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mmagnus / rna-tools

🔧rna-tools: a toolbox to analyze sequences, structures and simulations of RNA (and more) used by RNA CASP, RNA PUZZLES, and me ;-) docs @ http://rna-tools.rtfd.io web @ http://rna-tools.online
http://rna-tools.online
GNU General Public License v3.0
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a new format for rna_pdb_toolsx.py --get-seq #100

Closed mmagnus closed 4 years ago

mmagnus commented 5 years ago

instead of 

# solution_5iem
> A:1-57
GGGAUCUGUCACCCCAUUGAUCGCCUUCGGGCUGAUCUGGCUGGCUAGGCGGGUCCC
# solution_5lys
> A:24-48 60-87 101-101
GGGAUCUGUCACCCCAUUGAUCGCCGGCUGAUCUGGCUGGCUAGGCGGGUCCcu
> B:24-48 60-87 102-102
GGGAUCUGUCACCCCAUUGAUCGCCGGCUGAUCUGGCUGGCUAGGCGGGUCCcu
# solution_5lyu
> A:23-48 60-87 102-102
GGGGAUCUGUCACCCCAUUGAUCGCCGGCUGAUCUGGCUGGCUAGGCGGGUCCcl
> B:23-48 60-87
GGGGAUCUGUCACCCCAUUGAUCGCCGGCUGAUCUGGCUGGCUAGGCGGGUCCc
# solution_5lyv
> A:24-48 60-86 101-102
GGGAUCUGUCACCCCAUUGAUCGCCGGCUGAUCUGGCUGGCUAGGCGGGUCCcx
> B:24-48 60-86 101-101 103-103
GGGAUCUGUCACCCCAUUGAUCGCCGGCUGAUCUGGCUGGCUAGGCGGGUCCcl

get this

> solution_5iem A:1-57
GGGAUCUGUCACCCCAUUGAUCGCCUUCGGGCUGAUCUGGCUGGCUAGGCGGGUCCC
> solution_5lys A:24-48 60-87 101-101
GGGAUCUGUCACCCCAUUGAUCGCCGGCUGAUCUGGCUGGCUAGGCGGGUCCcu
> solution_5lys B:24-48 60-87 102-102
GGGAUCUGUCACCCCAUUGAUCGCCGGCUGAUCUGGCUGGCUAGGCGGGUCCcu
> solution_5lyu A:23-48 60-87 102-102
GGGGAUCUGUCACCCCAUUGAUCGCCGGCUGAUCUGGCUGGCUAGGCGGGUCCcl
> solution_5lyu B:23-48 60-87
GGGGAUCUGUCACCCCAUUGAUCGCCGGCUGAUCUGGCUGGCUAGGCGGGUCCc
> solution_5lyv A:24-48 60-86 101-102
GGGAUCUGUCACCCCAUUGAUCGCCGGCUGAUCUGGCUGGCUAGGCGGGUCCcx
> solution_5lyv B:24-48 60-86 101-101 103-103
GGGAUCUGUCACCCCAUUGAUCGCCGGCUGAUCUGGCUGGCUAGGCGGGUCCcl
mmagnus commented 4 years ago 
rna_pdb_toolsx.py --get-seq *.pdb --fasta
>solution_5lys.pdb A:24-48 60-87 101-101
GGGAUCUGUCACCCCAUUGAUCGCCGGCUGAUCUGGCUGGCUAGGCGGGUCCcu
>solution_5lys.pdb B:24-48 60-87 102-102
GGGAUCUGUCACCCCAUUGAUCGCCGGCUGAUCUGGCUGGCUAGGCGGGUCCcu
>solution_5lyu.pdb A:23-48 60-87 102-102
GGGGAUCUGUCACCCCAUUGAUCGCCGGCUGAUCUGGCUGGCUAGGCGGGUCCcl
>solution_5lyu.pdb B:23-48 60-87
GGGGAUCUGUCACCCCAUUGAUCGCCGGCUGAUCUGGCUGGCUAGGCGGGUCCc
>solution_5lyv.pdb A:24-48 60-86 101-102
GGGAUCUGUCACCCCAUUGAUCGCCGGCUGAUCUGGCUGGCUAGGCGGGUCCcx
>solution_5lyv.pdb B:24-48 60-86 101-101 103-103
GGGAUCUGUCACCCCAUUGAUCGCCGGCUGAUCUGGCUGGCUAGGCGGGUCCcl