public.general¶
canceljobs.py¶
Call scancel to cancel a consecutive set of cluster job numbers
usage: canceljobs.py [-h]
convert_fig.py¶
Converts images to TIFF figures at 300 DPI for publication using sips. Arguments: INFILE OUTFILE
usage: convert_fig.py [-h]
genscript_to_fasta.py¶
This script outputs fasta files from a genscript format. Pass the –format option to control which genscript format as input ~~~ Ex: python genscript_mut_to_fasta.py –format mutagenesis MutagenesisFormatU68 ~~~
usage: genscript_to_fasta.py [-h] --format {mutagenesis,GeneSynth} infile
Positional Arguments¶
infile | The mutagenesis format file. |
Named Arguments¶
--format | Possible choices: mutagenesis, GeneSynth The genscript file format |
get_seq.py¶
Uses Biopython to print sequence information. Example: get_seq.py –pdb 2j88_A.pdb –format fasta –outpath test.txt
usage: get_seq.py [-h] [--pdb PDB] [--pdblist PDBLIST]
[--pdblist_input_dir PDBLIST_INPUT_DIR] [--chain CHAIN]
[--cdr CDR]
[--format {basic,fasta,general_order,IgG_order,IgG_order_lambda,IgG_order_kappa,IgG_order_heavy}]
[--outpath OUTPATH] [--prefix PREFIX] [--region REGION]
[--strip_c_term STRIP_C_TERM] [--pad_c_term PAD_C_TERM]
[--output_original_seq]
Named Arguments¶
--pdb, -s | Input PDB path |
--pdblist, -l | Input PDB List |
--pdblist_input_dir, -i | |
Input directory if needed for PDB list | |
--chain, -c | A specific chain to output Default: “” |
--cdr | Pass a specific CDR to output alignments of. Default: “” |
--format | Possible choices: basic, fasta, general_order, IgG_order, IgG_order_lambda, IgG_order_kappa, IgG_order_heavy The output format requried. Default: “fasta” |
--outpath, -o | Output path. If none is specified it will write to screen. |
--prefix, -t | Tag to add before chain Default: “” |
--region | specify a particular region, start:end:chain |
--strip_c_term | Strip this sequence off the C-term of resulting sequences. (Useful for antibodies |
--pad_c_term | Pad this sequence with some C-term (Useful for antibodies |
--output_original_seq | |
Output the original sequence and the striped seqeunce if stripped. Default FALSE. Default: False |
rename_designs.py¶
Renames original files to new names for design ordering. Copy all models going to be ordered into a single directory first. Run from directory with pdb files already copied in!
usage: rename_designs.py [-h] -i NEW_NAMES
Named Arguments¶
-i, --new_names | |
File with new to old names. Example line: new_name * filename. Can have lines that don’t have all three. Will only rename if it has a star in the second column. |