def main():
try:
description = [
'~~~CRISPRessoMeta~~~',
'-Analysis of CRISPR/Cas9 outcomes from deep sequencing data using a metadata file-'
]
meta_string = r'''
________________________________________
| _________ ______ _______ ______ |
| | | | | | \ | | | | | | | | |
| | | | | | | | |---- | | | |__| | |
| |_| |_| |_| |_|____ |_| |_| |_| |
|________________________________________|
'''
print(CRISPRessoShared.get_crispresso_header(description, meta_string))
parser = CRISPRessoShared.getCRISPRessoArgParser(
parserTitle='CRISPRessoMeta Parameters')
#batch specific params
parser.add_argument(
'--metadata',
type=str,
help='Metadata file according to NIST specification',
required=True)
parser.add_argument(
'-mo',
'--meta_output_folder',
help='Directory where analysis output will be stored')
parser.add_argument(
'-p',
'--n_processes',
type=int,
help='Specify the number of processes to use for quantification.\
Please use with caution since increasing this parameter will increase the memory required to run CRISPResso.',
default=1)
parser.add_argument('--crispresso_command',
help='CRISPResso command to call',
default='CRISPResso')
args = parser.parse_args()
debug_flag = args.debug
crispresso_options = CRISPRessoShared.get_crispresso_options()
options_to_ignore = set(['name', 'output_folder'])
crispresso_options_for_meta = list(crispresso_options -
options_to_ignore)
CRISPRessoShared.check_file(args.metadata)
meta_params = pd.DataFrame(
columns=['name', 'guide_seq', 'amplicon_seq'])
with open(args.metadata) as metadata_file:
metadata = json.load(metadata_file)
exp = metadata['Experiment']
for guide in data['Experiment']:
print('Guide: ' + guide['name'])
print('Sequence: ' + guide['sequence'])
print('Amplicon: ' + guide['amplicon'])
print('Fastq_R1: ' + guide['fastq_r1'])
print('Fastq_R2: ' + guide['fastq_r2'])
meta_params.append({
'name': guide['name'],
'guide_seq': guide['sequence'],
'amplicon_seq': guide['amplicon'],
'fastq_r1': guide['fastq_r1'],
'fastq_r2': guide['fastq_r2']
})
print('table:')
print(meta_params)
#rename column "a" to "amplicon_seq", etc
meta_params.rename(
index=str,
columns=CRISPRessoShared.get_crispresso_options_lookup(),
inplace=True)
meta_count = meta_params.shape[0]
meta_params.index = range(meta_count)
if 'fastq_r1' not in meta_params:
raise CRISPRessoShared.BadParameterException(
"fastq_r1 must be specified in the meta settings file. Current headings are: "
+ str(meta_params.columns.values))
#add args from the command line to meta_params
for arg in vars(args):
if arg not in meta_params:
meta_params[arg] = getattr(args, arg)
else:
if (getattr(args, arg) is not None):
meta_params[arg].fillna(value=getattr(args, arg),
inplace=True)
#assert that all names are unique
#and clean names
for i in range(meta_count):
if meta_params.loc[i, 'name'] == '':
meta_params.at[i, 'name'] = i
meta_params.at[i, 'name'] = CRISPRessoShared.clean_filename(
meta_params.loc[i, 'name'])
if meta_params.drop_duplicates(
'name').shape[0] != meta_params.shape[0]:
raise CRISPRessoShared.BadParameterException(
'Sample input names must be unique. The given names are not unique: '
+ str(meta_params.loc[:, 'name']))
#Check files
meta_params[
"sgRNA_intervals"] = '' #create empty array for sgRNA intervals
meta_params["sgRNA_intervals"] = meta_params["sgRNA_intervals"].apply(
list)
meta_params[
"cut_point_include_idx"] = '' #create empty array for cut point intervals for each batch based on sgRNA
