def return_equal_charge_concentrations(protein_file,
RNA_file,
protein_conc=1000,
count_histidine=0,
count_gfp=1):
protein = list(SeqIO.parse(protein_file, 'fasta'))
RNAS = list(SeqIO.parse(RNA_file, 'fasta'))
pos_protein = 0
for p in protein:
protein_obj = SequenceParameters(str(p.seq))
pos_protein = protein_obj.get_countPos() - protein_obj.get_countNeg()
GFP = SequenceParameters(
"MVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITLGMDELYK"
)
if count_histidine:
pos_protein = pos_protein + 0.5 * protein_obj.get_amino_acid_fractions(
)['H'] * (protein_obj.get_length())
if count_gfp:
pos_protein = pos_protein + (GFP.get_countPos() - GFP.get_countNeg())
counter_conc_max = {}
for rna in RNAS:
counter_conc_max[rna.id.split('(')
[0]] = protein_conc * pos_protein / len(rna.seq)
return (counter_conc_max)
def get_features_charge(seq):
"""Return dictionary of all features associated with charge."""
SeqOb = SequenceParameters(seq)
return {'FCR': FCR(seq), 'NCPR': NCPR(seq),
'net_charge': net_charge(seq), 'net_charge_P': net_charge_P(seq),
'RK_ratio': RK_ratio(seq), 'ED_ratio': ED_ratio(seq),
'kappa': SeqOb.get_kappa(), 'omega': SeqOb.get_Omega(), 'SCD': SeqOb.get_SCD()}
def get_features_physchem(seq):
"""Return dictionary of all features associated with physiochemical properties."""
SeqOb = SequenceParameters(seq)
return {'fraction_acidic': fraction_acidic(seq), 'fraction_basic': fraction_basic(seq),
'fraction_aliphatic': fraction_aliphatic(seq), 'fraction_aromatic': fraction_aromatic(seq),
'fraction_polar': fraction_polar(seq), 'fraction_disorder': fraction_disorder(seq), 'fraction_chainexp': fraction_chainexp(seq),
'hydropathy': SeqOb.get_uversky_hydropathy(), 'isopoint': predict_isoelectric_point(seq),
'loglen': log2(len(seq)), 'PPII_propensity': SeqOb.get_PPII_propensity()}
def feat_charge(seq):
SeqOb = SequenceParameters(seq)
return {
'FCR': FCR(seq),
'NCPR': NCPR(seq),
'net_charge': net_charge(seq),
'net_charge_P': net_charge_P(seq),
'RK_ratio': RK_ratio(seq),
'ED_ratio': ED_ratio(seq),
'kappa': SeqOb.get_kappa(),
'omega': SeqOb.get_Omega(),
'SCD': SeqOb.get_SCD()
}
def feat_physchem(seq):
SeqOb = SequenceParameters(seq)
return {
'frac_acidic': frac_acidic(seq),
'frac_basic': frac_basic(seq),
'frac_aliphatic': frac_aliphatic(seq),
'frac_chainexp': frac_chainexp(seq),
'frac_polar': frac_polar(seq),
'frac_aromatic': frac_aromatic(seq),
'frac_disorder': frac_disorder(seq),
'loglen': log2(len(seq)),
'hydropathy': SeqOb.get_uversky_hydropathy(),
'iso_point': ProteinAnalysis(seq).isoelectric_point(),
'PPII_prop': SeqOb.get_PPII_propensity()
}
def test_get_reduced_alphabet_sequence_predefined_alphabets(self):
for i in [2,3,4,5,6,8,10,11, 12,15,18,20]:
