Mercurial > repos > rnateam > graphprot_predict_profile
changeset 4:4ad83aed5c3c draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit 15c382f71f1984aecff67ef9d268b992528996b2"
| author | bgruening |
|---|---|
| date | Thu, 28 Jan 2021 15:06:14 +0000 |
| parents | ace92c9a4653 |
| children | ddcf35a868b8 |
| files | graphprot_predict_wrapper.py |
| diffstat | 1 files changed, 12 insertions(+), 0 deletions(-) [+] |
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--- a/graphprot_predict_wrapper.py Wed Jan 27 19:27:47 2021 +0000 +++ b/graphprot_predict_wrapper.py Thu Jan 28 15:06:14 2021 +0000 @@ -221,6 +221,18 @@ print("# input .fa sequences: %i" % (c_in_fa)) # Read in FASTA sequences to check for uppercase sequences. seqs_dic = gplib.read_fasta_into_dic(args.in_fa) + # Check for lowercase only sequences, which cause GP to crash. + error_mess = "input sequences encountered containing "\ + "only lowercase characters or lowercase characters in between "\ + "uppercase characters. Please provide either all uppercase "\ + "sequences or sequences containing uppercase regions surrounded "\ + "by lowercase context regions for structure calculation (see "\ + "viewpoint concept in original GraphProt publication "\ + "for more details)" + if args.ws_pred: + bad_ids = gplib.check_seqs_dic_format(seqs_dic) + assert not bad_ids, "%s" % (error_mess) + c_uc_nt = gplib.seqs_dic_count_uc_nts(seqs_dic) assert c_uc_nt, "no uppercase nucleotides in input .fa sequences. "\ "Please change sequences to uppercase (keep in mind "\