def test_read_vcf(self):
#general
vcfvars, accessions = FileReader.read_vcf(self.vcf_path1)
self.assertEqual(len(vcfvars), 17)
#no annotations
self.assertWarnings(UserWarning, FileReader.read_vcf, self.vcf_path2)
#variation types
vcfvars, accessions = FileReader.read_vcf(self.vcf_path3)
self.assertEqual(len(vcfvars), 5) #stopgaininsertion will yield no variant
self.assertEqual(vcfvars[0].coding['NM_014675'].cdsMutationSyntax, 'c.6026C>G')
self.assertEqual(vcfvars[1].coding['NM_015237'].cdsMutationSyntax, 'c.1225C>T')
self.assertEqual(vcfvars[2].coding['NM_014826'].cdsMutationSyntax, 'c.2091delG')
self.assertEqual(vcfvars[2].coding['NM_003607'].cdsMutationSyntax, 'c.2334delG')
self.assertEqual(vcfvars[3].coding['NM_002318'].cdsMutationSyntax, 'c.142_162delCAGGCCCCCGCCAACGTGGCC')
self.assertEqual(vcfvars[4].coding['NM_152888'].cdsMutationSyntax, 'c.2086G>T')
def test_read_vcf(self):
#general
vcfvars, accessions = FileReader.read_vcf(self.vcf_path1)
self.assertEqual(len(vcfvars), 17)
#no annotations
self.assertWarnings(UserWarning, FileReader.read_vcf, self.vcf_path2)
#variation types
vcfvars, accessions = FileReader.read_vcf(self.vcf_path3)
self.assertEqual(len(vcfvars),
5) #stopgaininsertion will yield no variant
self.assertEqual(vcfvars[0].coding['NM_014675'].cdsMutationSyntax,
'c.6026C>G')
self.assertEqual(vcfvars[1].coding['NM_015237'].cdsMutationSyntax,
'c.1225C>T')
self.assertEqual(vcfvars[2].coding['NM_014826'].cdsMutationSyntax,
'c.2091delG')
self.assertEqual(vcfvars[2].coding['NM_003607'].cdsMutationSyntax,
'c.2334delG')
self.assertEqual(vcfvars[3].coding['NM_002318'].cdsMutationSyntax,
'c.142_162delCAGGCCCCCGCCAACGTGGCC')
self.assertEqual(vcfvars[4].coding['NM_152888'].cdsMutationSyntax,
'c.2086G>T')
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 __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)
