def __main__():
parser = argparse.ArgumentParser(description="""EPAA - Epitope Prediction And Annotation \n Pipeline for prediction of MHC class I and II epitopes from variants or peptides for a list of specified alleles.
Additionally predicted epitopes can be annotated with protein quantification values for the corresponding proteins, identified ligands, or differential expression values for the corresponding transcripts.""", 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="Dataset identifier")
parser.add_argument('-p', "--peptides", help="File with one peptide per line")
parser.add_argument('-c', "--mhcclass", default=1, help="MHC class I or II")
parser.add_argument('-l', "--max_length", help="Maximum peptide length")
parser.add_argument('-ml', "--min_length", help="Minimum peptide length")
parser.add_argument('-t', "--tools", help="Tools used for peptide predictions", required=True, type=str)
parser.add_argument('-sv', "--versions", help="File containing parsed software version numbers.", required=True)
parser.add_argument('-a', "--alleles", help="<Required> MHC Alleles", 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('-f', "--filter_self", help="Filter peptides against human proteom", required=False, action='store_true')
parser.add_argument('-wt', "--wild_type", help="Add wild type sequences of mutated peptides to output", required=False, action='store_true')
parser.add_argument('-fo', "--fasta_output", help="Create FASTA file with protein sequences", required=False, action='store_true')
parser.add_argument('-rp', "--reference_proteome", help="Reference proteome for self-filtering", required=False)
parser.add_argument('-gr', "--gene_reference", help="List of gene IDs for ID mapping.", required=False)
parser.add_argument('-pq', "--protein_quantification", help="File with protein quantification values")
parser.add_argument('-ge', "--gene_expression", help="File with expression analysis results")
parser.add_argument('-de', "--diff_gene_expression", help="File with differential expression analysis results (DESeq2)")
parser.add_argument('-li', "--ligandomics_id", help="Comma separated file with peptide sequence, score and median intensity of a ligandomics identification run.")
args = parser.parse_args()
if len(sys.argv) <= 1:
parser.print_help()
sys.exit(1)
logger.addHandler(logging.FileHandler('{}_prediction.log'.format(args.identifier)))
logger.info("Starting predictions at " + str(datetime.now().strftime("%Y-%m-%d %H:%M:%S")))
metadata = []
references = {'GRCh37': 'http://feb2014.archive.ensembl.org', 'GRCh38': 'http://dec2016.archive.ensembl.org'}
global transcriptProteinMap
global transcriptSwissProtMap
'''read in variants or peptides'''
if args.peptides:
peptides, metadata = read_peptide_input(args.peptides)
else:
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, metadata = read_vcf(args.somatic_mutations)
transcripts = list(set(transcripts))
transcriptProteinMap, transcriptSwissProtMap = get_protein_ids_for_transcripts(ID_SYSTEM_USED, transcripts, references[args.reference], args.reference)
# get the alleles
alleles = FileReader.read_lines(args.alleles, in_type=Allele)
# initialize MartsAdapter, GRCh37 or GRCh38 based
ma = MartsAdapter(biomart=references[args.reference])
# create protein db instance for filtering self-peptides
up_db = UniProtDB('sp')
if args.filter_self:
logger.info('Reading human proteome')
if os.path.isdir(args.reference_proteome):
for filename in os.listdir(args.reference_proteome):
if filename.endswith(".fasta") or filename.endswith(".fsa"):
up_db.read_seqs(os.path.join(args.reference_proteome, filename))
else:
up_db.read_seqs(args.reference_proteome)
selected_methods = [item for item in args.tools.split(',')]
with open(args.versions, 'r') as versions_file:
tool_version = [ (row[0], str(row[1][1:])) for row in csv.reader(versions_file, delimiter = "\t") ]
# NOTE this needs to be updated, if a newer version will be available via Fred2 and should be used in the future
tool_version.append(('syfpeithi', '1.0'))
# get for each selected method the corresponding tool version
methods = { method:version for tool, version in tool_version for method in selected_methods if tool.lower() in method.lower() }
for method, version in methods.items():
if version not in EpitopePredictorFactory.available_methods()[method]:
raise ValueError("The specified version " + version + " for " + method + " is not supported by Fred2.")
