def test_simple_incorporation(self):
"""
test simple variant incorporation. only 1 variant in 1 transcript.
input reference transcript: AAAAACCCCCGGGGG
variant 3: insert TT after pos 7
variant 1: SNP C -> T at pos 2
variant 4: del CCCCC after pos 9
"""
dummy_db = DummyAdapter()
# INSERTIONS:
dummy_vars = [var_3]
trans = Generator.generate_transcripts_from_variants(
dummy_vars, dummy_db, EIdentifierTypes.REFSEQ).next()
self.assertEqual(str(trans), "AAAAACCTTCCCGGGGG")
# SNPs:
dummy_vars = [var_1]
trans = Generator.generate_transcripts_from_variants(
dummy_vars, dummy_db, EIdentifierTypes.REFSEQ).next()
self.assertEqual(str(trans), "ATAAACCCCCGGGGG")
# DELETIONS:
dummy_vars = [var_4]
trans = Generator.generate_transcripts_from_variants(
dummy_vars, dummy_db, EIdentifierTypes.REFSEQ).next()
self.assertEqual(str(trans), "AAAAAGGGGG")
def test_peptides_from_varaints(self):
coding = {}
coding['NM_080751'] = MutationSyntax('NM_080751',2629,876,'c.2630C>T','p.Pro877Leu')
var = Variant('line0',0,20,2621905,'C','T',coding,True,False)
var.gene = 'TMC2'
ma = MartsAdapter(biomart="http://ensembl.org")
vars = [var, Variant("testInsertion", 2, 20, 2621899, "", "AAAAAA", {'NM_080751':MutationSyntax('NM_080751',2625,876,'c.2630C>T','p.Pro877Leu')}, True, False)]
test = Generator.generate_peptides_from_variants(vars, 9, ma, id_type=EIdentifierTypes.REFSEQ, peptides=None)
test2 = [x for x in test]
print(len(test2))
ts = list()
#using a tweaked generator that takes another sequence source if the sequence is too short in respect to the given variants
#in this case a newer/older sequence from mart in respect to what was given as reference in the annotation process
t = Generator.generate_transcripts_from_variants(vars, ma, id_type=EIdentifierTypes.REFSEQ)
ts = [x for x in t]
print(len(ts[0]))
p = Generator.generate_proteins_from_transcripts(ts, to_stop=True)
ps = [x for x in p]
e = Generator.generate_peptides_from_proteins(ps, 9)
es = [x for x in e]
print(len(es))
#print vars
print len(vars)
def test_simple_incorporation(self):
"""
test simple variant incorporation. only 1 variant in 1 transcript.
input reference transcript: AAAAACCCCCGGGGG
variant 3: insert TT after pos 7
variant 1: SNP C -> T at pos 2
variant 4: del CCCCC after pos 9
"""
dummy_db = DummyAdapter()
# INSERTIONS:
dummy_vars = [var_3]
trans = Generator.generate_transcripts_from_variants(dummy_vars, dummy_db).next()
self.assertEqual(str(trans), "AAAAACCTTCCCGGGGG")
# SNPs:
dummy_vars = [var_1]
trans = Generator.generate_transcripts_from_variants(dummy_vars, dummy_db).next()
self.assertEqual(str(trans), "ATAAACCCCCGGGGG")
# DELETIONS:
dummy_vars = [var_4]
trans = Generator.generate_transcripts_from_variants(dummy_vars, dummy_db).next()
self.assertEqual(str(trans), "AAAAAGGGGG")
def test_real_life_test(self):
mart = MartsAdapter(biomart="http://grch37.ensembl.org/biomart/martservice?query=")
ano_path = os.path.join(os.path.dirname(inspect.getfile(Fred2)), "Data/examples/test_annovar.out")
vars = read_annovar_exonic(ano_path)
peps = set(map(lambda x: str(x), Generator.generate_peptides_from_variants(vars, 9, mart,
EIdentifierTypes.REFSEQ)))
peps_from_prot = set(map(str, Generator.generate_peptides_from_proteins(
Generator.generate_proteins_from_transcripts(
Generator.generate_transcripts_from_variants(vars, mart, EIdentifierTypes.REFSEQ)), 9)))
self.assertTrue(len(peps - peps_from_prot) == 0)
self.assertTrue(len(peps_from_prot - peps) == 0)
def test_proteins_from_variants(self):
"""
Variants:
3-DEL(-2) , 5-INS(+3) , 7-DEL(-4)
HET-DEL(-2), HOM-INS(+3), HET-DEL(-1)
Reference sequence:set(['GLK', 'PPK', 'GFP', 'PQK', 'GFK', 'GGF', 'FPQ', 'FPP', 'GGL'])
AAATTTCGGGGG (DEL,INS,DEL)
AAATTTCCCCCGGGGG (DEL,INS)
AAAAATTTCCGGGG (INS,DEL)
AAAAATTTCCCCCGGGGG (INS)
GGGTTTCAAAAA (DEL,INS,DEL)
GGGTTTCCCCCAAAAA (DEL,INS)
GGGGGTTTCAAAAA (INS,DEL)
GGGGGTTTCCCCCAAAAA (INS)
Resulting protein sequences:
KFG
KNLG
KFPPG
KNFPRG
GFK
GGLK
GFPPK
GGFPQK
"""
dummy_db = DummyAdapter()
dummy_vars = [var_10, var_11, var_12]
exp_prot = set([
'KFG', 'KNLG', 'KFPPG', 'KNFPRG', 'GFK', 'GGLK', 'GFPPK', 'GFPPK',
'GGFPQK'
])
prot = set(
map(
lambda x: str(x),
Generator.generate_proteins_from_transcripts(
Generator.generate_transcripts_from_variants(
dummy_vars, dummy_db, EIdentifierTypes.REFSEQ))))
self.assertTrue(len(prot - exp_prot) == 0)
self.assertTrue(len(exp_prot - prot) == 0)
def test_offset_single(self):
"""
tests if offset is correctly handled when several variants for one
transcript occur. still only one transcript with one transcript variant.