meta_params["cut_point_include_idx"] = meta_params[
"cut_point_include_idx"].apply(list)
for idx, row in meta_params.iterrows():
if row.fastq_r1 is None:
raise CRISPRessoShared.BadParameterException(
"At least one fastq file must be given as a command line parameter or be specified in the meta settings file with the heading 'fastq_r1' (fastq_r1 on row %s '%s' is invalid)"
% (int(idx) + 1, row.fastq_r1))
CRISPRessoShared.check_file(row.fastq_r1)
if row.fastq_r2 != "":
CRISPRessoShared.check_file(row.fastq_r2)
if args.auto:
continue
curr_amplicon_seq_str = row.amplicon_seq
if curr_amplicon_seq_str is None:
raise CRISPRessoShared.BadParameterException(
"Amplicon sequence must be given as a command line parameter or be specified in the meta settings file with the heading 'amplicon_seq' (Amplicon seq on row %s '%s' is invalid)"
% (int(idx) + 1, curr_amplicon_seq_str))
guides_are_in_amplicon = {
} #dict of whether a guide is in at least one amplicon sequence
#iterate through amplicons
for curr_amplicon_seq in curr_amplicon_seq_str.split(','):
this_include_idxs = [
] #mask for bp to include for this amplicon seq, as specified by sgRNA cut points
this_sgRNA_intervals = []
wrong_nt = CRISPRessoShared.find_wrong_nt(curr_amplicon_seq)
if wrong_nt:
raise CRISPRessoShared.NTException(
'The amplicon sequence in row %d (%s) contains incorrect characters:%s'
% (idx + 1, curr_amplicon_seq_str, ' '.join(wrong_nt)))
#iterate through guides
curr_guide_seq_string = row.guide_seq
if curr_guide_seq_string is not None and curr_guide_seq_string != "":
guides = curr_guide_seq_string.strip().upper().split(',')
for curr_guide_seq in guides:
wrong_nt = CRISPRessoShared.find_wrong_nt(
curr_guide_seq)
if wrong_nt:
raise CRISPRessoShared.NTException(
'The sgRNA sequence in row %d (%s) contains incorrect characters:%s'
%
(idx + 1, curr_guide_seq, ' '.join(wrong_nt)))
guide_names = [''] * len(guides)
guide_mismatches = [[]] * len(guides)
guide_qw_centers = CRISPRessoShared.set_guide_array(
row.quantification_window_center, guides,
'guide quantification center')
guide_qw_sizes = CRISPRessoShared.set_guide_array(
row.quantification_window_size, guides,
'guide quantification size')
guide_plot_cut_points = [1] * len(guides)
discard_guide_positions_overhanging_amplicon_edge = False
if 'discard_guide_positions_overhanging_amplicon_edge' in row:
discard_guide_positions_overhanging_amplicon_edge = row.discard_guide_positions_overhanging_amplicon_edge
(this_sgRNA_sequences, this_sgRNA_intervals,
this_sgRNA_cut_points, this_sgRNA_plot_cut_points,
this_sgRNA_plot_idxs, this_sgRNA_names, this_include_idxs,
this_exclude_idxs
) = CRISPRessoShared.get_amplicon_info_for_guides(
curr_amplicon_seq, guides, guide_mismatches,
guide_names, guide_qw_centers, guide_qw_sizes,
row.quantification_window_coordinates,
row.exclude_bp_from_left, row.exclude_bp_from_right,
row.plot_window_size, guide_plot_cut_points,
discard_guide_positions_overhanging_amplicon_edge)
for guide_seq in this_sgRNA_sequences:
guides_are_in_amplicon[guide_seq] = 1
meta_params.ix[idx, "cut_point_include_idx"].append(
this_include_idxs)
meta_params.ix[idx,
"sgRNA_intervals"].append(this_sgRNA_intervals)
for guide_seq in guides_are_in_amplicon:
if guides_are_in_amplicon[guide_seq] != 1:
warn(
'\nThe guide sequence provided on row %d (%s) is not present in any amplicon sequence:%s! \nNOTE: The guide will be ignored for the analysis. Please check your input!'