# MHC class I or II predictions
if args.mhcclass is 1:
if args.peptides:
pred_dataframes, statistics = make_predictions_from_peptides(peptides, methods, alleles, up_db, args.identifier, metadata)
else:
pred_dataframes, statistics, all_peptides_filtered, proteins = make_predictions_from_variants(vl, methods, alleles, int(args.min_length), int(args.max_length) + 1, ma, up_db, args.identifier, metadata, transcriptProteinMap)
else:
if args.peptides:
pred_dataframes, statistics = make_predictions_from_peptides(peptides, methods, alleles, up_db, args.identifier, metadata)
else:
pred_dataframes, statistics, all_peptides_filtered, proteins = make_predictions_from_variants(vl, methods, alleles, int(args.min_length), int(args.max_length) + 1, ma, up_db, args.identifier, metadata, transcriptProteinMap)
# concat dataframes for all peptide lengths
try:
complete_df = pd.concat(pred_dataframes)
except:
complete_df = pd.DataFrame()
logger.error("No predictions available.")
# replace method names with method names with version
# complete_df.replace({'method': methods}, inplace=True)
complete_df['method'] = complete_df['method'].apply(lambda x : x + '-' + methods[x] )
# include wild type sequences to dataframe if specified
if args.wild_type:
wt_sequences = generate_wt_seqs(all_peptides_filtered)
complete_df['wt sequence'] = complete_df.apply(lambda row: create_wt_seq_column_value(row, wt_sequences), axis=1)
columns_tiles = ['sequence', 'wt sequence', 'length', 'chr', 'pos', 'gene', 'transcripts', 'proteins', 'variant type', 'method']
# Change the order (the index) of the columns
else:
columns_tiles = ['sequence', 'length', 'chr', 'pos', 'gene', 'transcripts', 'proteins', 'variant type', 'method']
for c in complete_df.columns:
if c not in columns_tiles:
columns_tiles.append(c)
complete_df = complete_df.reindex(columns=columns_tiles)
binder_cols = [col for col in complete_df.columns if 'binder' in col]
binders = []
non_binders = []
pos_predictions = []
neg_predictions = []
for i, r in complete_df.iterrows():
binder = False
for c in binder_cols:
if r[c] is True:
binder = True
continue
if binder:
binders.append(str(r['sequence']))
pos_predictions.append(str(r['sequence']))
else:
neg_predictions.append(str(r['sequence']))
if str(r['sequence']) not in binders:
non_binders.append(str(r['sequence']))
# parse protein quantification results, annotate proteins for samples
if args.protein_quantification is not None:
protein_quant = read_protein_quant(args.protein_quantification)
first_entry = protein_quant[protein_quant.keys()[0]]
for k in first_entry.keys():
complete_df['{} log2 protein LFQ intensity'.format(k)] = complete_df.apply(lambda row: create_quant_column_value_for_result(row, protein_quant, transcriptSwissProtMap, k), axis=1)
# parse (differential) expression analysis results, annotate features (genes/transcripts)
if args.gene_expression is not None:
fold_changes = read_diff_expression_values(args.gene_expression)
gene_id_lengths = {}
col_name = 'RNA expression (RPKM)'
with open(args.gene_reference, 'r') as gene_list:
for l in gene_list:
ids = l.split('\t')
gene_id_in_df = complete_df.iloc[1]['gene']
if 'ENSG' in gene_id_in_df:
gene_id_lengths[ids[0]] = float(ids[2].strip())
else:
gene_id_lengths[ids[1]] = float(ids[2].strip())
deseq = False
# add column to result dataframe
complete_df[col_name] = complete_df.apply(lambda row: create_expression_column_value_for_result(row, fold_changes, deseq, gene_id_lengths), axis=1)
if args.diff_gene_expression is not None:
gene_id_lengths = {}
fold_changes = read_diff_expression_values(args.diff_gene_expression)
col_name = 'RNA normal_vs_tumor.log2FoldChange'
deseq = True