reference transcript: AAAAACCCCCGGGGG
Each variant so that it is clearly down stream of
it's predecessor
"""
dummy_db = DummyAdapter()
# 1) INS, SNP, DEL
dummy_vars = [var_3, var_7, var_6]
trans = Generator.generate_transcripts_from_variants(dummy_vars, dummy_db).next()
self.assertEqual(str(trans), "AAAAACCTTCTGGGG")
# 2.) INS, DEL, INS
dummy_vars = [var_9, var_4, var_8]
trans = Generator.generate_transcripts_from_variants(dummy_vars, dummy_db).next()
self.assertEqual(str(trans), "AATTAAAGGGGGTTT")
def test_offset_single(self):
"""
tests if offset is correctly handled when several variants for one
transcript occur. still only one transcript with one transcript variant.
reference transcript: AAAAACCCCCGGGGG
Each variant so that it is clearly down stream of
it's predecessor
"""
dummy_db = DummyAdapter()
# 1) INS, SNP, DEL
dummy_vars = [var_3, var_7, var_6]
trans = Generator.generate_transcripts_from_variants(dummy_vars, dummy_db, EIdentifierTypes.REFSEQ).next()
self.assertEqual(str(trans), "AAAAACCTTCTGGGG")
# 2.) INS, DEL, INS
dummy_vars = [var_9, var_4, var_8]
trans = Generator.generate_transcripts_from_variants(dummy_vars, dummy_db, EIdentifierTypes.REFSEQ).next()
self.assertEqual(str(trans), "AATTAAAGGGGGTTT")
def test_proteins_from_variants(self):
"""
Variants:
3-DEL(-2) , 5-INS(+3) , 7-DEL(-4)
HET-DEL(-2), HOM-INS(+3), HET-DEL(-1)
Reference sequence:set(['GLK', 'PPK', 'GFP', 'PQK', 'GFK', 'GGF', 'FPQ', 'FPP', 'GGL'])
AAATTTCGGGGG (DEL,INS,DEL)
AAATTTCCCCCGGGGG (DEL,INS)
AAAAATTTCCGGGG (INS,DEL)
AAAAATTTCCCCCGGGGG (INS)
GGGTTTCAAAAA (DEL,INS,DEL)
GGGTTTCCCCCAAAAA (DEL,INS)
GGGGGTTTCAAAAA (INS,DEL)
GGGGGTTTCCCCCAAAAA (INS)
Resulting protein sequences:
KFG
KNLG
KFPPG
KNFPRG
GFK
GGLK
GFPPK
GGFPQK
"""
dummy_db = DummyAdapter()
dummy_vars = [var_10, var_11, var_12]
exp_prot = set(['KFG', 'KNLG', 'KFPPG', 'KNFPRG', 'GFK', 'GGLK', 'GFPPK', 'GFPPK', 'GGFPQK'])
prot = set(map(lambda x: str(x),
Generator.generate_proteins_from_transcripts(
Generator.generate_transcripts_from_variants(dummy_vars, dummy_db, EIdentifierTypes.REFSEQ)))
)
self.assertTrue(len(prot-exp_prot) == 0)
self.assertTrue(len(exp_prot-prot) == 0)
def test_non_syn_hetero_snp_trans_number(self):
"""
tests if the number of generated transcripts for a heterozygous
transcript is correct
1 hetero vars = 2 transcripts
:return:
"""
vars_ = \
[self.non_syn_hetero_snp, self.non_frame_shift_del, self.syn_homo_snp]
trans = \
[t for t in Generator.generate_transcripts_from_variants(vars_, self.db_adapter, EIdentifierTypes.REFSEQ)]
self.assertTrue(len(trans) == 2**sum(not v.isHomozygous for v in vars_))
def test_non_syn_hetero_snp_trans_number(self):
"""
tests if the number of generated transcripts for a heterozygous
transcript is correct
1 hetero vars = 2 transcripts
:return:
"""
vars_ = \
[self.non_syn_hetero_snp, self.non_frame_shift_del,self.syn_homo_snp]
trans = \
[t for t in Generator.generate_transcripts_from_variants(vars_, self.db_adapter)]
self.assertTrue(len(trans) == 2**sum(not v.isHomozygous for v in vars_))
def test_real_life_test(self):
mart = MartsAdapter(
biomart="http://grch37.ensembl.org/biomart/martservice?query=")
ano_path = os.path.join(os.path.dirname(inspect.getfile(Fred2)),
"Data/examples/test_annovar.out")
vars = read_annovar_exonic(ano_path)
peps = set(
map(
lambda x: str(x),
Generator.generate_peptides_from_variants(
vars, 9, mart, EIdentifierTypes.REFSEQ)))
peps_from_prot = set(
map(
str,
Generator.generate_peptides_from_proteins(
Generator.generate_proteins_from_transcripts(
Generator.generate_transcripts_from_variants(
vars, mart, EIdentifierTypes.REFSEQ)), 9)))
self.assertTrue(len(peps - peps_from_prot) == 0)
self.assertTrue(len(peps_from_prot - peps) == 0)
def test_heterozygous_variants(self):
"""
Create multiple transcript variants for a transcript, given a set
containing heterozygous variants .