% (idx + 1, row.guide_seq, curr_amplicon_seq))
meta_folder_name = os.path.splitext(os.path.basename(args.metadata))[0]
if args.name and args.name != "":
meta_folder_name = args.name
output_folder_name = 'CRISPRessoMeta_on_%s' % meta_folder_name
OUTPUT_DIRECTORY = os.path.abspath(output_folder_name)
if args.meta_output_folder:
OUTPUT_DIRECTORY = os.path.join(
os.path.abspath(args.meta_output_folder), output_folder_name)
_jp = lambda filename: os.path.join(
OUTPUT_DIRECTORY, filename
) #handy function to put a file in the output directory
try:
info('Creating Folder %s' % OUTPUT_DIRECTORY)
os.makedirs(OUTPUT_DIRECTORY)
except:
warn('Folder %s already exists.' % OUTPUT_DIRECTORY)
log_filename = _jp('CRISPRessoMeta_RUNNING_LOG.txt')
logging.getLogger().addHandler(logging.FileHandler(log_filename))
with open(log_filename, 'w+') as outfile:
outfile.write('[Command used]:\n%s\n\n[Execution log]:\n' %
' '.join(sys.argv))
crispresso2Meta_info_file = os.path.join(
OUTPUT_DIRECTORY, 'CRISPResso2Meta_info.pickle')
crispresso2_info = {
} #keep track of all information for this run to be pickled and saved at the end of the run
crispresso2_info['version'] = CRISPRessoShared.__version__
crispresso2_info['args'] = deepcopy(args)
crispresso2_info['log_filename'] = os.path.basename(log_filename)
crispresso_cmds = []
meta_names_arr = []
meta_input_names = {}
for idx, row in meta_params.iterrows():
metaName = CRISPRessoShared.slugify(row["name"])
meta_names_arr.append(metaName)
meta_input_names[metaName] = row["name"]
crispresso_cmd = args.crispresso_command + ' -o %s --name %s' % (
OUTPUT_DIRECTORY, metaName)
crispresso_cmd = propagate_options(crispresso_cmd,
crispresso_options_for_meta,
meta_params, idx)
crispresso_cmds.append(crispresso_cmd)
crispresso2_info['meta_names_arr'] = meta_names_arr
crispresso2_info['meta_input_names'] = meta_input_names
CRISPRessoMultiProcessing.run_crispresso_cmds(crispresso_cmds,
args.n_processes, 'meta',
args.skip_failed)
run_datas = [] #crispresso2 info from each row
all_amplicons = set()
amplicon_names = {}
amplicon_counts = {}
completed_meta_arr = []
for idx, row in meta_params.iterrows():
metaName = CRISPRessoShared.slugify(row["name"])
folder_name = os.path.join(OUTPUT_DIRECTORY,
'CRISPResso_on_%s' % metaName)
run_data_file = os.path.join(folder_name,
'CRISPResso2_info.pickle')
if os.path.isfile(run_data_file) is False:
info("Skipping folder '%s'. Cannot find run data at '%s'." %
(folder_name, run_data_file))
run_datas.append(None)
continue
run_data = cp.load(open(run_data_file, 'rb'))
run_datas.append(run_data)
for ref_name in run_data['ref_names']:
ref_seq = run_data['refs'][ref_name]['sequence']
all_amplicons.add(ref_seq)
#if this amplicon is called something else in another sample, just call it the amplicon
if ref_name in amplicon_names and amplicon_names[
ref_seq] != ref_name:
amplicon_names[ref_seq] = ref_seq
else:
amplicon_names[ref_seq] = ref_name
if ref_seq not in amplicon_counts:
amplicon_counts[ref_seq] = 0
amplicon_counts[ref_seq] += 1
completed_meta_arr.append(metaName)
crispresso2_info['completed_meta_arr'] = completed_meta_arr
#make sure amplicon names aren't super long
for amplicon in all_amplicons:
if len(amplicon_names[amplicon]) > 20:
amplicon_names[amplicon] = amplicon_names[amplicon][0:20]
#make sure no duplicate names (same name for the different amplicons)
seen_names = {}
for amplicon in all_amplicons:
suffix_counter = 2
while amplicon_names[amplicon] in seen_names:
amplicon_names[amplicon] = amplicon_names[
amplicon] + "_" + str(suffix_counter)
suffix_counter += 1
seen_names[amplicon_names[amplicon]] = 1
save_png = True
if args.suppress_report:
save_png = False
#summarize amplicon modifications
with open(
_jp('CRISPRessoBatch_quantification_of_editing_frequency.txt'),
'w') as outfile:
wrote_header = False
for idx, row in meta_params.iterrows():
metaName = CRISPRessoShared.slugify(row["name"])
folder_name = os.path.join(OUTPUT_DIRECTORY,
'CRISPResso_on_%s' % metaName)
run_data = run_datas[idx]
if run_data is None:
continue
amplicon_modification_file = os.path.join(
folder_name, run_data['quant_of_editing_freq_filename'])
with open(amplicon_modification_file, 'r') as infile:
file_head = infile.readline()
if not wrote_header:
outfile.write('Batch\t' + file_head)
wrote_header = True