# add column to result dataframe
complete_df[col_name] = complete_df.apply(lambda row: create_expression_column_value_for_result(row, fold_changes, deseq, gene_id_lengths), axis=1)
# parse ligandomics identification results, annotate peptides for samples
if args.ligandomics_id is not None:
lig_id = read_lig_ID_values(args.ligandomics_id)
# add columns to result dataframe
complete_df['ligand score'] = complete_df.apply(lambda row: create_ligandomics_column_value_for_result(row, lig_id, 0, False), axis=1)
complete_df['ligand intensity'] = complete_df.apply(lambda row: create_ligandomics_column_value_for_result(row, lig_id, 1, False), axis=1)
if args.wild_type != None:
complete_df['wt ligand score'] = complete_df.apply(lambda row: create_ligandomics_column_value_for_result(row, lig_id, 0, True), axis=1)
complete_df['wt ligand intensity'] = complete_df.apply(lambda row: create_ligandomics_column_value_for_result(row, lig_id, 1, True), axis=1)
# write mutated protein sequences to fasta file
if args.fasta_output:
with open('{}_prediction_proteins.fasta'.format(args.identifier), 'w') as protein_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)])
protein_outfile.write('>{}:{}:{}\n'.format(p.transcript_id, aas, cds))
protein_outfile.write('{}\n'.format(str(p)))
# write dataframe to tsv
complete_df.fillna('')
complete_df.to_csv("{}_prediction_results.tsv".format(args.identifier), '\t', index=False)
statistics['number_of_predictions'] = len(complete_df)
statistics['number_of_binders'] = len(pos_predictions)
statistics['number_of_nonbinders'] = len(neg_predictions)
statistics['number_of_unique_binders'] = list(set(binders))
statistics['number_of_unique_nonbinders'] = list(set(non_binders) - set(binders))
with open('{}_report.json'.format(args.identifier), 'w') as json_out:
json.dump(statistics, json_out)
logger.info("Finished predictions at " + str(datetime.now().strftime("%Y-%m-%d %H:%M:%S")))
def __main__():
parser = argparse.ArgumentParser(
description=
"""EPAA - Epitope Prediction And Annotation \n Pipeline for prediction of MHC class I and II epitopes from variants or peptides for a list of specified alleles.
Additionally predicted epitopes can be annotated with protein quantification values for the corresponding proteins, identified ligands, or differential expression values for the corresponding transcripts.""",
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="Dataset identifier")
parser.add_argument('-p',
"--peptides",
help="File with one peptide per line")
parser.add_argument('-c',
"--mhcclass",
default="I",
help="MHC class I or II")
parser.add_argument('-l', "--length", help="Maximum peptide length")
parser.add_argument('-a',
"--alleles",
help="<Required> MHC Alleles",
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('-f',
"--filter_self",
help="Filter peptides against human proteom",
required=False,
action='store_true')
parser.add_argument(
'-wt',
"--wild_type",
help="Add wild type sequences of mutated peptides to output",
required=False,
action='store_true')
parser.add_argument('-rp',
"--reference_proteome",
help="Reference proteome for self-filtering",
required=False)
parser.add_argument('-gr',
"--gene_reference",
help="List of gene IDs for ID mapping.",
required=False)
parser.add_argument('-pq',
"--protein_quantification",
help="File with protein quantification values")
parser.add_argument('-ge',
"--gene_expression",
help="File with expression analysis results")
parser.add_argument(
'-de',
"--diff_gene_expression",
help="File with differential expression analysis results (DESeq2)")
parser.add_argument(
'-li',
"--ligandomics_id",
help=
"Comma separated file with peptide sequence, score and median intensity of a ligandomics identification run."