Variants:
3-DEL(-2) , 5-INS(+3) , 7-DEL(-4)
HET-DEL(-2), HOM-INS(+3), HET-DEL(-1)
Reference sequence:
AAAAACCCCCGGGGG
AAATTTCGGGGG (DEL,INS,DEL)
AAATTTCCCCCGGGGG (DEL,INS)
AAAAATTTCCGGGG (INS,DEL)
AAAAATTTCCCCCGGGGG (INS)
GGGGGCCCCCAAAAA
GGGTTTCAAAAA (DEL,INS,DEL)
GGGTTTCCCCCAAAAA (DEL,INS)
GGGGGTTTCAAAAA (INS,DEL)
GGGGGTTTCCCCCAAAAA (INS)
"""
dummy_db = DummyAdapter()
# 1) INS, SNP, DEL
dummy_vars = [var_10, var_11, var_12]
trans_gener = Generator.generate_transcripts_from_variants(
dummy_vars, dummy_db, EIdentifierTypes.REFSEQ)
trans = [t for t in trans_gener]
trans = map(str, trans)
self.assertEqual(len(trans), 8)
self.assertTrue("AAATTTGGGGG" in trans)
self.assertTrue("AAAAATTTGGGGG" in trans)
self.assertTrue("AAATTTCCCCCGGGGG" in trans)
self.assertTrue("AAAAATTTCCCCCGGGGG" in trans)
self.assertTrue("GGGTTTAAAAA" in trans)
self.assertTrue("GGGGGTTTAAAAA" in trans)
self.assertTrue("GGGTTTCCCCCAAAAA" in trans)
self.assertTrue("GGGGGTTTCCCCCAAAAA" in trans)
def test_heterozygous_variants(self):
"""
Create multiple transcript variants for a transcript, given a set
containing heterozygous variants .
Variants:
3-DEL(-2) , 5-INS(+3) , 7-DEL(-4)
HET-DEL(-2), HOM-INS(+3), HET-DEL(-1)
Reference sequence:
AAAAACCCCCGGGGG
AAATTTCGGGGG (DEL,INS,DEL)
AAATTTCCCCCGGGGG (DEL,INS)
AAAAATTTCCGGGG (INS,DEL)
AAAAATTTCCCCCGGGGG (INS)
GGGGGCCCCCAAAAA
GGGTTTCAAAAA (DEL,INS,DEL)
GGGTTTCCCCCAAAAA (DEL,INS)
GGGGGTTTCAAAAA (INS,DEL)
GGGGGTTTCCCCCAAAAA (INS)
"""
dummy_db = DummyAdapter()
# 1) INS, SNP, DEL
dummy_vars = [var_10, var_11, var_12]
trans_gener = Generator.generate_transcripts_from_variants(dummy_vars, dummy_db)
trans = [t for t in trans_gener]
trans = map(str, trans)
self.assertEqual(len(trans), 8)
self.assertTrue("AAATTTGGGGG" in trans)
self.assertTrue("AAAAATTTGGGGG" in trans)
self.assertTrue("AAATTTCCCCCGGGGG" in trans)
self.assertTrue("AAAAATTTCCCCCGGGGG" in trans)
self.assertTrue("GGGTTTAAAAA" in trans)
self.assertTrue("GGGGGTTTAAAAA" in trans)
self.assertTrue("GGGTTTCCCCCAAAAA" in trans)
self.assertTrue("GGGGGTTTCCCCCAAAAA" in trans)
def __main__():
parser = argparse.ArgumentParser(version=VERSION)
parser.add_argument('-V',
'--variations',
dest="var_file",
help='<Required> full path to the input variations',
required=True)
parser.add_argument('-o',
"--outfile",
dest="outfile_path",
help="Created fasta file",
required=True)
parser.add_argument(
'-d',
"--digest",
dest="digest",
type=int,
help="Length of peptides for predigestion and prediction, default 9.")
parser.add_argument('-a',
"--alleles",
dest="alleles",
help="Input alleles for prediction")
parser.add_argument(
'-p',
"--predict",
dest="predict_with",
help="Method of prediction, needs alleles & length, allowed:[{m}]".
format(m=PRED_METH))
parser.add_argument(
'-f',
"--filter",
dest="filter",
type=float,
help=
"Only include sequences with predictions above the given threshold (e.g. 0.4256 for at least weak binder), needs predict"
)
parser.add_argument('-P',
"--Proteins",
dest="only_proteins",
action='store_true',
help="Will write only proteins.")
parser.add_argument(
'-b',
"--base",
dest="basefasta_path",
help="If given, entries are replaced by the variation.")
options = parser.parse_args()
if len(sys.argv) <= 1:
parser.print_help()
sys.exit(1)
if options.filter and not options.predict_with:
parser.print_help()
print "Need alleles with predict option, aborting!"
sys.exit(1)
if options.predict_with and not options.alleles:
parser.print_help()
print "Need alleles with predict option, aborting!"