for line in infile:
outfile.write(metaName + "\t" + line)
#summarize alignment
with open(_jp('CRISPRessoBatch_mapping_statistics.txt'),
'w') as outfile:
wrote_header = False
for idx, row in meta_params.iterrows():
metaName = CRISPRessoShared.slugify(row["name"])
folder_name = os.path.join(OUTPUT_DIRECTORY,
'CRISPResso_on_%s' % metaName)
run_data = run_datas[idx]
if run_data is None:
continue
amplicon_modification_file = os.path.join(
folder_name, run_data['mapping_stats_filename'])
with open(amplicon_modification_file, 'r') as infile:
file_head = infile.readline()
if not wrote_header:
outfile.write('Batch\t' + file_head)
wrote_header = True
for line in infile:
outfile.write(metaName + "\t" + line)
if not args.suppress_report:
if (args.place_report_in_output_folder):
report_name = _jp("CRISPResso2Meta_report.html")
else:
report_name = OUTPUT_DIRECTORY + '.html'
CRISPRessoReport.make_meta_report_from_folder(
report_name, crispresso2_info, OUTPUT_DIRECTORY, _ROOT)
crispresso2_info['report_location'] = report_name
crispresso2_info['report_filename'] = os.path.basename(report_name)
cp.dump(crispresso2_info, open(crispresso2Meta_info_file, 'wb'))
info('Analysis Complete!')
print(CRISPRessoShared.get_crispresso_footer())
sys.exit(0)
except Exception as e:
debug_flag = False
if 'args' in vars() and 'debug' in args:
debug_flag = args.debug
if debug_flag:
traceback.print_exc(file=sys.stdout)
error('\n\nERROR: %s' % e)
sys.exit(-1)
def main():
try:
description = [
'~~~CRISPRessoBatch~~~',
'-Analysis of CRISPR/Cas9 outcomes from batch deep sequencing data-'
]
batch_string = r'''
_________________
| __ ___ __ |
||__) /\ | / |__||
||__)/--\| \__| ||
|_________________|
'''
print(CRISPRessoShared.get_crispresso_header(description,
batch_string))
parser = CRISPRessoShared.getCRISPRessoArgParser(
parserTitle='CRISPRessoBatch Parameters')
#batch specific params
parser.add_argument(
'-bs',
'--batch_settings',
type=str,
help=
'Settings file for batch. Must be tab-separated text file. The header row contains CRISPResso parameters (e.g., fastq_r1, fastq_r2, amplicon_seq, and other optional parameters). Each following row sets parameters for an additional batch.',
required=True)
parser.add_argument(
'--skip_failed',
help='Continue with batch analysis even if one sample fails',
action='store_true')
parser.add_argument(
'--min_reads_for_inclusion',
help=
'Minimum number of reads for a batch to be included in the batch summary',
type=int)
parser.add_argument(
'-p',
'--n_processes',
type=int,
help='Specify the number of processes to use for quantification.\
Please use with caution since increasing this parameter will increase the memory required to run CRISPResso.',
default=1)
parser.add_argument(
'-bo',
'--batch_output_folder',
help='Directory where batch analysis output will be stored')
parser.add_argument('--crispresso_command',
help='CRISPResso command to call',
default='CRISPResso')
args = parser.parse_args()
debug_flag = args.debug
crispresso_options = CRISPRessoShared.get_crispresso_options()
options_to_ignore = set(['name', 'output_folder'])
crispresso_options_for_batch = list(crispresso_options -
options_to_ignore)
CRISPRessoShared.check_file(args.batch_settings)
##parse excel sheet
batch_params = pd.read_csv(args.batch_settings, comment='#', sep='\t')
#pandas either allows for auto-detect sep or for comment. not both
# batch_params=pd.read_csv(args.batch_settings,sep=None,engine='python',error_bad_lines=False)
batch_params.columns = batch_params.columns.str.strip(' -\xd0')
#rename column "a" to "amplicon_seq", etc
batch_params.rename(
index=str,
columns=CRISPRessoShared.get_crispresso_options_lookup(),
inplace=True)
batch_count = batch_params.shape[0]
batch_params.index = range(batch_count)
if 'fastq_r1' not in batch_params and 'bam_input' not in batch_params:
raise CRISPRessoShared.BadParameterException(
"fastq_r1 must be specified in the batch settings file. Current headings are: "
+ str(batch_params.columns.values))
#add args from the command line to batch_params_df
for arg in vars(args):
if arg not in batch_params:
batch_params[arg] = getattr(args, arg)
else:
if (getattr(args, arg) is not None):
batch_params[arg].fillna(value=getattr(args, arg),
inplace=True)
#assert that all names are unique
#and clean names