)
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)
if args.output_dir is not None:
try:
os.chdir(args.output_dir)
logging.basicConfig(filename=os.path.join(
args.output_dir, '{}_prediction.log'.format(args.identifier)),
filemode='w+',
level=logging.DEBUG)
logging.info("Using provided data directory: {}".format(
str(args.output_dir)))
except:
logging.info("No such directory, using current.")
else:
logging.basicConfig(filename='{}_prediction.log'.format(
args.identifier),
filemode='w+',
level=logging.DEBUG)
logging.info("Using current data directory.")
logging.info("Starting predictions at " +
str(datetime.now().strftime("%Y-%m-%d %H:%M:%S")))
metadata = []
references = {
'GRCh37': 'http://feb2014.archive.ensembl.org',
'GRCh38': 'http://dec2016.archive.ensembl.org'
}
global transcriptProteinMap
global transcriptSwissProtMap
'''read in variants or peptides'''
if args.peptides:
peptides, metadata = read_peptide_input(args.peptides)
else:
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)
transcripts = list(set(transcripts))
transcriptProteinMap, transcriptSwissProtMap = get_protein_ids_for_transcripts(
ID_SYSTEM_USED, transcripts, references[args.reference],
args.reference)
# get the alleles
alleles = FileReader.read_lines(args.alleles, in_type=Allele)
# initialize MartsAdapter, GRCh37 or GRCh38 based
ma = MartsAdapter(biomart=references[args.reference])
# create protein db instance for filtering self-peptides
up_db = UniProtDB('sp')
if args.filter_self:
logging.info('Reading human proteome')
if os.path.isdir(args.reference_proteome):
for filename in os.listdir(args.reference_proteome):
if filename.endswith(".fasta") or filename.endswith(".fsa"):
up_db.read_seqs(
os.path.join(args.reference_proteome, filename))
else:
up_db.read_seqs(args.reference_proteome)
# MHC class I or II predictions
if args.mhcclass == "I":
#methods = ['netmhc-4.0', 'syfpeithi-1.0', 'netmhcpan-3.0']
methods = ['syfpeithi-1.0']
if args.peptides:
pred_dataframes, statistics = make_predictions_from_peptides(
peptides, methods, alleles, up_db, args.identifier, metadata)
else:
pred_dataframes, statistics, all_peptides_filtered = make_predictions_from_variants(
vl, methods, alleles, 8,
int(args.length) + 1, ma, up_db, args.identifier, metadata,
transcriptProteinMap)
else:
methods = ['netmhcII-2.2', 'syfpeithi-1.0', 'netmhcIIpan-3.1']
if args.peptides:
pred_dataframes, statistics = make_predictions_from_peptides(
peptides, methods, alleles, up_db, args.identifier, metadata)
else:
pred_dataframes, statistics, all_peptides_filtered = make_predictions_from_variants(
vl, methods, alleles, 15,
int(args.length) + 1, ma, up_db, args.identifier, metadata,
transcriptProteinMap)
# concat dataframes for all peptide lengths
try:
complete_df = pd.concat(pred_dataframes)
except:
complete_df = pd.DataFrame()
logging.error("No predictions available.")
# store version of used methods
method_map = {}
for m in methods:
method_map[m.split('-')[0]] = m
# replace method names with method names with version
complete_df.replace({'method': method_map}, inplace=True)
# include wild type sequences to dataframe if specified
if args.wild_type:
wt_sequences = generate_wt_seqs(all_peptides_filtered)
complete_df['wt sequence'] = complete_df.apply(
lambda row: create_wt_seq_column_value(row, wt_sequences), axis=1)
columns_tiles = [
'sequence', 'wt sequence', 'length', 'chr', 'pos', 'gene',
'transcripts', 'proteins', 'variant type', 'method'
]
# Change the order (the index) of the columns
else:
columns_tiles = [
'sequence', 'length', 'chr', 'pos', 'gene', 'transcripts',
'proteins', 'variant type', 'method'
]
for c in complete_df.columns:
if c not in columns_tiles:
columns_tiles.append(c)
complete_df = complete_df.reindex(columns=columns_tiles)
binder_cols = [col for col in complete_df.columns if 'binder' in col]
binders = []
non_binders = []
pos_predictions = []
neg_predictions = []
for i, r in complete_df.iterrows():
binder = False
for c in binder_cols:
if r[c] is True:
binder = True
continue
if binder:
binders.append(str(r['sequence']))