# checks that a sequence with all 20 amino acids returns a reduced-alphabet sequence
# made up of i-residues which contains exactly i residues!
self.assertEqual(len(set(self.SP_60.get_reduced_alphabet_sequence(i)[0])),i)
random_seqs = testTools.generate_random_sequence(10)
for j in random_seqs:
# build obj
SP = SequenceParameters(j)
# check reduced alphabet sequence length matches
self.assertEqual(len(SP.get_reduced_alphabet_sequence(i)[0]), len(j))
def test_get_reduced_alphabet_sequence_predefined_alphabets(self):
for i in [2,3,4,5,6,8,10,11, 12,15,18,20]:
# checks that a sequence with all 20 amino acids returns a reduced-alphabet sequence
# made up of i-residues which contains exactly i residues!
self.assertEqual(len(set(self.SP_60.get_reduced_alphabet_sequence(i)[0])),i)
random_seqs = testTools.generate_random_sequence(10)
for j in random_seqs:
# build obj
SP = SequenceParameters(j)
# check reduced alphabet sequence length matches
self.assertEqual(len(SP.get_reduced_alphabet_sequence(i)[0]), len(j))
def encode(cdr3):
#print cdr3
cdr3 = cdr3.replace("X", "V")
cdr3 = cdr3[1:-3]
#print cdr3
cidercdr3 = SequenceParameters(str(cdr3))
a = cidercdr3.get_linear_sequence_composition(blobLen=1, grps=grps)
res = np.where(a[1][0]==1, "N",a[1][0])
res = np.where(a[1][1]==1, "P", res)
res = np.where(a[1][2]==1, "H", res)
res = np.where(a[1][3]==1, "H", res)
res = np.where(res=="0.0", "X", res)
res = "".join(res)
return res
def feat_complexity(seq):
return {
'wf_complexity':
SequenceParameters(seq).get_linear_complexity(blobLen=len(seq))[1]
[0], # Returns a 2xN matrix containing the complexity vector and the corresponding residue positions distributed equally along the sequence
**rep_fractions(seq)
}
def get_features_complexity(seq):
"""Return dictionary of all features associated with sequence complexity."""
repeats = ['Q', 'N', 'S', 'G', 'E', 'D', 'K', 'R', 'P',
'QN', 'RG', 'FG', 'SG', 'SR', 'KAP', 'PTS']
features = {}
for repeat in repeats:
features['repeat_' + repeat] = fraction_regex(seq, f'[{repeat}]' + '{2,}')
features['wf_complexity'] = SequenceParameters(seq).get_linear_complexity(blobLen=len(seq))[1][0] # Returns a 2xN matrix containing the complexity vector and the corresponding residue positions distributed equally along the sequence
return features
def test_get_linear_WF_complexity(self):
# general test
random_seqs = testTools.generate_random_sequence_list(10, minLen=15, maxLen=500)
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('WF',alphabetSize=5)
# test all alphabets
for i in [2,3,4,5,6,8,10,11, 12,15,18,20]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('WF',alphabetSize=i)
# test a range of window sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('WF',blobLen=i)
# test a range of window sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('WF',blobLen=i)
# test a range of step-sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('WF',stepSize=i)
# test a range of word-sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('WF',wordSize=i)
def get_polyamp_regions(inputFasta,outputFile):
# look for mixed charge regions in each protein. Each entry is preceeded by its accession
seqs,out,added = [],[],{}
with open(inputFasta,'rU') as infile, open(outputFile,'wb') as outf:
reader = SeqIO.parse(infile,'fasta')
writer = csv.writer(outf, delimiter='\t')
writer.writerow(['accession','name','highly charged region','r/(r+k)','d/(d+e)','length','charge_density','kappa'])
for s in reader:
tmp = s.id.split('|')
acc = tmp[1]
tmp2 = s.description.split()[-3]
name = tmp2[tmp2.find('=')+1:]
t2=score_polyamp(str(s.seq),window_size,cut_off*window_size)
if len(t2)>0:
for i in range(len(t2)):
to_write = [acc,name, '', 0,0, 0,0,1]
r,k = t2[i].count('R'), t2[i].count('K')
d,e = t2[i].count('D'), t2[i].count('E')
neg = d+e #+t2[i].count('X')
pos = r+k
if pos>0 and neg>0 and pos/neg>=charge_bal and neg/pos>=charge_bal:
l = len(t2[i])
r_ratio = r/pos
d_ratio = d/neg
region_noX = ''