sys.exit(1)
temp_dir = "/tmp/"
logging.basicConfig(
filename=os.path.splitext(options.outfile_path)[0] +
"_{:%d-%m-%Y_%H-%M-%S}".format(datetime.datetime.now()) + '.log',
filemode='w+',
level=logging.DEBUG) #, format='%(levelname)s:%(message)s'
logging.info("Starting variant fasta creation " + options.outfile_path +
" at " + str(datetime.datetime.now()))
logging.warning("verbosity turned on")
#... look at theos filter, ligandoqc, fasta-distributions, lica and the morgenstellen server conten scripts
# complete proteins?
# only containing binders?
# k-mers?
# binders only?
# FastaSlicer.py?
# remove original if homozygous (needs fasta input)?
# add germline variant option? or expect all to be in one vcf?
# MyObject = type('MyObject', (object,), {})
# options = MyObject()
# setattr(options,"var_file","/home/walzer/immuno-tools/Fred2/Fred2/Data/examples/vcftestfile3.vcf")
#
# vt = os.path.splitext(options.var_file)[-1]
# if ".vcf" == vt:
# vcfvars, accessions = FileReader.read_vcf(options.var_file)
#
# mart_db = MartsAdapter(biomart="http://grch37.ensembl.org")
#
# transcript_gen = g.generate_transcripts_from_variants(vcfvars, mart_db, id_type=EIdentifierTypes.REFSEQ)
# transcripts = [x for x in transcript_gen if x.vars]
# transcript_gen = g.generate_transcripts_from_variants(vcfvars, mart_db, id_type=EIdentifierTypes.REFSEQ)
# protein_gen = g.generate_proteins_from_transcripts(transcript_gen)
# proteins = [x for x in protein_gen if x.vars]
# for p in proteins:
# p.gene_id = p.vars.values()[0][0].gene
#
#
# for t in transcripts:
# t.gene_id = t.vars.values()[0].gene
#
vt = os.path.splitext(options.var_file)[-1]
if ".vcf" == vt:
vcfvars, accessions = FileReader.read_vcf(options.var_file)
elif ".GSvar" == vt:
pass
# vcfvars = FileReader.read_GSvar(options.var_file)
else:
m = "Could not read variants {f}, aborting.".format(f=options.var_file)
logging.error(m)
print m
sys.exit(1)
mart_db = MartsAdapter(biomart="http://grch37.ensembl.org"
) # TODO guess id_type for mart_db from accessions
transcript_gen = g.generate_transcripts_from_variants(
vcfvars, mart_db, id_type=EIdentifierTypes.REFSEQ)
protein_gen = g.generate_proteins_from_transcripts(transcript_gen)
proteins = [x for x in protein_gen if x.vars] # removing unvaried
for p in proteins:
p.gene_id = p.vars.values(
)[0][0].gene # assume gene name from first variant
proteins = [p for p in proteins
if not is_stop_gain(p)] # kick out stop gains
# First exit option
if not (options.predict_with or options.filter) and options.only_proteins:
if options.basefasta_path:
# TODO - replace from base fasta
print "N/A"
sys.exit(0)
else:
e = proteins_to_fasta(proteins)
with open(options.outfile_path, 'w') as f:
f.write(e)
sys.exit(0)
# From now on, digestion must be set somehow
if not options.digest:
digest = 9
else:
digest = options.digest
peptide_gen = g.generate_peptides_from_proteins(proteins, digest)
peptides = [x for x in peptide_gen]
peptides_var = [
x for x in peptides if any(
x.get_variants_by_protein(y) for y in x.proteins.keys())
] # removing unvaried
# Second exit option
if not (options.predict_with or options.filter):
e = peptides_to_fasta(peptides_var)
with open(options.outfile_path, 'w') as f:
f.write(e)
sys.exit(0)
# From now on, predictions are needed
try:
target_alleles_set = set(
FileReader.read_lines(options.alleles, in_type=Allele))
except Exception as e:
m = "Could not read alleles file {f}, aborting.".format(
f=options.alleles)
logging.error(m)
print m, "what:", str(e)
sys.exit(1)
try:
ttn = EpitopePredictorFactory(options.predict_with)
except Exception as e:
m = "Could not initialize prediction method {f}, aborting.".format(
f=options.predict_with)
logging.error(m)
print m
sys.exit(1)
try:
preds = ttn.predict(peptides_var, alleles=target_alleles_set)
except Exception as e:
print "something went wrong with the prediction", options.inf, options.predict_with, "what:", str(
e)
sys.exit(1)
# punch prediction results in peptide metadata (inside pandas dataframe)
#PRED_METH = set()
for i, row in preds.iterrows():
for j in i[1:]:
i[0].log_metadata(j, dict(zip(row.index, row.values)))
#PRED_METH.add(j) # need that later
# Third exit option
if not options.filter:
if options.only_proteins:
if options.basefasta_path:
# TODO - replace from base fasta plus prediction annotation
print "N/A"
sys.exit(0)
else:
prs = annotate_protein_from_peptides(preds)
e = proteins_to_fasta(prs)
with open(options.outfile_path, 'w') as f:
f.write(e)
sys.exit(0)
else:
e = peptides_to_fasta(preds)
with open(options.outfile_path, 'w') as f:
f.write(e)
sys.exit(0)
# kick out nonbinder
preds_f = preds[(preds > options.filter).any(axis=1)]
# Fourth exit option
if options.only_proteins:
if options.basefasta_path:
# TODO - replace from base fasta binders only plus prediction annotation
print "N/A"
sys.exit(0)
else:
prs = annotate_protein_from_peptides(preds_f)
e = proteins_to_fasta(prs)
with open(options.outfile_path, 'w') as f:
f.write(e)
sys.exit(0)
else:
e = peptides_to_fasta(preds_f)
with open(options.outfile_path, 'w') as f:
f.write(e)
sys.exit(0)
def test__check_for_problematic_variants(self):
self.assertTrue(
Generator._check_for_problematic_variants([var_2, var_1]))
self.assertFalse(
Generator._check_for_problematic_variants([var_5, var_6]))
def test__incorp_deletion(self):
ts = list("TESTSEQUEASDFGNCES")
self.assertEqual(Generator._incorp_deletion(ts, var_4, "tsc_1", 0, 0),
-5)
self.assertEqual(Generator._incorp_deletion(ts, var_6, "tsc_1", 0, 0),
-2)
def test__incorp_insertion(self):
ts = list("TESTSEQUENCE")
self.assertEqual(Generator._incorp_insertion(ts, var_3, "tsc_1", 0, 0),
2)
def test__incorp_snp(self):
ts = list("TESTSEQUENCE")
self.assertEqual(Generator._incorp_snp(ts, var_2, "tsc_1", 6, 6), 6)
def test__incorp_deletion(self):
ts = list("TESTSEQUEASDFGNCES")
self.assertEqual(Generator._incorp_deletion(ts, var_4, "tsc_1", 0, 0), -5)
self.assertEqual(Generator._incorp_deletion(ts, var_6, "tsc_1",0, 0), -2)
def test_peptides_from_variants(self):
"""
Create multiple peptides, given a set
containing heterozygous variants .