pos_predictions.append(str(r['sequence']))
else:
neg_predictions.append(str(r['sequence']))
if str(r['sequence']) not in binders:
non_binders.append(str(r['sequence']))
# parse protein quantification results, annotate proteins for samples
if args.protein_quantification is not None:
protein_quant = read_protein_quant(args.protein_quantification)
first_entry = protein_quant[protein_quant.keys()[0]]
for k in first_entry.keys():
complete_df['{} log2 protein LFQ intensity'.format(
k)] = complete_df.apply(
lambda row: create_quant_column_value_for_result(
row, protein_quant, transcriptSwissProtMap, k),
axis=1)
# parse (differential) expression analysis results, annotate features (genes/transcripts)
if args.gene_expression is not None:
fold_changes = read_diff_expression_values(args.gene_expression)
gene_id_lengths = {}
col_name = 'RNA expression (RPKM)'
with open(args.gene_reference, 'r') as gene_list:
for l in gene_list:
ids = l.split('\t')
gene_id_in_df = complete_df.iloc[1]['gene']
if 'ENSG' in gene_id_in_df:
gene_id_lengths[ids[0]] = float(ids[2].strip())
else:
gene_id_lengths[ids[1]] = float(ids[2].strip())
deseq = False
# add column to result dataframe
complete_df[col_name] = complete_df.apply(
lambda row: create_expression_column_value_for_result(
row, fold_changes, deseq, gene_id_lengths),
axis=1)
if args.diff_gene_expression is not None:
gene_id_lengths = {}
fold_changes = read_diff_expression_values(args.diff_gene_expression)
col_name = 'RNA normal_vs_tumor.log2FoldChange'
deseq = True
# add column to result dataframe
complete_df[col_name] = complete_df.apply(
lambda row: create_expression_column_value_for_result(
row, fold_changes, deseq, gene_id_lengths),
axis=1)
# parse ligandomics identification results, annotate peptides for samples
if args.ligandomics_id is not None:
lig_id = read_lig_ID_values(args.ligandomics_id)
# add columns to result dataframe
complete_df['ligand score'] = complete_df.apply(
lambda row: create_ligandomics_column_value_for_result(
row, lig_id, 0, False),
axis=1)
complete_df['ligand intensity'] = complete_df.apply(
lambda row: create_ligandomics_column_value_for_result(
row, lig_id, 1, False),
axis=1)
if args.wild_type != None:
complete_df['wt ligand score'] = complete_df.apply(
lambda row: create_ligandomics_column_value_for_result(
row, lig_id, 0, True),
axis=1)
complete_df['wt ligand intensity'] = complete_df.apply(
lambda row: create_ligandomics_column_value_for_result(
row, lig_id, 1, True),
axis=1)
# write dataframe to tsv
complete_df.fillna('')
complete_df.to_csv("{}_prediction_results.tsv".format(args.identifier),
'\t',
index=False)
statistics['number_of_predictions'] = complete_df.shape[0]
statistics['number_of_binders'] = len(pos_predictions)
statistics['number_of_nonbinders'] = len(neg_predictions)
statistics['number_of_unique_binders'] = list(set(binders))
statistics['number_of_unique_nonbinders'] = list(
set(non_binders) - set(binders))
with open('{}_report.json'.format(args.identifier), 'w') as json_out:
json.dump(statistics, json_out)
def main():
parser = argparse.ArgumentParser(description="Reads protein or peptide sequences and predicts peptides "+
"for a specified prediction method and HLA alleles.")
parser.add_argument("-i", "--input",
nargs="+",
required=True,
help="Input data can be RefSeq ID, UniProt ID, fasta file, peptide file (one peptide per line),"
+" or peptide sequences as sequences (max 50)"
)
input_types = parser.add_mutually_exclusive_group(required=True)
input_types.add_argument("-p","--protein",
action="store_true",
help= "Specifies if IDs are protein IDs")
input_types.add_argument("-r","--rna",
action="store_true",
help= "Specifies the input as rna IDs")
input_types.add_argument("-f","--fasta",
action="store_true",
help= "Specifies the input as protein (multi-)Fasta file")
parser.add_argument("-a", "--alleles",
nargs="+",
required=True,
help="Specifies for which alleles prediction should be made. " +
"Input either can be alleles as string (new nomenclature), or a file with one allele per line.")