for char in t2[i]:
if char=='X':
region_noX = region_noX+'S'
elif char=='S' or char == 'U':
region_noX = region_noX+'T'
else:
region_noX = region_noX+char
SeqOb = SequenceParameters(region_noX)
kap = SeqOb.get_kappa_X(grp1 = ['E','D'], grp2 = ['K','R'])
if kap<=kappa:
to_write = [acc,name, t2[i], str(r_ratio),str(d_ratio), l,(pos+neg)/l ,str(kap)]
writer.writerow(to_write)
def get_polyamp_regions(inputFasta,outputFile):
# look for polyamph regions in each protein, write all of them in the outfile, separated by a space. Each entry is preceeded by its accession
seqs,out,added = [],[],{}
with open(inputFasta,'rU') as infile, open(outputFile,'wb') as outf:
reader = SeqIO.parse(infile,'fasta')
writer = csv.writer(outf, delimiter='\t')
writer.writerow(['accession','name','highly charged region','r/(r+k)','d/(d+e)','length','charge_density','kappa'])
for s in reader:
tmp = s.id.split('|')
acc = tmp[1]
tmp2 = s.description.split()[-3]
name = tmp2[tmp2.find('=')+1:]
t2=score_polyamp(str(s.seq),window_size,cut_off*window_size)
if len(t2)>0:
for i in range(len(t2)):
to_write = [acc,name, '', 0,0, 0,0,1]
r,k = t2[i].count('R'), t2[i].count('K')
d,e = t2[i].count('D'), t2[i].count('E')
neg = d+e #+t2[i].count('X')
pos = r+k
if pos>0 and neg>0 and pos/neg>=charge_bal and neg/pos>=charge_bal:
l = len(t2[i])
r_ratio = r/pos
d_ratio = d/neg
region_noX = ''
for char in t2[i]:
if char=='X':
region_noX = region_noX+'S'
elif char=='S' or char == 'U':
region_noX = region_noX+'T'
else:
region_noX = region_noX+char
SeqOb = SequenceParameters(region_noX)
kap = SeqOb.get_kappa_X(grp1 = ['E','D'], grp2 = ['K','R'])
if kap<=kappa:
to_write = [acc,name, t2[i], str(r_ratio),str(d_ratio), l,(pos+neg)/l ,str(kap)]
writer.writerow(to_write)
def apply_attribute_kappa(proteome):
interface_tools.check_proteome(proteome,
'apply_attribute_kappa (apis.localcider)')
for protein in proteome:
# get the protein sequence
seq = protein.sequence
# this is where we convert sequence into NCPR
kappa = SequenceParameters(protein.sequence).get_kappa()
# this is where we add the NCPR track
protein.add_attribute('kappa', kappa)
def in_out_kappa(self):
df = pd.read_csv(self.train_fpi, sep='\t', index_col=0)
df = df[df['y'] == 0]
seqs = list(df['Sequence'])
for seq in seqs:
ms = motif_seq.LcSeq(seq, self.k, self.lca, 'lca')
in_seq, out_seq = ms.seq_in_motif()
SeqOb = SequenceParameters(in_seq)
print(SeqOb.get_kappa())
seqOb = SequenceParameters(out_seq)
print(seqOb.get_kappa())
print('')
def get_kappa(sequence):
####-CREATE A SEQUENCEOBJECT FROM THE AMINO ACID SEQUENCE-##############################################################
SeqOb = SequenceParameters(sequence)
####-KAPPA RANGES: 0 < K < 1 --------------- LOW KAPPA:EXTENDED ---- HIGH KAPPA:COMPACTED --------------################
kappa = SeqOb.get_kappa()
return kappa
from localcider.sequenceParameters import SequenceParameters
from natsort import natsorted
import matplotlib.pyplot as plt
#Assigning path and fasta files to be analyzed
path = "ecoli/input/"
filelist = os.listdir(path)
#Sorting them in an order
filelist=natsorted(filelist)
#create an empty lists for sequences to be processed
list_of_SeqObjs = []
#First cider command to load the fasta files into the list of sequences
for file in filelist:
file= path + file
list_of_SeqObjs.append(SequenceParameters(sequenceFile=file))
#output file
f = open("cider_ecoli.dat", "w")
#Cider commands to get the parameters of interest
for obj in list_of_SeqObjs:
f_pos=obj.get_fraction_positive()
f_neg=obj.get_fraction_negative()
mhyd=obj.get_uversky_hydropathy()
mnc=obj.get_mean_net_charge(pH=7)
kappa=obj.get_kappa()
f.write("%s %f %f %f %f %f\n"%(filelist[list_of_SeqObjs.index(obj)],f_pos,f_neg,mhyd,mnc,kappa))
#closing the output file
f.close()
#For plotting mean net charge vs mean hydropathy
print(file)
contents = open(file).read().split('>')
#can't use SeqParam(seqfile=file)
#because all the sequences are appended to each other.