for i in range(batch_count):
if batch_params.loc[i, 'name'] == '':
batch_params.at[i, 'name'] = i
batch_params.at[i, 'name'] = CRISPRessoShared.clean_filename(
batch_params.loc[i, 'name'])
if batch_params.drop_duplicates(
'name').shape[0] != batch_params.shape[0]:
raise CRISPRessoShared.BadParameterException(
'Batch input names must be unique. The given names are not unique: '
+ str(batch_params.loc[:, 'name']))
#Check files
batch_params[
"sgRNA_intervals"] = '' #create empty array for sgRNA intervals
batch_params["sgRNA_intervals"] = batch_params[
"sgRNA_intervals"].apply(list)
batch_params[
"cut_point_include_idx"] = '' #create empty array for cut point intervals for each batch based on sgRNA
batch_params["cut_point_include_idx"] = batch_params[
"cut_point_include_idx"].apply(list)
for idx, row in batch_params.iterrows():
if 'fastq_r1' in row:
if row.fastq_r1 is None:
raise CRISPRessoShared.BadParameterException(
"At least one fastq file must be given as a command line parameter or be specified in the batch settings file with the heading 'fastq_r1' (fastq_r1 on row %s '%s' is invalid)"
% (int(idx) + 1, row.fastq_r1))
else:
CRISPRessoShared.check_file(row.fastq_r1)
if 'fastq_r2' in row and row.fastq_r2 != "":
CRISPRessoShared.check_file(row.fastq_r2)
if 'input_bam' in row:
if row.input_bam is None:
raise CRISPRessoShared.BadParameterException(
"At least one input file must be given as a command line parameter or be specified in the batch settings file with the heading 'fastq_r1' or 'input_bam' (input_bam on row %s '%s' is invalid)"
% (int(idx) + 1, row.input_bam))
else:
CRISPRessoShared.check_file(row.input_bam)
if args.auto:
continue
curr_amplicon_seq_str = row.amplicon_seq
if curr_amplicon_seq_str is None:
raise CRISPRessoShared.BadParameterException(
"Amplicon sequence must be given as a command line parameter or be specified in the batch settings file with the heading 'amplicon_seq' (Amplicon seq on row %s '%s' is invalid)"
% (int(idx) + 1, curr_amplicon_seq_str))
guides_are_in_amplicon = {
} #dict of whether a guide is in at least one amplicon sequence
#iterate through amplicons
for curr_amplicon_seq in curr_amplicon_seq_str.split(','):
this_include_idxs = [
] #mask for bp to include for this amplicon seq, as specified by sgRNA cut points
this_sgRNA_intervals = []
wrong_nt = CRISPRessoShared.find_wrong_nt(curr_amplicon_seq)
if wrong_nt:
raise CRISPRessoShared.NTException(
'The amplicon sequence in row %d (%s) contains incorrect characters:%s'
% (idx + 1, curr_amplicon_seq_str, ' '.join(wrong_nt)))
#iterate through guides
curr_guide_seq_string = row.guide_seq
if curr_guide_seq_string is not None and curr_guide_seq_string != "":
guides = curr_guide_seq_string.strip().upper().split(',')
for curr_guide_seq in guides:
wrong_nt = CRISPRessoShared.find_wrong_nt(
curr_guide_seq)
if wrong_nt:
raise CRISPRessoShared.NTException(
'The sgRNA sequence in row %d (%s) contains incorrect characters:%s'
%
(idx + 1, curr_guide_seq, ' '.join(wrong_nt)))
guide_mismatches = [[]] * len(guides)
guide_names = [""] * len(guides)
guide_qw_centers = CRISPRessoShared.set_guide_array(
row.quantification_window_center, guides,
'guide quantification center')
guide_qw_sizes = CRISPRessoShared.set_guide_array(
row.quantification_window_size, guides,
'guide quantification size')
guide_plot_cut_points = [1] * len(guides)
(this_sgRNA_sequences, this_sgRNA_intervals,
this_sgRNA_cut_points, this_sgRNA_plot_cut_points,
this_sgRNA_plot_idxs, this_sgRNA_mismatches,
this_sgRNA_names, this_include_idxs, this_exclude_idxs
) = CRISPRessoShared.get_amplicon_info_for_guides(
curr_amplicon_seq, guides, guide_mismatches,
guide_names, guide_qw_centers, guide_qw_sizes,
row.quantification_window_coordinates,
row.exclude_bp_from_left, row.exclude_bp_from_right,
row.plot_window_size, guide_plot_cut_points)
for guide_seq in this_sgRNA_sequences:
guides_are_in_amplicon[guide_seq] = 1
batch_params.ix[idx, "cut_point_include_idx"].append(
this_include_idxs)
batch_params.ix[idx,
"sgRNA_intervals"].append(this_sgRNA_intervals)
for guide_seq in guides_are_in_amplicon:
if guides_are_in_amplicon[guide_seq] != 1:
warn(
'\nThe guide sequence provided on row %d (%s) is not present in any amplicon sequence:%s! \nNOTE: The guide will be ignored for the analysis. Please check your input!'