allele_types = parser.add_mutually_exclusive_group(required=True)
allele_types.add_argument("-af", "--allelefile",
action="store_true",
help="Specifies the allele input as allele file.")
allele_types.add_argument("-as", "--allelestring",
action="store_true",
help="Specifies the allele input as allele string.")
parser.add_argument("-m", "--method",
required=True,
nargs="+",
help="Specifies the method used for prediction.")
parser.add_argument("-l", "--length",
required=False,
type=int,
default=9,
help="Specifies the length of the peptides (default=9).")
parser.add_argument("-o", "--output",
required=True,
help="Specifies the output path. Results will be written to CSV")
parser.add_argument("-am", "--available",
required=False,
action="store_true",
help="Returns all available methods and their allele models.")
#COMMENT: These options are hidden and only used for ETK2
parser.add_argument("-html", "--html",
required=False,
action="store_true",
help=argparse.SUPPRESS)
parser.add_argument("-od", "--outdir",
required=False,
default="",
help=argparse.SUPPRESS)
args = parser.parse_args()
if args.available:
for pred, obj in AEpitopePrediction.registry.iteritems():
if pred not in ["AEpitopePrediction", "APSSMEpitopePredictor", "ANetMHC", "ASVMEpitopePrediction"]:
print "Method: ",pred
print "Supported Alleles: ", " ".join(getattr(obj, "_"+pred+"__alleles" ))
print "Supported Length: ", " ".join(map(str, getattr(obj, "_"+pred+"__supported_length")))
print
sys.exit(0)
mart = MartsAdapter()
#RefSeq
transcripts = []
if args.protein:
for pid in args.input:
ids = mart.get_transcript_information_from_protein_id(pid)
#UniProt
elif args.uniprot:
pass
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_MartsAdapter(self):
ma = MartsAdapter(biomart="http://grch37.ensembl.org")
self.assertEqual((1515, 1529), ma.get_transcript_position('ENST00000361221', '17953929', '17953943', type=EIdentifierTypes.ENSEMBL))
self.assertIsNone(ma.get_transcript_position("ENST00000614237", 7566927, 7566927, type=EIdentifierTypes.ENSEMBL))
#logging.captureWarnings(True)
#result = ma.get_transcript_position("ENST00000614237", 7566927, 7566927, type=EIdentifierTypes.ENSEMBL)
self.assertEqual("TP53", ma.get_gene_by_position(17, 7566927, 7566927))
self.assertIsNone(ma.get_product_sequence("Q15942", type=EIdentifierTypes.UNIPROT))
self.assertEqual(self.NP_001005353, ma.get_product_sequence("NP_001005353", type=EIdentifierTypes.REFSEQ))
self.assertEqual(self.ENSP00000369497, ma.get_product_sequence("ENSP00000369497", type=EIdentifierTypes.ENSEMBL))
self.assertEqual(self.ENST00000361221[2], ma.get_transcript_sequence('ENST00000361221', type=EIdentifierTypes.ENSEMBL))
self.assertIsNone(ma.get_transcript_sequence("ENST00000614237", type=EIdentifierTypes.ENSEMBL))
self.assertDictEqual(self.ENST00000361221, ma.get_transcript_information('ENST00000361221', type=EIdentifierTypes.ENSEMBL))
self.assertIsNone(ma.get_transcript_information("ENST00000614237", type=EIdentifierTypes.ENSEMBL))
self.assertEqual(str(ma.get_ensembl_ids_from_id('TP53', type=EIdentifierTypes.GENENAME)), "[{0: 'ENSG00000141510', 1: '-', 3: 'ENST00000413465', 4: 'ENSP00000410739'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000359597', 4: 'ENSP00000352610'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000504290', 4: ''}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000510385', 4: ''}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000504937', 4: ''}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000269305', 4: 'ENSP00000269305'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000455263', 