Variants:
3-DEL(-2) , 5-INS(+3) , 7-DEL(-4)
HET-DEL(-2), HOM-INS(+3), HET-DEL(-1)
Reference sequence:
AAAAACCCCCGGGGG
AAATTTGGGGG (DEL,INS,DEL)
AAATTTCCCCCGGGGG (DEL,INS)
AAAAATTTGGGGG (INS,DEL)
AAAAATTTCCCCCGGGGG (INS)
GGGGGCCCCCAAAAA
GGGTTTCAAAAA (DEL,INS,DEL)
GGGTTTCCCCCAAAAA (DEL,INS)
GGGGGTTTCAAAAA (INS,DEL)
GGGGGTTTCCCCCAAAAA (INS)
Resulting protein sequences:
KFG
KNLG
KFPPG
KNFPRG
GFK
GGLK
GFPPK
GGFPQK
Resulting peptides of length 3:
KFG +
KNL +
NLG +
KFP +
FPP +
PPG +
KNF +
NFP +
FPR +
PRG +
GFK +
GGL +
GLK +
GFP +
FPP +
PPK +
GGF +
GFP +
FPQ +
PQK +
"""
dummy_db = DummyAdapter()
exp_peps = set([
'PRG', 'GLK', 'PPG', 'KFP', 'GFK', 'PPK', 'GFP', 'PQK', 'KNL',
'KFG', 'GGF', 'FPQ', 'FPP', 'NLG', 'FPR', 'KNF', 'GGL', 'NFP'
])
# 1) INS, SNP, DEL
dummy_vars = [var_10, var_11, var_12]
peps = set(
map(
lambda x: str(x),
Generator.generate_peptides_from_variants(
dummy_vars, 3, dummy_db, EIdentifierTypes.REFSEQ)))
peps_from_prot = set(
map(
str,
Generator.generate_peptides_from_proteins(
Generator.generate_proteins_from_transcripts(
Generator.generate_transcripts_from_variants(
dummy_vars, dummy_db, EIdentifierTypes.REFSEQ)),
3)))
self.assertTrue(len(peps - peps_from_prot) == 0)
self.assertTrue(len(peps_from_prot - peps) == 0)
self.assertTrue(len(peps - exp_peps) == 0)
self.assertTrue(len(exp_peps - peps) == 0)
def test__incorp_snp(self):
ts = list("TESTSEQUENCE")
print self.assertEqual(Generator._incorp_snp(ts, var_2, "tsc_1", 6, 6), 6)
def __main__():
parser = argparse.ArgumentParser(
description=
"""Individualized Proteins 2.0 \n Script for generation of protein sequences which contain provided variants.""",
version=VERSION)
parser.add_argument('-s', "--somatic_mutations", help='Somatic variants')
parser.add_argument('-g', "--germline_mutations", help="Germline variants")
parser.add_argument(
'-i',
"--identifier",
help="<Required> Predictions will be written with this name prefix",
required=True)
parser.add_argument(
'-r',
"--reference",
help=
"Reference, retrieved information will be based on this ensembl version",
required=False,
default='GRCh37',
choices=['GRCh37', 'GRCh38'])
parser.add_argument(
'-db',
"--database",
help=
"Proteome sequence reference database to be attached to individualized sequences",
required=True)
parser.add_argument('-o',
"--output_dir",
help="All files written will be put in this directory")
args = parser.parse_args()
if len(sys.argv) <= 1:
parser.print_help()
sys.exit(1)
logging.basicConfig(filename=os.path.join(
args.output_dir, '{}_indproteinsDB.log'.format(args.identifier)),
filemode='w+',
level=logging.DEBUG)
logging.info("Starting generation of protein sequences at " +
str(datetime.now().strftime("%Y-%m-%d %H:%M:%S")))
if args.output_dir is not None:
try:
os.chdir(args.output_dir)
logging.info("Using provided data directory: {}".format(
str(args.output_dir)))
except:
logging.info("No such directory, using current.")
else:
logging.info("Using current data directory.")