% (idx + 1, row.guide_seq, curr_amplicon_seq))
batch_folder_name = os.path.splitext(
os.path.basename(args.batch_settings))[0]
if args.name and args.name != "":
batch_folder_name = args.name
output_folder_name = 'CRISPRessoBatch_on_%s' % batch_folder_name
OUTPUT_DIRECTORY = os.path.abspath(output_folder_name)
if args.batch_output_folder:
OUTPUT_DIRECTORY = os.path.join(
os.path.abspath(args.batch_output_folder), output_folder_name)
_jp = lambda filename: os.path.join(
OUTPUT_DIRECTORY, filename
) #handy function to put a file in the output directory
try:
info('Creating Folder %s' % OUTPUT_DIRECTORY)
os.makedirs(OUTPUT_DIRECTORY)
except:
warn('Folder %s already exists.' % OUTPUT_DIRECTORY)
log_filename = _jp('CRISPRessoBatch_RUNNING_LOG.txt')
logging.getLogger().addHandler(logging.FileHandler(log_filename))
with open(log_filename, 'w+') as outfile:
outfile.write('[Command used]:\n%s\n\n[Execution log]:\n' %
' '.join(sys.argv))
crispresso2Batch_info_file = os.path.join(
OUTPUT_DIRECTORY, 'CRISPResso2Batch_info.pickle')
crispresso2_info = {
} #keep track of all information for this run to be pickled and saved at the end of the run
crispresso2_info['version'] = CRISPRessoShared.__version__
crispresso2_info['args'] = deepcopy(args)
crispresso2_info['log_filename'] = os.path.basename(log_filename)
crispresso_cmds = []
batch_names_arr = []
batch_input_names = {}
for idx, row in batch_params.iterrows():
batchName = CRISPRessoShared.slugify(row["name"])
batch_names_arr.append(batchName)
batch_input_names[batchName] = row["name"]
crispresso_cmd = args.crispresso_command + ' -o %s --name %s' % (
OUTPUT_DIRECTORY, batchName)
crispresso_cmd = propagate_options(crispresso_cmd,
crispresso_options_for_batch,
batch_params, idx)
crispresso_cmds.append(crispresso_cmd)
crispresso2_info['batch_names_arr'] = batch_names_arr
crispresso2_info['batch_input_names'] = batch_input_names
CRISPRessoMultiProcessing.run_crispresso_cmds(crispresso_cmds,
args.n_processes,
'batch',
args.skip_failed)
run_datas = [] #crispresso2 info from each row
all_amplicons = set()
amplicon_names = {}
amplicon_counts = {}
completed_batch_arr = []
for idx, row in batch_params.iterrows():
batchName = CRISPRessoShared.slugify(row["name"])
file_prefix = row['file_prefix']
folder_name = os.path.join(OUTPUT_DIRECTORY,
'CRISPResso_on_%s' % batchName)
run_data_file = os.path.join(folder_name,
'CRISPResso2_info.pickle')
if os.path.isfile(run_data_file) is False:
info("Skipping folder '%s'. Cannot find run data at '%s'." %
(folder_name, run_data_file))
run_datas.append(None)
continue
run_data = cp.load(open(run_data_file, 'rb'))
run_datas.append(run_data)
for ref_name in run_data['ref_names']:
ref_seq = run_data['refs'][ref_name]['sequence']
all_amplicons.add(ref_seq)
#if this amplicon is called something else in another sample, just call it the amplicon
if ref_name in amplicon_names and amplicon_names[
ref_seq] != ref_name:
amplicon_names[ref_seq] = ref_seq
else:
amplicon_names[ref_seq] = ref_name
if ref_seq not in amplicon_counts:
amplicon_counts[ref_seq] = 0
amplicon_counts[ref_seq] += 1
completed_batch_arr.append(batchName)
crispresso2_info['completed_batch_arr'] = completed_batch_arr
#make sure amplicon names aren't super long
for amplicon in all_amplicons:
if len(amplicon_names[amplicon]) > 20:
