def _get_feature_map(index='JOND920101'):
""" To get the feature mapping object
using the amino acid index given.
The mapping is created using AAindex.
'-' is mapped to 0.0.
"""
# Create a Feature object
aaindex_map = get_aaindex_file(index)
aaindex_map.mapping['-'] = 0.0
feat_map = Feature(aaindex_map)
return feat_map
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
'avg_abs': average_absolute,
'rec': recurrence,
'det': determinism,
'pal': palindromism,
'ratio_det': ratio_determinism,
'ratio_pal': ratio_palindromism,
'entropy': entropy
}
args = parser.parse_args()
# Retrieve AAindex mappings for the properties if and as requested
# property1
if args.property1 is not None:
try:
aa_mapping1 = get_aaindex_file(args.property1)
except ValueError:
aa_mapping1 = get_aaindex_www(args.property1)
try:
aa_mapping1.default = float(args.default1)
except (TypeError, ValueError):
aa_mapping1.default = args.default1
feat1 = Feature(aa_mapping1)
else:
feat1 = Feature(identity)
# property2
if args.property2 is not None:
try:
aa_mapping2 = get_aaindex_file(args.property2)
except ValueError:
fastaLength.append(len(seq.data))
fastaID.append(seq.identifier)
for leng in fastaLength:
count += leng
print(fastaLength)
# Set of features
fs = FeatureSet("Basic Features")
# Add feature names to set of features
# Hydrophobicity (Zimmerman et al., 1968)
fs.add(get_aaindex_file("ZIMJ680101"))
# Average flexibility indices (Bhaskaran-Ponnuswamy, 1988)
fs.add(get_aaindex_file("BHAR880101"))
# Hydrophilicity value (Hopp-Woods, 1981)
fs.add(get_aaindex_file("HOPT810101"))
# Polarity (Grantham, 1974)
fs.add(get_aaindex_file("GRAR740102"))
# Conformational parameter of beta-structure (Beghin-Dirkx, 1975)
fs.add(get_aaindex_file("BEGF750102"))
# Hydrophobicity (Jones, 1975)
fs.add(get_aaindex_file("JOND750101"))
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
try:
aa_mapping.default = float(args.default)
except (TypeError, ValueError):
aa_mapping.default = args.default
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)
net_charge = Feature(get_aaindex_file("KLEP840101")).then(average)
glycine = Feature(pattern_count, pattern='G')
RGD = Feature(pattern_count, pattern='RGD')
GFPGER = Feature(pattern_count, pattern='GFPGER')
#Build the feature set
fs = FeatureSet("my set")
fs1 = FeatureSet("test")
fs2 = FeatureSet("glycine")
fs3 = FeatureSet("GFPGER")
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
from quantiprot.metrics.aaindex import get_aaindex_file
from quantiprot.metrics.basic import identity
# Load the 'data/Alphasyn.fasta' sequence set, which contains several
# peptides from alpha-synuclein deposed in the Amyload database:
alphasyn_seq = load_fasta_file("data/Alphasyn.fasta")
# Retrieve predefined mapping from aminoacids to formal charge,
# and AAindex mapping to relative frequency of occurence (entry: JOND920101)
aa2charge_map = get_aa2charge()
aa2freq_map = get_aaindex_file("JOND920101")
print aa2charge_map
print aa2freq_map
# Make Feature objects based on Mappings:
charge_feat = Feature(aa2charge_map)
freq_feat = Feature(aa2freq_map)
print charge_feat
print freq_feat
# And use them to covert 1st sequence in 'alphasyn_seq':
print charge_feat(alphasyn_seq[0])
print freq_feat(alphasyn_seq[0])
# Make a FeatureSet from a Feature and Mappings:
fs = FeatureSet("basic features")