'''start the actual IRMA functions'''
metadata = []
#references = {'GRCh37': 'http://grch37.ensembl.org', 'GRCh38': 'http://ensembl.org'}
references = {
'GRCh37': 'http://feb2014.archive.ensembl.org',
'GRCh38': 'http://dec2016.archive.ensembl.org'
}
global transcriptProteinMap
'''read in variants'''
if args.somatic_mutations.endswith(
'.GSvar') or args.somatic_mutations.endswith('.tsv'):
vl, transcripts, metadata = read_GSvar(args.somatic_mutations)
elif args.somatic_mutations.endswith('.vcf'):
vl, transcripts = read_vcf(args.somatic_mutations)
if args.germline_mutations is not None:
if args.germline_mutations.endswith(
'.GSvar') or args.germline_mutations.endswith('.tsv'):
vl_normal, transcripts_germline, metadata = read_GSvar(
args.germline_mutations)
elif args.germline_mutations.endswith('.vcf'):
vl_normal, transcripts_germline = read_vcf(args.germline_mutations)
# combine germline and somatic variants
vl = vl + vl_normal
transcripts = transcripts_germline + transcripts
transcripts = list(set(transcripts))
# initialize MartsAdapter, GRCh37 or GRCh38 based
ma = MartsAdapter(biomart=references[args.reference])
#generate transcripts containing variants, filter for unmutated sequences
transcripts = [
g for g in generator.generate_transcripts_from_variants(
vl, ma, ID_SYSTEM_USED) if g.vars
]
#generate proteins from transcripts, table='Standard', stop_symbol='*', to_stop=True, cds=False
proteins = generator.generate_proteins_from_transcripts(transcripts)
diff_sequences = {}
out_ref = args.database.split('/')[-1].replace(
'.fasta',
'_{}_individualized_protein_DB.fasta'.format(args.identifier))
cpRef = 'cp {f} {o}'.format(f=args.database, o=out_ref)
subprocess.call(cpRef.split())
with open(out_ref, 'a') as outfile:
for p in proteins:
variants = []
for v in p.vars:
variants = variants + p.vars[v]
c = [x.coding.values() for x in variants]
cf = list(itertools.chain.from_iterable(c))
cds = ','.join([y.cdsMutationSyntax for y in set(cf)])
aas = ','.join([y.aaMutationSyntax for y in set(cf)])
outfile.write('>{}:{}\n'.format(p.transcript_id, aas))
outfile.write('{}\n'.format(str(p)))
logging.info("Finished generation of protein sequences at " +
str(datetime.now().strftime("%Y-%m-%d %H:%M:%S")))
def test__check_for_problematic_variants(self):
self.assertTrue(Generator._check_for_problematic_variants([var_2, var_1]))
self.assertFalse(Generator._check_for_problematic_variants([var_5, var_6]))
def make_predictions_from_variants(variants_all, methods, alleles, minlength,
maxlength, martsadapter, protein_db,
identifier, metadata, transcriptProteinMap):
# list for all peptides and filtered peptides
all_peptides = []
all_peptides_filtered = []
# dictionaries for syfpeithi matrices max values and allele mapping
max_values_matrices = {}
allele_string_map = {}
# list to hold dataframes for all predictions
pred_dataframes = []
prots = [
p for p in generator.generate_proteins_from_transcripts(
generator.generate_transcripts_from_variants(
variants_all, martsadapter, ID_SYSTEM_USED))
]
for peplen in range(minlength, maxlength):
peptide_gen = generator.generate_peptides_from_proteins(prots, peplen)
peptides_var = [x for x in peptide_gen]
# remove peptides which are not 'variant relevant'
peptides = [
x for x in peptides_var if any(
x.get_variants_by_protein(y) for y in x.proteins.keys())
]
# filter out self peptides
selfies = [str(p) for p in peptides if protein_db.exists(str(p))]
filtered_peptides = [p for p in peptides if str(p) not in selfies]
all_peptides = all_peptides + peptides
all_peptides_filtered = all_peptides_filtered + filtered_peptides
results = []
if len(filtered_peptides) > 0:
for m in methods:
try:
results.extend([
EpitopePredictorFactory(
m.split('-')[0],
version=m.split('-')[1]).predict(filtered_peptides,
alleles=alleles)
])
except:
logging.warning(
"Prediction for length {length} and allele {allele} not possible with {method}."
