Merge pull request #11 from edilytics/pooled_mixed_changes

Pooled mixed changes

CRISPResso2/CRISPRessoPooledCORE.py

@@ -303,7 +303,7 @@ def main():
         \nquantification_window_coordinates (OPTIONAL): Bp positions in the amplicon sequence specifying the quantification window. This parameter overrides values of the "--quantification_window_center", "-- cleavage_offset", "--window_around_sgrna" or "-- window_around_sgrna" values. Any indels/substitutions outside this window are excluded. Indexes are 0-based, meaning that the first nucleotide is position 0. Ranges are separated by the dash sign like "start-stop", and multiple ranges can be separated by the underscore (\_). A value of 0 disables this filter. (can be comma-separated list of values, corresponding to amplicon sequences given in --amplicon_seq e.g. 5-10,5-10_20-30 would specify the 5th-10th bp in the first reference and the 5th-10th and 20th-30th bp in the second reference) (default: None)\
         \nquantification_window_size (OPTIONAL): Defines the size (in bp) of the quantification window extending from the position specified by the "--cleavage_offset" or "--quantification_window_center" parameter in relation to the provided guide RNA sequence(s) (--sgRNA). Mutations within this number of bp from the quantification window center are used in classifying reads as modified or unmodified. A value of 0 disables this window and indels in the entire amplicon are considered. Default is 1, 1bp on each side of the cleavage position for a total length of 2bp.\
         \nquantification_window_center (OPTIONAL): Center of quantification window to use within respect to the 3\' end of the provided sgRNA sequence. Remember that the sgRNA sequence must be entered without the PAM. For cleaving nucleases, this is the predicted cleavage position. The default is -3 and is suitable for the Cas9 system. For alternate nucleases, other cleavage offsets may be appropriate, for example, if using Cpf1 this parameter would be set to 1. For base editors, this could be set to -17.', default='')
-        
+
         #tool specific optional
         parser.add_argument('--gene_annotations', type=str, help='Gene Annotation Table from UCSC Genome Browser Tables (http://genome.ucsc.edu/cgi-bin/hgTables?command=start), \
         please select as table "knownGene", as output format "all fields from selected table" and as file returned "gzip compressed"', default='')
@@ -664,7 +664,7 @@ def main():
                     headers.append(match[0])
                 if args.debug and match:
                     info(f'Matching header {head} with {match[0]}.')
-                
+
             if not has_header or has_unmatched_header_el:
                 # Default header
                 headers = []
@@ -842,12 +842,16 @@ def main():
                 crispresso_cmd= args.crispresso_command + ' -r1 %s -a %s %s -o %s --name %s' % (row['Demultiplexed_fastq.gz_filename'], this_amp_seq, this_amp_name_string, OUTPUT_DIRECTORY, idx)
 
                 if n_reads_aligned_amplicons[-1] > args.min_reads_to_use_region:
-                    this_run_args = deepcopy(args)
+                    this_run_args_from_amplicons_file = {}
                     for column_name in default_input_amplicon_headers:
                         if column_name in df_template.columns and row[column_name] and not pd.isnull(row[column_name]):
-                            setattr(this_run_args, column_name, row[column_name])
+                            this_run_args_from_amplicons_file[column_name] = row[column_name]
 
-                    crispresso_cmd = CRISPRessoShared.propagate_crispresso_options(crispresso_cmd, crispresso_options_for_pooled, this_run_args)
+                    #first, set the general CRISPResso options for this sub-run (e.g. plotting options, etc)
+                    #note that the crispresso_options_for_pooled doesn't include e.g. amplicon_seq so when someone calls CRISPRessoPooled with -a that won't get passed on here
+                    crispresso_cmd = CRISPRessoShared.propagate_crispresso_options(crispresso_cmd, crispresso_options_for_pooled, args)
+                    #next set the per-amplicon options we read from the Amplicons file (and are stored in this_run_args_from_amplicons_file)
+                    crispresso_cmd = CRISPRessoShared.propagate_crispresso_options(crispresso_cmd, default_input_amplicon_headers, this_run_args_from_amplicons_file)
 
                     crispresso_cmds.append(crispresso_cmd)
 
@@ -1211,12 +1215,16 @@ def rreplace(s, old, new):
 
                             crispresso_cmd = args.crispresso_command + ' -r1 %s -o %s --name %s' % (fastq_filename_region, OUTPUT_DIRECTORY, idx)
 
-                            this_run_args = deepcopy(args)
+                            this_run_args_from_amplicons_file = {}
                             for column_name in default_input_amplicon_headers:
                                 if column_name in df_template.columns and row[column_name] and not pd.isnull(row[column_name]):
-                                    setattr(this_run_args, column_name, row[column_name])
+                                    this_run_args_from_amplicons_file[column_name] = row[column_name]
 
-                            crispresso_cmd = CRISPRessoShared.propagate_crispresso_options(crispresso_cmd, crispresso_options_for_pooled, this_run_args)
+                            #first, set the general CRISPResso options for this sub-run (e.g. plotting options, etc)
+                            #note that the crispresso_options_for_pooled doesn't include e.g. amplicon_seq so when someone calls CRISPRessoPooled with -a that won't get passed on here
+                            crispresso_cmd = CRISPRessoShared.propagate_crispresso_options(crispresso_cmd, crispresso_options_for_pooled, args)
+                            #next set the per-amplicon options we read from the Amplicons file (and are stored in this_run_args_from_amplicons_file)
+                            crispresso_cmd = CRISPRessoShared.propagate_crispresso_options(crispresso_cmd, default_input_amplicon_headers, this_run_args_from_amplicons_file)
                             info('Running CRISPResso:%s' % crispresso_cmd)
                             crispresso_cmds.append(crispresso_cmd)
 

CRISPResso2/CRISPRessoShared.py

@@ -397,7 +397,10 @@ def propagate_crispresso_options(cmd, options, params, paramInd=None):
         if option:
             if option in params:
                 if paramInd is None:
-                    val = getattr(params, option)
+                    if type(params) == dict:
+                        val = params[option]
+                    else:
+                        val = getattr(params, option)
                 else:
                     val = params.loc[paramInd, option]
                 if val is None:
@@ -1672,7 +1675,7 @@ def get_crispresso_header(description, header_str):
                 term_width) + "\n" + output_line
 
     output_line += '\n' + ('[CRISPResso version ' + __version__ + ']').center(term_width) + '\n' + (
-        '[Note that starting in version 2.3.0 FLASh and Trimmomatic will be replaced by fastp for read merging and trimming. Accordingly, the --flash_command and --trimmomatic_command parameters will be replaced with --fastp_command. Also, --trimmomatic_options_string will be replaced with --fastp_options_string.]').center(
+        '[Note that starting in version 2.3.0 FLASh and Trimmomatic will be replaced by fastp for read merging and trimming. Accordingly, the --flash_command and --trimmomatic_command parameters will be replaced with --fastp_command. Also, --trimmomatic_options_string will be replaced with --fastp_options_string.\n\nAlso in version 2.3.0, when running CRISPRessoPooled in mixed-mode (amplicon file and genome are provided) the default behavior will be as if the --demultiplex_only_at_amplicons parameter is provided. This change means that reads and amplicons do not need to align to the exact locations.]').center(
         term_width) + "\n" + ('[For support contact [email protected] or [email protected]]').center(term_width) + "\n"
 
     description_str = ""