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About Proprecess data #12
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Hi,you need to generate pssm features by PSI-Blast and intrinsic features by IUPred with your own data. |
Hi, twopin
Thanks, |
I seem to output an empty raw_score_dict, why is this happening? The following is one of the files output by my IUPred. Is there any problem with this file?
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hi, here are two of the results I got when I wrote these codes 1 years ago (I'm not sure if the output format changes recently). The fasta names for each sequence can be changed according to the input fasta files. |
Hi, Thanks for your reply, let me have solved this problem, there is still a small question, for this piece of code:
Here will report an error |
Hi, I encountered another troubles in preprocess_features.py, the following is my error:
I guess the
How can I solve this problem? look forward to your reply. |
It seems that the key 'MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFYLKMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGDEGDAGEGEN' is not in the dict? Actually I'm not sure about that, you can use the debug function to check. |
#12 (comment): Yes |
So
The following is my
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I think this bug is due to the naming of variable seq_ss_set twice. I just fixed the bug and revised the script. |
Hi,
According to Data curation, I need to format the peptide-protein data like "
protein sequence, peptide sequence, protein_ss, peptide_ss
", but in fact preprocess_features.py needs me to provide theProtein_pssm_dict, Protein_Intrinsic_dict and Peptide_Intrinsic_dict_v3
files, if I understand correctly.I can get pssm_dict according to step3_generate_features.py, but what are the next two files?
Thanks,
LeeLee
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