.format(length=peplen,
allele=','.join([str(a) for a in alleles]),
method=m))
if (len(results) == 0):
continue
df = results[0].merge_results(results[1:])
for a in alleles:
conv_allele = "%s_%s%s" % (a.locus, a.supertype, a.subtype)
allele_string_map['%s_%s' %
(a, peplen)] = '%s_%i' % (conv_allele, peplen)
max_values_matrices['%s_%i' %
(conv_allele, peplen)] = get_matrix_max_score(
conv_allele, peplen)
df.insert(0, 'length', df.index.map(create_length_column_value))
df['chr'] = df.index.map(create_variant_chr_column_value)
df['pos'] = df.index.map(create_variant_pos_column_value)
df['gene'] = df.index.map(create_gene_column_value)
df['transcripts'] = df.index.map(create_transcript_column_value)
df['proteins'] = df.index.map(create_protein_column_value)
df['variant type'] = df.index.map(create_variant_type_column_value)
df['synonymous'] = df.index.map(create_variant_syn_column_value)
df['homozygous'] = df.index.map(create_variant_hom_column_value)
df['variant details (genomic)'] = df.index.map(
create_mutationsyntax_genome_column_value)
df['variant details (protein)'] = df.index.map(
create_mutationsyntax_column_value)
# reset index to have index as columns
df.reset_index(inplace=True)
for c in df.columns:
if '*' in str(c):
idx = df.columns.get_loc(c)
df.insert(
idx + 1, '%s affinity' % c,
df.apply(lambda x: create_affinity_values(
str(c), int(x['length']), float(x[c]), x['Method'],
max_values_matrices, allele_string_map),
axis=1))
df.insert(
idx + 2, '%s binder' % c,
df.apply(lambda x: create_binder_values(
float(x['%s affinity' % c]), x['Method']),
axis=1))
df = df.rename(columns={c: '%s score' % c})
df['%s score' % c] = df['%s score' %
c].map(lambda x: round(x, 4))
for c in metadata:
df[c] = df.apply(lambda row: create_metadata_column_value(row, c),
axis=1)
df = df.rename(columns={'Seq': 'sequence'})
df = df.rename(columns={'Method': 'method'})
pred_dataframes.append(df)
statistics = {
'prediction_methods': methods,
'number_of_variants': len(variants_all),
'number_of_peptides': len(all_peptides),
'number_of_peptides_after_filtering': len(all_peptides_filtered)
}
return pred_dataframes, statistics, all_peptides_filtered
def test_peptides_from_variants(self):
"""
Create multiple peptides, given a set
containing heterozygous variants .
Variants:
3-DEL(-2) , 5-INS(+3) , 7-DEL(-4)
HET-DEL(-2), HOM-INS(+3), HET-DEL(-1)
Reference sequence:
AAAAACCCCCGGGGG
AAATTTGGGGG (DEL,INS,DEL)
AAATTTCCCCCGGGGG (DEL,INS)
AAAAATTTGGGGG (INS,DEL)
AAAAATTTCCCCCGGGGG (INS)
GGGGGCCCCCAAAAA
GGGTTTCAAAAA (DEL,INS,DEL)
GGGTTTCCCCCAAAAA (DEL,INS)
GGGGGTTTCAAAAA (INS,DEL)
GGGGGTTTCCCCCAAAAA (INS)
Resulting protein sequences:
KFG
KNLG
KFPPG
KNFPRG
GFK
GGLK
GFPPK
GGFPQK
Resulting peptides of length 3:
KFG +
KNL +
NLG +
KFP +
FPP +
PPG +
KNF +
NFP +
FPR +
PRG +
GFK +
GGL +
GLK +
GFP +
FPP +
PPK +
GGF +
GFP +
FPQ +
PQK +
"""
dummy_db = DummyAdapter()
exp_peps = set(['PRG', 'GLK', 'PPG', 'KFP', 'GFK', 'PPK', 'GFP', 'PQK', 'KNL', 'KFG', 'GGF', 'FPQ',
'FPP', 'NLG', 'FPR', 'KNF', 'GGL', 'NFP'])
# 1) INS, SNP, DEL
dummy_vars = [var_10, var_11, var_12]
peps = set(map(lambda x: str(x), Generator.generate_peptides_from_variants(dummy_vars, 3, dummy_db)))
self.assertTrue(len(peps-exp_peps) == 0)
self.assertTrue(len(exp_peps-peps) == 0)
def __main__():
parser = argparse.ArgumentParser(version=VERSION)
parser.add_argument('-V', '--variations', dest="var_file", help='<Required> full path to the input variations', required=True)
parser.add_argument('-o', "--outfile", dest="outfile_path", help="Created fasta file", required=True)
parser.add_argument('-d', "--digest", dest="digest", type=int, help="Length of peptides for predigestion and prediction, default 9.")
parser.add_argument('-a', "--alleles", dest="alleles", help="Input alleles for prediction")
parser.add_argument('-p', "--predict", dest="predict_with", help="Method of prediction, needs alleles & length, allowed:[{m}]".format(m=PRED_METH))
parser.add_argument('-f', "--filter", dest="filter", type=float, help="Only include sequences with predictions above the given threshold (e.g. 0.4256 for at least weak binder), needs predict")
parser.add_argument('-P', "--Proteins", dest="only_proteins", action='store_true', help="Will write only proteins.")
parser.add_argument('-b', "--base", dest="basefasta_path", help="If given, entries are replaced by the variation.")
options = parser.parse_args()
if len(sys.argv) <= 1:
parser.print_help()
sys.exit(1)
if options.filter and not options.predict_with:
parser.print_help()
print "Need alleles with predict option, aborting!"
sys.exit(1)
if options.predict_with and not options.alleles:
parser.print_help()
print "Need alleles with predict option, aborting!"
