search

openvax / topiary

Predict mutated T-cell epitopes from sequencing data
Apache License 2.0
27 stars 9 forks source link

'Namespace' object has no attribute 'rna_gene_fpkm_file' #59

Closed cedarice closed 7 years ago

cedarice commented 8 years ago

Hey guys, My command line input:

topiary --vcf Hep-3B2.FilterOut1000G.vcf --mhc-predictor netmhcpan --mhc-alleles HLA-A_74:01,HLA-A_68:02 --ic50-cutoff 500 --percentile-cutoff 2.0 --mhc-epitope-length 8-11 --rna-gene-fpkm-tracking-file genes.fpkm_tracking --rna-min-gene-expression 4.0 --rna-transcript-fpkm-tracking-file isoforms.fpkm_tracking --rna-min-transcript-expression 1.5 --output-csv Hep-3B2.epitopes.csv --output-html Hep-3B2.epitope.html --rna-transcript-fpkm-gtf-file transcripts.gtf

But get the following errors: Topiary commandline arguments: Namespace(ic50_cutoff=500.0, json_variant_files=[], maf=[], mhc_alleles='HLA-A_74:01,HLA-A_68:02', mhc_alleles_file=None, mhc_epitope_lengths=[8, 9, 10, 11], mhc_predictor='netmhcpan', only_novel_epitopes=False, output_csv='Hep-3B2.epitopes.csv', output_csv_sep=',', output_html='Hep-3B2.epitope.html', padding_around_mutation=None, percentile_cutoff=2.0, print_columns=False, reference_name=None, rename_output_column=None, rna_gene_fpkm_tracking_file='genes.fpkm_tracking', rna_min_gene_expression=4.0, rna_min_transcript_expression=1.5, rna_transcript_fpkm_gtf_file='transcripts.gtf', rna_transcript_fpkm_tracking_file='isoforms.fpkm_tracking', skip_variant_errors=False, subset_output_columns=None, variant=[], vcf=['Hep-3B2.FilterOut1000G.vcf'], wildtype_ligandome_directory=None) INFO:root:Building MHC binding prediction type for alleles ['HLA-A_74:01', 'HLA-A_68:02'] and epitope lengths [8, 9, 10, 11] INFO:root:Skipping allele SLA-1-CHANGDA: Malformed MHC type 1 INFO:root:Skipping allele SLA-1-HB01: Malformed MHC type 1 INFO:root:Skipping allele SLA-1-HB02: Malformed MHC type 1 INFO:root:Skipping allele SLA-1-HB03: Malformed MHC type 1 INFO:root:Skipping allele SLA-1-HB04: Malformed MHC type 1 INFO:root:Skipping allele SLA-1-LWH: Malformed MHC type 1 INFO:root:Skipping allele SLA-1-TPK: Malformed MHC type 1 INFO:root:Skipping allele SLA-1-YC: Malformed MHC type 1 INFO:root:Skipping allele SLA-1-YDL01: Malformed MHC type 1 INFO:root:Skipping allele SLA-1-YTH: Malformed MHC type 1 INFO:root:Skipping allele SLA-2-YDL02: Malformed MHC type 2 INFO:root:Skipping allele SLA-3-CDY: Malformed MHC type 3 INFO:root:Skipping allele SLA-3-HB01: Malformed MHC type 3 INFO:root:Skipping allele SLA-3-LWH: Malformed MHC type 3 INFO:root:Skipping allele SLA-3-TPK: Malformed MHC type 3 INFO:root:Skipping allele SLA-3-YC: Malformed MHC type 3 INFO:root:Skipping allele SLA-3-YDL: Malformed MHC type 3 INFO:root:Skipping allele SLA-3-YDY01: Malformed MHC type 3 INFO:root:Skipping allele SLA-3-YDY02: Malformed MHC type 3 INFO:root:Skipping allele SLA-3-YTH: Malformed MHC type 3 INFO:root:Skipping allele H-2-Qa2: Malformed mouse MHC allele: H-2-Qa2, parse error at a2 INFO:root:Skipping allele H-2-Qa1: Malformed mouse MHC allele: H-2-Qa1, parse error at a1 Traceback (most recent call last): File "/home/qianlab/soft/topiary/ENV/bin/topiary", line 4, in import('pkg_resources').run_script('topiary==0.0.20', 'topiary') File "/home/qianlab/soft/topiary/ENV/local/lib/python2.7/site-packages/pkg_resources/init.py", line 719, in run_script self.require(requires)[0].run_script(script_name, ns) File "/home/qianlab/soft/topiary/ENV/local/lib/python2.7/site-packages/pkg_resources/init.py", line 1504, in run_script exec(code, namespace, namespace) File "/home/qianlab/soft/topiary/ENV/lib/python2.7/site-packages/topiary-0.0.20-py2.7.egg/EGG-INFO/scripts/topiary", line 58, in main(args) File "/home/qianlab/soft/topiary/ENV/lib/python2.7/site-packages/topiary-0.0.20-py2.7.egg/EGG-INFO/scripts/topiary", line 43, in main epitopes = predict_epitopes_from_args(args) File "/home/qianlab/soft/topiary/ENV/local/lib/python2.7/site-packages/topiary-0.0.20-py2.7.egg/topiary/predict_epitopes.py", line 277, in predict_epitopes_from_args gene_expression_dict = rna_gene_expression_dict_from_args(args) File "/home/qianlab/soft/topiary/ENV/local/lib/python2.7/site-packages/topiary-0.0.20-py2.7.egg/topiary/commandline_args/rna.py", line 72, in rna_gene_expression_dict_from_args return load_cufflinks_fpkm_dict(args.rna_gene_fpkm_file) AttributeError: 'Namespace' object has no attribute 'rna_gene_fpkm_file'

Any ideas?

iskandr commented 8 years ago

Looks like there was a small typo in parsing of RNA args, should be fixed by: https://github.com/hammerlab/topiary/commit/8a63a0fafe54d1561c1af52468db57ac7f5b440b -- let me know if that works!

cedarice commented 8 years ago

It works, thank you!