output = open(file + "_charge", 'w+')
for protein in [x for x in contents if x]:
header = protein[0:protein.index('\n')]
seq = protein[protein.index('\n'):-1]
print(header)
if ('X' in seq):
print("Warning: unspecified protein encountered.")
seq = seq.replace('X', '')
seq_param = SequenceParameters(seq)
#mean_net_charge is always positive, whereas
# net_charge_per_residue is alternating
net_charge = seq_param.get_NCPR(pH=7.0) * seq_param.get_length()
print(net_charge)
output.write(header)
output.write(", ")
output.write(str(7.0))
output.write(str(", "))
output.write(str(seq_param.get_molecular_weight()))
output.write(str(", "))
output.write(str(net_charge))
output.write('\n')
class TestComplexityFunctions(unittest.TestCase):
def setUp(self):
self.SP_60 = SequenceParameters('QWERTYIPASDFGHKLCVNMQWERTYIPASDFGHKLCVNMQWERTYIPASDFGHKLCVNM')
self.SP_10 = SequenceParameters('KDNIKHVPGG')
def test_get_reduced_alphabet_sequence_predefined_alphabets(self):
for i in [2,3,4,5,6,8,10,11, 12,15,18,20]:
# checks that a sequence with all 20 amino acids returns a reduced-alphabet sequence
# made up of i-residues which contains exactly i residues!
self.assertEqual(len(set(self.SP_60.get_reduced_alphabet_sequence(i)[0])),i)
random_seqs = testTools.generate_random_sequence(10)
for j in random_seqs:
# build obj
SP = SequenceParameters(j)
# check reduced alphabet sequence length matches
self.assertEqual(len(SP.get_reduced_alphabet_sequence(i)[0]), len(j))
def test_get_linear_WF_complexity(self):
# general test
random_seqs = testTools.generate_random_sequence_list(10, minLen=15, maxLen=500)
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('WF',alphabetSize=5)
# test all alphabets
for i in [2,3,4,5,6,8,10,11, 12,15,18,20]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('WF',alphabetSize=i)
# test a range of window sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('WF',blobLen=i)
# test a range of window sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('WF',blobLen=i)
# test a range of step-sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('WF',stepSize=i)
# test a range of word-sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('WF',wordSize=i)
def test_get_linear_LC_complexity(self):
# general test
random_seqs = testTools.generate_random_sequence_list(10, minLen=15, maxLen=500)
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LC',alphabetSize=5)
# test all alphabets
for i in [2,3,4,5,6,8,10,11, 12,15,18,20]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LC',alphabetSize=i)
# test a range of window sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LC',blobLen=i)
# test a range of window sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LC',blobLen=i)
# test a range of step-sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LC',stepSize=i)
# test a range of word-sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LC',wordSize=i)
def test_get_linear_LZW_complexity(self):