sys.exit(1)
temp_dir = "/tmp/"
logging.basicConfig(filename=os.path.splitext(options.outfile_path)[0] + "_{:%d-%m-%Y_%H-%M-%S}".format(datetime.datetime.now()) + '.log',
filemode='w+', level=logging.DEBUG) #, format='%(levelname)s:%(message)s'
logging.info("Starting variant fasta creation " + options.outfile_path + " at " + str(datetime.datetime.now()))
logging.warning("verbosity turned on")
#... look at theos filter, ligandoqc, fasta-distributions, lica and the morgenstellen server conten scripts
# complete proteins?
# only containing binders?
# k-mers?
# binders only?
# FastaSlicer.py?
# remove original if homozygous (needs fasta input)?
# add germline variant option? or expect all to be in one vcf?
# MyObject = type('MyObject', (object,), {})
# options = MyObject()
# setattr(options,"var_file","/home/walzer/immuno-tools/Fred2/Fred2/Data/examples/vcftestfile3.vcf")
#
# vt = os.path.splitext(options.var_file)[-1]
# if ".vcf" == vt:
# vcfvars, accessions = FileReader.read_vcf(options.var_file)
#
# mart_db = MartsAdapter(biomart="http://grch37.ensembl.org")
#
# transcript_gen = g.generate_transcripts_from_variants(vcfvars, mart_db, id_type=EIdentifierTypes.REFSEQ)
# transcripts = [x for x in transcript_gen if x.vars]
# transcript_gen = g.generate_transcripts_from_variants(vcfvars, mart_db, id_type=EIdentifierTypes.REFSEQ)
# protein_gen = g.generate_proteins_from_transcripts(transcript_gen)
# proteins = [x for x in protein_gen if x.vars]
# for p in proteins:
# p.gene_id = p.vars.values()[0][0].gene
#
#
# for t in transcripts:
# t.gene_id = t.vars.values()[0].gene
#
vt = os.path.splitext(options.var_file)[-1]
if ".vcf" == vt:
vcfvars, accessions = FileReader.read_vcf(options.var_file)
elif ".GSvar" == vt:
pass
# vcfvars = FileReader.read_GSvar(options.var_file)
else:
m = "Could not read variants {f}, aborting.".format(f=options.var_file)
logging.error(m)
print m
sys.exit(1)
mart_db = MartsAdapter(biomart="http://grch37.ensembl.org") # TODO guess id_type for mart_db from accessions
transcript_gen = g.generate_transcripts_from_variants(vcfvars, mart_db, id_type=EIdentifierTypes.REFSEQ)
protein_gen = g.generate_proteins_from_transcripts(transcript_gen)
proteins = [x for x in protein_gen if x.vars] # removing unvaried
for p in proteins:
p.gene_id = p.vars.values()[0][0].gene # assume gene name from first variant
proteins = [p for p in proteins if not is_stop_gain(p)] # kick out stop gains
# First exit option
if not (options.predict_with or options.filter) and options.only_proteins:
if options.basefasta_path:
# TODO - replace from base fasta
print "N/A"
sys.exit(0)
else:
e = proteins_to_fasta(proteins)
with open(options.outfile_path, 'w') as f:
f.write(e)
sys.exit(0)
# From now on, digestion must be set somehow
if not options.digest:
digest = 9
else:
digest = options.digest
peptide_gen = g.generate_peptides_from_proteins(proteins, digest)
peptides = [x for x in peptide_gen]
peptides_var = [x for x in peptides if any(x.get_variants_by_protein(y) for y in x.proteins.keys())] # removing unvaried
# Second exit option
if not (options.predict_with or options.filter):
e = peptides_to_fasta(peptides_var)
with open(options.outfile_path, 'w') as f:
f.write(e)
sys.exit(0)
# From now on, predictions are needed
try:
target_alleles_set = set(FileReader.read_lines(options.alleles, in_type=Allele))
except Exception as e:
m = "Could not read alleles file {f}, aborting.".format(f=options.alleles)
logging.error(m)
print m, "what:", str(e)
sys.exit(1)
try:
ttn = EpitopePredictorFactory(options.predict_with)
except Exception as e:
m = "Could not initialize prediction method {f}, aborting.".format(f=options.predict_with)
logging.error(m)
print m
sys.exit(1)
try:
preds = ttn.predict(peptides_var, alleles=target_alleles_set)
except Exception as e:
print "something went wrong with the prediction", options.inf, options.predict_with, "what:", str(e)
sys.exit(1)
# punch prediction results in peptide metadata (inside pandas dataframe)
#PRED_METH = set()
for i, row in preds.iterrows():
for j in i[1:]:
i[0].log_metadata(j, dict(zip(row.index, row.values)))
#PRED_METH.add(j) # need that later
# Third exit option
if not options.filter:
if options.only_proteins:
if options.basefasta_path:
# TODO - replace from base fasta plus prediction annotation
print "N/A"
sys.exit(0)
else:
prs = annotate_protein_from_peptides(preds)
e = proteins_to_fasta(prs)
with open(options.outfile_path, 'w') as f:
f.write(e)
sys.exit(0)
else:
e = peptides_to_fasta(preds)
with open(options.outfile_path, 'w') as f:
f.write(e)
sys.exit(0)
# kick out nonbinder
preds_f = preds[(preds > options.filter).any(axis=1)]
# Fourth exit option
if options.only_proteins:
if options.basefasta_path:
# TODO - replace from base fasta binders only plus prediction annotation
print "N/A"
sys.exit(0)
else:
prs = annotate_protein_from_peptides(preds_f)
e = proteins_to_fasta(prs)
with open(options.outfile_path, 'w') as f:
f.write(e)
sys.exit(0)
else:
e = peptides_to_fasta(preds_f)
with open(options.outfile_path, 'w') as f:
f.write(e)
sys.exit(0)
def test__incorp_insertion(self):
ts = list("TESTSEQUENCE")
self.assertEqual(Generator._incorp_insertion(ts, var_3, "tsc_1", 0, 0), 2)