# Load the HET-E1 sequence with WD40 repeats:
hete1_seq = load_fasta_file("data/HETE1_PODAS.fasta")
# Prepare FeatureSet for conversion from aa to Miyazawa-Jernigan hydrophobicity:
mj_fs = FeatureSet("mj")
mj_fs.add(get_aa2mj())
# Prepare specialized FeatureSet with basic RQA parameters calculated
# over 100aa window, then smoothed over the 10aa window:
rqa_fs = RQAFeatureSet("rqa",
features=['recurrence', 'determinism'],
window=100,
metric='taxi',
radius=4,
dim=4,
det_len=8)
rqa_fs.then_all(average, window=10)
print rqa_fs
import os
import sys
sys.path.insert(0, os.path.abspath('..'))
# Uversky plot
from quantiprot.utils.io import load_fasta_file
from quantiprot.utils.feature import Feature, FeatureSet
from quantiprot.utils.sequence import compact
from quantiprot.metrics.aaindex import get_aa2charge, get_aa2hydropathy
from quantiprot.metrics.basic import average, average_absolute
from matplotlib import pyplot as plt
amyload_seq = load_fasta_file("data/Amyload_positive.fasta")
disprot_seq = load_fasta_file("data/Disprot.fasta")
# Non-standard letters in Disprot assigned neutral charge and hydropathy:
net_abs_charge = Feature(get_aa2charge(default=0)).then(average_absolute)
mean_hydropathy = Feature(get_aa2hydropathy(default=0)).then(average)
uversky_fs = FeatureSet("uversky")
uversky_fs.add(mean_hydropathy, name="mean_hydropathy")
uversky_fs.add(net_abs_charge, name="net_abs_charge")
amyload_uversky_seq = uversky_fs(amyload_seq)
disprot_uversky_seq = uversky_fs(disprot_seq)
# First approach to get hydrophobicity/charge pairs
amyload_data_x = amyload_uversky_seq.columns(feature="mean_hydropathy")[0]
amyload_data_y = amyload_uversky_seq.columns(feature="net_abs_charge")[0]
plt.plot(amyload_data_x, amyload_data_y, '.', label="Amyload")
default=1,
help='rqa: embedding dimension (default: 1)')
group_rqa.add_argument('-u',
'--tau',
default=0,
help='rqa: embedding delay tau (default: 0)')
group_rqa.add_argument(
'-l',
'--diaglen',
default=2,
help='rqa: minimal diagonal length for det/pal (default: 2)')
args = parser.parse_args()
# Load the 'input' sequence set
input_seq = load_fasta_file(args.input)
# Retrieve AAindex mapping for the 'property'
if args.property is not None:
try:
aa_mapping = get_aaindex_file(args.property)
except ValueError:
aa_mapping = get_aaindex_www(args.property)
# Assign 'default' value for the Mapping
try:
aa_mapping.default = float(args.default)
except (TypeError, ValueError):
aa_mapping.default = args.default
# Simplify if and as requested