amplicon_names[amplicon] = amplicon_names[amplicon][0:20]
#make sure no duplicate names (same name for the different amplicons)
seen_names = {}
for amplicon in all_amplicons:
suffix_counter = 2
orig_name = amplicon_names[amplicon]
while amplicon_names[amplicon] in seen_names:
amplicon_names[amplicon] = orig_name + "_" + str(
suffix_counter)
suffix_counter += 1
seen_names[amplicon_names[amplicon]] = 1
save_png = True
if args.suppress_report:
save_png = False
window_nuc_pct_quilt_plot_names = []
nuc_pct_quilt_plot_names = []
window_nuc_conv_plot_names = []
nuc_conv_plot_names = []
#report for amplicons that appear multiple times
for amplicon_index, amplicon_seq in enumerate(all_amplicons):
#only perform comparison if amplicon seen in more than one sample
if amplicon_counts[amplicon_seq] < 2:
continue
amplicon_name = amplicon_names[amplicon_seq]
info('Reporting summary for amplicon: "' + amplicon_name + '"')
consensus_sequence = ""
nucleotide_frequency_summary = []
nucleotide_percentage_summary = []
modification_frequency_summary = []
modification_percentage_summary = []
amp_found_count = 0 #how many folders had information for this amplicon
consensus_guides = []
consensus_include_idxs = []
consensus_sgRNA_plot_idxs = []
consensus_sgRNA_intervals = []
guides_all_same = True
batches_with_this_amplicon = []
for idx, row in batch_params.iterrows():
batchName = CRISPRessoShared.slugify(row["name"])
file_prefix = row['file_prefix']
folder_name = os.path.join(OUTPUT_DIRECTORY,
'CRISPResso_on_%s' % batchName)
run_data = run_datas[idx]
if run_data is None:
continue
batch_has_amplicon = False
batch_amplicon_name = ''
for ref_name in run_data['ref_names']:
if amplicon_seq == run_data['refs'][ref_name]['sequence']:
batch_has_amplicon = True
batch_amplicon_name = ref_name
if not batch_has_amplicon:
continue
batches_with_this_amplicon.append(idx)
if consensus_guides == []:
consensus_guides = run_data['refs'][batch_amplicon_name][
'sgRNA_sequences']
consensus_include_idxs = run_data['refs'][
batch_amplicon_name]['include_idxs']
consensus_sgRNA_intervals = run_data['refs'][
batch_amplicon_name]['sgRNA_intervals']
consensus_sgRNA_plot_idxs = run_data['refs'][
batch_amplicon_name]['sgRNA_plot_idxs']
if run_data['refs'][batch_amplicon_name][
'sgRNA_sequences'] != consensus_guides:
guides_all_same = False
if set(run_data['refs'][batch_amplicon_name]
['include_idxs']) != set(consensus_include_idxs):
guides_all_same = False
if 'nuc_freq_filename' not in run_data['refs'][
batch_amplicon_name]:
info(
"Skipping the amplicon '%s' in folder '%s'. Cannot find nucleotide information."
% (batch_amplicon_name, folder_name))
continue
nucleotide_frequency_file = os.path.join(
folder_name,
run_data['refs'][batch_amplicon_name]['nuc_freq_filename'])
ampSeq_nf, nuc_freqs = CRISPRessoShared.parse_count_file(
nucleotide_frequency_file)
nucleotide_pct_file = os.path.join(
folder_name,
run_data['refs'][batch_amplicon_name]['nuc_pct_filename'])
ampSeq_np, nuc_pcts = CRISPRessoShared.parse_count_file(
nucleotide_pct_file)
count_file = os.path.join(
folder_name, run_data['refs'][batch_amplicon_name]
['mod_count_filename'])
ampSeq_cf, mod_freqs = CRISPRessoShared.parse_count_file(
count_file)
if ampSeq_nf is None or ampSeq_np is None or ampSeq_cf is None:
info(
"Skipping the amplicon '%s' in folder '%s'. Could not parse batch output."