4: 'ENSP00000398846'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000420246', 4: 'ENSP00000391127'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000445888', 4: 'ENSP00000391478'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000576024', 4: 'ENSP00000458393'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000509690', 4: 'ENSP00000425104'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000514944', 4: 'ENSP00000423862'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000574684', 4: ''}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000505014', 4: ''}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000508793', 4: 'ENSP00000424104'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000604348', 4: 'ENSP00000473895'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000503591', 4: 'ENSP00000426252'}, {0: 'LRG_321', 1: '+', 3: 'LRG_321t8', 4: 'LRG_321p8'}, {0: 'LRG_321', 1: '+', 3: 'LRG_321t7', 4: 'LRG_321p13'}, {0: 'LRG_321', 1: '+', 3: 'LRG_321t6', 4: 'LRG_321p12'}, {0: 'LRG_321', 1: '+', 3: 'LRG_321t5', 4: 'LRG_321p11'}, {0: 'LRG_321', 1: '+', 3: 'LRG_321t4', 4: 'LRG_321p10'}, {0: 'LRG_321', 1: '+', 3: 'LRG_321t3', 4: 'LRG_321p3'}, {0: 'LRG_321', 1: '+', 3: 'LRG_321t2', 4: 'LRG_321p2'}, {0: 'LRG_321', 1: '+', 3: 'LRG_321t1', 4: 'LRG_321p1'}]")
def test_MartsAdapter(self):
ma = MartsAdapter(biomart="http://grch37.ensembl.org")
self.assertEqual(
(1515, 1529),
ma.get_transcript_position('ENST00000361221',
'17953929',
'17953943',
type=EIdentifierTypes.ENSEMBL))
self.assertIsNone(
ma.get_transcript_position("ENST00000614237",
7566927,
7566927,
type=EIdentifierTypes.ENSEMBL))
#logging.captureWarnings(True)
#result = ma.get_transcript_position("ENST00000614237", 7566927, 7566927, type=EIdentifierTypes.ENSEMBL)
self.assertEqual("TP53", ma.get_gene_by_position(17, 7566927, 7566927))
self.assertIsNone(
ma.get_product_sequence("Q15942", type=EIdentifierTypes.UNIPROT))
self.assertEqual(
self.NP_001005353,
ma.get_product_sequence("NP_001005353",
type=EIdentifierTypes.REFSEQ))
self.assertEqual(
self.ENSP00000369497,
ma.get_product_sequence("ENSP00000369497",
type=EIdentifierTypes.ENSEMBL))
self.assertEqual(
self.ENST00000361221[2],
ma.get_transcript_sequence('ENST00000361221',
type=EIdentifierTypes.ENSEMBL))
self.assertIsNone(
ma.get_transcript_sequence("ENST00000614237",
type=EIdentifierTypes.ENSEMBL))
self.assertDictEqual(
self.ENST00000361221,
ma.get_transcript_information('ENST00000361221',
type=EIdentifierTypes.ENSEMBL))
self.assertIsNone(
ma.get_transcript_information("ENST00000614237",
type=EIdentifierTypes.ENSEMBL))
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_MartsAdapter(self):
ma = MartsAdapter(biomart="http://grch37.ensembl.org")
self.assertEqual((1515, 1529), ma.get_transcript_position('ENST00000361221', '17953929', '17953943', type=EIdentifierTypes.ENSEMBL))
self.assertIsNone(ma.get_transcript_position("ENST00000614237", 7566927, 7566927, type=EIdentifierTypes.ENSEMBL))
#logging.captureWarnings(True)
#result = ma.get_transcript_position("ENST00000614237", 7566927, 7566927, type=EIdentifierTypes.ENSEMBL)
self.assertEqual("TP53", ma.get_gene_by_position(17, 7566927, 7566927))
self.assertIsNone(ma.get_product_sequence("Q15942", type=EIdentifierTypes.UNIPROT))
self.assertEqual(self.NP_001005353, ma.get_product_sequence("NP_001005353", type=EIdentifierTypes.REFSEQ))
self.assertEqual(self.ENSP00000369497, ma.get_product_sequence("ENSP00000369497", type=EIdentifierTypes.ENSEMBL))
self.assertEqual(self.ENST00000361221[2], ma.get_transcript_sequence('ENST00000361221', type=EIdentifierTypes.ENSEMBL))