# general test
random_seqs = testTools.generate_random_sequence_list(10, minLen=15, maxLen=500)
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LZW',alphabetSize=5)
# test all alphabets
for i in [2,3,4,5,6,8,10,11, 12,15,18,20]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LZW',alphabetSize=i)
# test a range of window sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LZW',blobLen=i)
# test a range of window sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LZW',blobLen=i)
# test a range of step-sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LZW',stepSize=i)
# test a range of word-sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LZW',wordSize=i)
def test_complexity_values(self):
out = {}
# WF alphatbetsize 4
out['WF'] = np.array([ 0.92321967, 0.92321967, 0.92321967, 0.88048202, 0.88048202,
0.92321967, 0.92321967, 0.92321967, 0.94773092, 0.92321967,
0.86096405, 0.86096405, 0.86096405, 0.68048202, 0.68048202,
0.86096405, 0.92321967, 0.92321967, 0.96096405, 0.9854753 ,
0.92321967, 0.92321967, 0.92321967, 0.88048202, 0.88048202,
0.92321967, 0.92321967, 0.92321967, 0.94773092, 0.92321967,
0.86096405, 0.86096405, 0.86096405, 0.68048202, 0.68048202,
0.86096405, 0.92321967, 0.92321967, 0.96096405, 0.9854753 ,
0.92321967, 0.92321967, 0.92321967, 0.88048202, 0.88048202,
0.92321967, 0.92321967, 0.92321967, 0.94773092, 0.92321967,
0.86096405])
# LZW alphabate size=4
out['LZW'] = np.array([ 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.8, 0.8, 0.8,
0.8, 0.8, 0.8, 0.8, 0.9, 0.9, 0.9, 1. , 1. , 0.9, 0.9,
0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.8, 0.8, 0.8, 0.8, 0.8,
0.8, 0.8, 0.9, 0.9, 0.9, 1. , 1. , 0.9, 0.9, 0.9, 0.9,
0.9, 0.9, 0.9, 0.9, 0.8, 0.8, 0.8])
# LC alphabet size = 2
out['LC'] = np.array([ 0.625, 0.5 , 0.5 , 0.5 , 0.5 , 0.5 , 0.625, 0.75 ,
0.625, 0.75 , 0.625, 0.75 , 0.875, 0.75 , 0.625, 0.625,
0.625, 0.625, 0.75 , 0.75 , 0.625, 0.5 , 0.5 , 0.5 ,
0.5 , 0.5 , 0.625, 0.75 , 0.625, 0.75 , 0.625, 0.75 ,
0.875, 0.75 , 0.625, 0.625, 0.625, 0.625, 0.75 , 0.75 ,
0.625, 0.5 , 0.5 , 0.5 , 0.5 , 0.5 , 0.625, 0.75 ,
0.625, 0.75 , 0.625])
self.assertEqual((self.SP_60.get_linear_complexity('WF', alphabetSize=4)[1] - out['WF'] < 0.00001).all(), True)
self.assertEqual((self.SP_60.get_linear_complexity('LZW', alphabetSize=4)[1] - out['LZW'] < 0.00001).all(), True)
self.assertEqual((self.SP_60.get_linear_complexity('LC', alphabetSize=2)[1] - out['LC'] < 0.00001).all(), True)
def setUp(self):
self.SP_60 = SequenceParameters('QWERTYIPASDFGHKLCVNMQWERTYIPASDFGHKLCVNMQWERTYIPASDFGHKLCVNM')
self.SP_10 = SequenceParameters('KDNIKHVPGG')
class TestComplexityFunctions(unittest.TestCase):
def setUp(self):
self.SP_60 = SequenceParameters('QWERTYIPASDFGHKLCVNMQWERTYIPASDFGHKLCVNMQWERTYIPASDFGHKLCVNM')
self.SP_10 = SequenceParameters('KDNIKHVPGG')
def test_get_reduced_alphabet_sequence_predefined_alphabets(self):
for i in [2,3,4,5,6,8,10,11, 12,15,18,20]:
