search

IdoSpringer / ERGO-II

ERGO-II, an updated version of ERGO including more features for TCR-peptide binding prediction
MIT License
29 stars 6 forks source link

Error with "Bad input-file, please choose a different input file" #11

Open wu-yc opened 2 years ago

wu-yc commented 2 years ago

Dear Springer,

Thanks for developing this fantastic package. It is really useful.

When I used the web server, it says "Bad input-file, please choose a different input file". Here is my test csv file,

TRA,TRB,TRAV,TRAJ,TRBV,TRBJ,T-Cell-Type,Peptide,MHC ,CASGAQGTNTEAFF,,,TRBV5-4,TRBJ1-1,CD8,KLLPENNVL,HLA-B08 CAAGYFTGGGNKLTF,,TRAV23/DV6,TRAJ10,,,CD8,KLLPENNVL,HLA-B08 CAVSYSGYSTLTF,,TRAV1-2,TRAJ11,,,CD8,KLLPENNVL,HLA-B08 ,CSAVDTTSSTDTQYF,,,TRBV20-1,TRBJ2-3,CD8,KLLPENNVL,HLA-B08 CAVRPRGTGGFKTIF,,TRAV1-1,TRAJ9,,,CD8,KLLPENNVL,HLA-B08 ,CASSQAQGGYEQYF,,,TRBV14,TRBJ2-7,CD8,KLLPENNVL,HLA-B08 ,CASSLTDNSYEQYF,,,TRBV11-2,TRBJ2-7,CD8,KLLPENNVL,HLA-B08 CLVGGGYSGSARQLTF,,TRAV4,TRAJ22,,,CD8,KLLPENNVL,HLA-B08 CAENGGISSGSARQLTF,,TRAV13-2,TRAJ22,,,CD8,KLLPENNVL,HLA-B08 CAMRPSGGYQKVTF,,TRAV14/DV4,TRAJ13,,,CD8,KLLPENNVL,HLA-B08 ,CASSLDRNLDTGELFF,,,TRBV11-2,TRBJ2-2,CD8,KLLPENNVL,HLA-B08 CAMRLLYNFNKFYF,,TRAV14/DV4,TRAJ21,,,CD8,KLLPENNVL,HLA-B08 ,CASSKRQQVNEQFF,,,TRBV19,TRBJ2-1,CD8,KLLPENNVL,HLA-B08 ,CASSLVLGATGELSF,,,TRBV13,TRBJ2-2,CD8,KLLPENNVL,HLA-B08 CATDALAAGNKLTF,,TRAV17,TRAJ17,,,CD8,KLLPENNVL,HLA-B08 ,CASSFARGRADTQYN,,,TRBV28,TRBJ2-3,CD8,KLLPENNVL,HLA-B08 CAGRASGTSYGKLTF,,TRAV35,TRAJ52,,,CD8,KLLPENNVL,HLA-B08 CALTRANSKLTF,,TRAV9-2,TRAJ56,,,CD8,KLLPENNVL,HLA-B08 CAASPNTGNQFYF,,TRAV29/DV5,TRAJ49,,,CD8,KLLPENNVL,HLA-B08 ,CASSLSGGGHGYTF,,,TRBV28,TRBJ1-2,CD8,KLLPENNVL,HLA-B08 CAMRENHRDDKIIF,,TRAV14/DV4,TRAJ30,,,CD8,KLLPENNVL,HLA-B08 ,CACDEWGVSTDKLIF,,,TRDV2,TRDJ1,CD8,KLLPENNVL,HLA-B08 ,CSAPITGSYEQYF,,,TRBV20-1,TRBJ2-7,CD8,KLLPENNVL,HLA-B08 CAASPSMNRQLTF,,TRAV23/DV6,TRAJ22,,,CD8,KLLPENNVL,HLA-B08 ,CASSLLPGHLTDPGGEQYF,,,TRBV7-2,TRBJ2-7,CD8,KLLPENNVL,HLA-B08 CALSDELTGANNLFF,,TRAV9-2,TRAJ36,,,CD8,KLLPENNVL,HLA-B08

Would you kindly tell what's going wrong?

Best, Yingcheng

IdoSpringer commented 2 years ago

Hi, notice that ERGO-II always includes the TCR beta sequence, hence it must be supplied in each row. see here: https://tcr2.cs.biu.ac.il/help