self.assertIsNone(ma.get_transcript_sequence("ENST00000614237", type=EIdentifierTypes.ENSEMBL))
self.assertDictEqual(self.ENST00000361221, ma.get_transcript_information('ENST00000361221', type=EIdentifierTypes.ENSEMBL))
self.assertIsNone(ma.get_transcript_information("ENST00000614237", type=EIdentifierTypes.ENSEMBL))
def test_MartsAdapter(self):
ma = MartsAdapter(biomart="http://grch37.ensembl.org")
self.assertEqual(
(1515, 1529),
ma.get_transcript_position('ENST00000361221',
'17953929',
'17953943',
type=EIdentifierTypes.ENSEMBL))
self.assertIsNone(
ma.get_transcript_position("ENST00000614237",
7566927,
7566927,
type=EIdentifierTypes.ENSEMBL))
#logging.captureWarnings(True)
#result = ma.get_transcript_position("ENST00000614237", 7566927, 7566927, type=EIdentifierTypes.ENSEMBL)
self.assertEqual("TP53", ma.get_gene_by_position(17, 7566927, 7566927))
self.assertIsNone(
ma.get_product_sequence("Q15942", type=EIdentifierTypes.UNIPROT))
self.assertEqual(
self.NP_001005353,
ma.get_product_sequence("NP_001005353",
type=EIdentifierTypes.REFSEQ))
self.assertEqual(
self.ENSP00000369497,
ma.get_product_sequence("ENSP00000369497",
type=EIdentifierTypes.ENSEMBL))
self.assertEqual(
self.ENST00000361221[2],
ma.get_transcript_sequence('ENST00000361221',
type=EIdentifierTypes.ENSEMBL))
self.assertIsNone(
ma.get_transcript_sequence("ENST00000614237",
type=EIdentifierTypes.ENSEMBL))
self.assertDictEqual(
self.ENST00000361221,
ma.get_transcript_information('ENST00000361221',
type=EIdentifierTypes.ENSEMBL))
self.assertIsNone(
ma.get_transcript_information("ENST00000614237",
type=EIdentifierTypes.ENSEMBL))
self.assertEqual(
str(
ma.get_ensembl_ids_from_id('TP53',
type=EIdentifierTypes.GENENAME)),
"[{0: 'ENSG00000141510', 1: '-', 3: 'ENST00000413465', 4: 'ENSP00000410739'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000359597', 4: 'ENSP00000352610'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000504290', 4: ''}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000510385', 4: ''}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000504937', 4: ''}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000269305', 4: 'ENSP00000269305'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000455263', 4: 'ENSP00000398846'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000420246', 4: 'ENSP00000391127'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000445888', 4: 'ENSP00000391478'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000576024', 4: 'ENSP00000458393'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000509690', 4: 'ENSP00000425104'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000514944', 4: 'ENSP00000423862'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000574684', 4: ''}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000505014', 4: ''}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000508793', 4: 'ENSP00000424104'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000604348', 4: 'ENSP00000473895'}, {0: 'ENSG00000141510', 1: '-', 3: 'ENST00000503591', 4: 'ENSP00000426252'}, {0: 'LRG_321', 1: '+', 3: 'LRG_321t8', 4: 'LRG_321p8'}, {0: 'LRG_321', 1: '+', 3: 'LRG_321t7', 4: 'LRG_321p13'}, {0: 'LRG_321', 1: '+', 3: 'LRG_321t6', 4: 'LRG_321p12'}, {0: 'LRG_321', 1: '+', 3: 'LRG_321t5', 4: 'LRG_321p11'}, {0: 'LRG_321', 1: '+', 3: 'LRG_321t4', 4: 'LRG_321p10'}, {0: 'LRG_321', 1: '+', 3: 'LRG_321t3', 4: 'LRG_321p3'}, {0: 'LRG_321', 1: '+', 3: 'LRG_321t2', 4: 'LRG_321p2'}, {0: 'LRG_321', 1: '+', 3: 'LRG_321t1', 4: 'LRG_321p1'}]"
)