# checks that a sequence with all 20 amino acids returns a reduced-alphabet sequence
# made up of i-residues which contains exactly i residues!
self.assertEqual(len(set(self.SP_60.get_reduced_alphabet_sequence(i)[0])),i)
random_seqs = testTools.generate_random_sequence(10)
for j in random_seqs:
# build obj
SP = SequenceParameters(j)
# check reduced alphabet sequence length matches
self.assertEqual(len(SP.get_reduced_alphabet_sequence(i)[0]), len(j))
def test_get_linear_WF_complexity(self):
# general test
random_seqs = testTools.generate_random_sequence_list(10, minLen=15, maxLen=500)
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('WF',alphabetSize=5)
# test all alphabets
for i in [2,3,4,5,6,8,10,11, 12,15,18,20]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('WF',alphabetSize=i)
# test a range of window sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('WF',blobLen=i)
# test a range of window sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('WF',blobLen=i)
# test a range of step-sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('WF',stepSize=i)
# test a range of word-sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('WF',wordSize=i)
def test_get_linear_LC_complexity(self):
# general test
random_seqs = testTools.generate_random_sequence_list(10, minLen=15, maxLen=500)
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LC',alphabetSize=5)
# test all alphabets
for i in [2,3,4,5,6,8,10,11, 12,15,18,20]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LC',alphabetSize=i)
# test a range of window sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LC',blobLen=i)
# test a range of window sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LC',blobLen=i)
# test a range of step-sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LC',stepSize=i)
# test a range of word-sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LC',wordSize=i)
def test_get_linear_LZW_complexity(self):
# general test
random_seqs = testTools.generate_random_sequence_list(10, minLen=15, maxLen=500)
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LZW',alphabetSize=5)
# test all alphabets
for i in [2,3,4,5,6,8,10,11, 12,15,18,20]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LZW',alphabetSize=i)
# test a range of window sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LZW',blobLen=i)
# test a range of window sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LZW',blobLen=i)
# test a range of step-sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LZW',stepSize=i)
# test a range of word-sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LZW',wordSize=i)
def test_complexity_values(self):
out = {}
# WF alphatbetsize 4
out['WF'] = np.array([ 0.92321967, 0.92321967, 0.92321967, 0.88048202, 0.88048202,
0.92321967, 0.92321967, 0.92321967, 0.94773092, 0.92321967,
0.86096405, 0.86096405, 0.86096405, 0.68048202, 0.68048202,
0.86096405, 0.92321967, 0.92321967, 0.96096405, 0.9854753 ,
0.92321967, 0.92321967, 0.92321967, 0.88048202, 0.88048202,
0.92321967, 0.92321967, 0.92321967, 0.94773092, 0.92321967,
0.86096405, 0.86096405, 0.86096405, 0.68048202, 0.68048202,
0.86096405, 0.92321967, 0.92321967, 0.96096405, 0.9854753 ,
0.92321967, 0.92321967, 0.92321967, 0.88048202, 0.88048202,
0.92321967, 0.92321967, 0.92321967, 0.94773092, 0.92321967,
0.86096405])
