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Update primedesign.py #7

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6 changes: 3 additions & 3 deletions PrimeDesign/command_line/primedesign.py
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Original file line number Diff line number Diff line change
Expand Up @@ -54,8 +54,8 @@
# parser.add_argument('-pe_format', '--pe_format', type = str, default = 'NNNNNNNNNNNNNNNNN/NNN[NGG]', help = "***** Prime editing formatting including the spacer, cut index -> /, and protospacer adjacent motif (PAM) -> [PAM] (Default: NNNNNNNNNNNNNNNNN/NNN[NGG]). Examples: NNNNNNNNNNNNNNNNN/NNN[NGG], NNNNNNNNNNNNNNNNN/NNN[NG] *****\n\n")
parser.add_argument('-pbs', '--pbs_length_list', type = int, default = 0, nargs = '+', help = '***** List of primer binding site (PBS) lengths for the pegRNA extension (Default: 10 to 16 nt). Example: 12 13 14 15 *****\n\n')
parser.add_argument('-rtt', '--rtt_length_list', type = int, default = 0, nargs = '+', help = '***** List of reverse transcription (RT) template lengths for the pegRNA extension (Default: 10 to 16 nt). Example: 10 15 20 *****\n')
parser.add_argument('-nick_dist_min', '--nicking_distance_minimum', type = int, default = 0, nargs = '+', help = '***** Minimum nicking distance for designing ngRNAs upstream and downstream of a pegRNA (Default: 0). *****\n\n')
parser.add_argument('-nick_dist_max', '--nicking_distance_maximum', type = int, default = 120, nargs = '+', help = '***** Maximum nicking distance for designing ngRNAs upstream and downstream of a pegRNA (Default: 100). *****\n\n')
parser.add_argument('-nick_dist_min', '--nicking_distance_minimum', type = int, default = 0, nargs = '?', help = '***** Minimum nicking distance for designing ngRNAs upstream and downstream of a pegRNA (Default: 0). *****\n\n')
parser.add_argument('-nick_dist_max', '--nicking_distance_maximum', type = int, default = 120, nargs = '?', help = '***** Maximum nicking distance for designing ngRNAs upstream and downstream of a pegRNA (Default: 100). *****\n\n')
parser.add_argument('-filter_c1', '--filter_c1_extension', action='store_true', help = '***** Option to filter against pegRNA extensions that start with a C base. *****\n\n')
parser.add_argument('-filter_homopolymer_ts', '--filter_homopolymer_ts', action='store_true', help = '***** Option to filter out spacer sequences with homopolymer Ts (>3). *****\n\n')
parser.add_argument('-silent_mut', '--silent_mutation', action='store_true', help = '***** Introduce silent mutation into PAM assuming sequence is in-frame. Currently only available with SpCas9 PE (Default: N). *****\n\n')
Expand Down Expand Up @@ -1803,4 +1803,4 @@ def saturating_mutagenesis_input_sequences(target_name, target_sequence, sm_type

f.write(','.join(map(str, [target_name, target_design[target_name]['target_sequence'], counter, 'ngRNA', ng_spacer_sequence_edit, spacer_gc_content, ng_pam_edit, '', ng_strand, ng_annotate, '', ng_nick_ref_idx, nick_distance, '', '', '', '', '', spacer_oligo_top, spacer_oligo_bottom, '', ''])) + '\n')

counter += 1
counter += 1