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.