# LZW alphabate size=4
out['LZW'] = np.array([ 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.8, 0.8, 0.8,
0.8, 0.8, 0.8, 0.8, 0.9, 0.9, 0.9, 1. , 1. , 0.9, 0.9,
0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.8, 0.8, 0.8, 0.8, 0.8,
0.8, 0.8, 0.9, 0.9, 0.9, 1. , 1. , 0.9, 0.9, 0.9, 0.9,
0.9, 0.9, 0.9, 0.9, 0.8, 0.8, 0.8])
# LC alphabet size = 2
out['LC'] = np.array([ 0.625, 0.5 , 0.5 , 0.5 , 0.5 , 0.5 , 0.625, 0.75 ,
0.625, 0.75 , 0.625, 0.75 , 0.875, 0.75 , 0.625, 0.625,
0.625, 0.625, 0.75 , 0.75 , 0.625, 0.5 , 0.5 , 0.5 ,
0.5 , 0.5 , 0.625, 0.75 , 0.625, 0.75 , 0.625, 0.75 ,
0.875, 0.75 , 0.625, 0.625, 0.625, 0.625, 0.75 , 0.75 ,
0.625, 0.5 , 0.5 , 0.5 , 0.5 , 0.5 , 0.625, 0.75 ,
0.625, 0.75 , 0.625])
self.assertEquals((self.SP_60.get_linear_complexity('WF', alphabetSize=4)[1] - out['WF'] < 0.00001).all(), True)
self.assertEquals((self.SP_60.get_linear_complexity('LZW', alphabetSize=4)[1] - out['LZW'] < 0.00001).all(), True)
self.assertEquals((self.SP_60.get_linear_complexity('LC', alphabetSize=2)[1] - out['LC'] < 0.00001).all(), True)
def aa_analysis(df, property):
if property == "ncpr":
df = df[pd.notnull(df['Amino_acids'])]
df[["AA1","AA2"]] = df['Amino_acids'].str.split('/',expand=True)
isoelectric_point = []
for sequence in df["AA1"]:
try:
cdr3 = ProteinAnalysis(str(sequence))
cidercdr3 = SequenceParameters(str(sequence))
isoelectric_point.append(cidercdr3.get_NCPR())
except:
isoelectric_point.append(0)
pass
df["AA1_Iso"] = isoelectric_point
isoelectric_point2 = []
for sequence in df["AA2"]:
try:
cdr3 = ProteinAnalysis(str(sequence))
cidercdr3 = SequenceParameters(str(sequence))
isoelectric_point2.append(cidercdr3.get_NCPR())
except:
isoelectric_point2.append(0)
pass
df["AA2_Iso"] = isoelectric_point2
df["AA_Iso_Delta"] = df["AA2_Iso"] - df["AA1_Iso"]
df = df[["AA1_Iso", "AA2_Iso", "AA_Iso_Delta"]]
elif property == "uversky_hydropathy":
df = df[pd.notnull(df['Amino_acids'])]
df[["AA1","AA2"]] = df['Amino_acids'].str.split('/',expand=True)
isoelectric_point = []
for sequence in df["AA1"]:
try:
cdr3 = ProteinAnalysis(str(sequence))
cidercdr3 = SequenceParameters(str(sequence))
isoelectric_point.append(cidercdr3.get_uversky_hydropathy())
except:
isoelectric_point.append(0)
pass
df["AA1_Iso"] = isoelectric_point
isoelectric_point2 = []
for sequence in df["AA2"]:
try:
cdr3 = ProteinAnalysis(str(sequence))
cidercdr3 = SequenceParameters(str(sequence))
isoelectric_point2.append(cidercdr3.get_uversky_hydropathy())
except:
isoelectric_point2.append(0)
pass
df["AA2_Iso"] = isoelectric_point2
df["AA_Iso_Delta"] = df["AA2_Iso"] - df["AA1_Iso"]
df = df[["AA1_Iso", "AA2_Iso", "AA_Iso_Delta"]]
return df
def setUp(self):
self.SP_60 = SequenceParameters('QWERTYIPASDFGHKLCVNMQWERTYIPASDFGHKLCVNMQWERTYIPASDFGHKLCVNM')
self.SP_10 = SequenceParameters('KDNIKHVPGG')
#!/usr/bin/env python
import sys
import os
import json
import numpy as np
from pandas import *
# import the relevant code
import localcider
from localcider.sequenceParameters import SequenceParameters
# create an empty list
list_of_SeqObjs = []
with open("FUS_mammals.seq") as f:
#for each ortholog in the file
for seq in f:
try:
list_of_SeqObjs.append(SequenceParameters(seq))
except localcider.SequenceFileParserException:
# if we encounter a file parsing error just skip that sequence
continue
# for each
for obj in list_of_SeqObjs:
print obj.get_kappa()