% (batch_amplicon_name, folder_name))
info(
"Nucleotide frequency amplicon: '%s', Nucleotide percentage amplicon: '%s', Count vectors amplicon: '%s'"
% (ampSeq_nf, ampSeq_np, ampSeq_cf))
continue
if ampSeq_nf != ampSeq_np or ampSeq_np != ampSeq_cf:
warn(
"Skipping the amplicon '%s' in folder '%s'. Parsed amplicon sequences do not match\nnf:%s\nnp:%s\ncf:%s\nrf:%s"
% (batch_amplicon_name, folder_name, ampSeq_nf,
ampSeq_np, ampSeq_cf, amplicon_seq))
continue
if consensus_sequence == "":
consensus_sequence = ampSeq_nf
if ampSeq_nf != consensus_sequence:
info(
"Skipping the amplicon '%s' in folder '%s'. Amplicon sequences do not match."
% (batch_amplicon_name, folder_name))
continue
if 'Total' not in mod_freqs:
info(
"Skipping the amplicon '%s' in folder '%s'. Processing did not complete."
% (batch_amplicon_name, folder_name))
continue
if mod_freqs['Total'][0] == 0 or mod_freqs['Total'][0] == "0":
info(
"Skipping the amplicon '%s' in folder '%s'. Got no reads for amplicon."
% (batch_amplicon_name, folder_name))
continue
if (args.min_reads_for_inclusion is not None) and (int(
mod_freqs['Total'][0]) < args.min_reads_for_inclusion):
info(
"Skipping the amplicon '%s' in folder '%s'. Got %s reads (min_reads_for_inclusion is %d)."
% (batch_amplicon_name, folder_name,
str(mod_freqs['Total'][0]),
args.min_reads_for_inclusion))
continue
mod_pcts = {}
for key in mod_freqs:
mod_pcts[key] = np.array(mod_freqs[key]).astype(
np.float) / float(mod_freqs['Total'][0])
amp_found_count += 1
for nuc in ['A', 'T', 'C', 'G', 'N', '-']:
row = [batchName, nuc]
row.extend(nuc_freqs[nuc])
nucleotide_frequency_summary.append(row)
pct_row = [batchName, nuc]
pct_row.extend(nuc_pcts[nuc])
nucleotide_percentage_summary.append(pct_row)
for mod in [
'Insertions', 'Insertions_Left', 'Deletions',
'Substitutions', 'All_modifications'
]:
row = [batchName, mod]
row.extend(mod_freqs[mod])
modification_frequency_summary.append(row)
pct_row = [batchName, mod]
pct_row.extend(mod_pcts[mod])
modification_percentage_summary.append(pct_row)
if amp_found_count == 0:
info(
"Couldn't find any data for amplicon '%s'. Not compiling results."
% amplicon_name)
else:
amplicon_plot_name = amplicon_name + "."
if len(amplicon_names) == 1 and amplicon_name == "Reference":
amplicon_plot_name = ""
colnames = ['Batch', 'Nucleotide']
colnames.extend(list(consensus_sequence))
nucleotide_frequency_summary_df = pd.DataFrame(
nucleotide_frequency_summary, columns=colnames)
nucleotide_frequency_summary_df = pd.concat([
nucleotide_frequency_summary_df.iloc[:, 0:2],
nucleotide_frequency_summary_df.iloc[:, 2:].apply(
pd.to_numeric)
],
axis=1)
nucleotide_frequency_summary_filename = _jp(
amplicon_plot_name + 'Nucleotide_frequency_summary.txt')
nucleotide_frequency_summary_df.to_csv(
nucleotide_frequency_summary_filename,
sep='\t',
index=None)
nucleotide_percentage_summary_df = pd.DataFrame(
nucleotide_percentage_summary, columns=colnames)
nucleotide_percentage_summary_df = pd.concat([
nucleotide_percentage_summary_df.iloc[:, 0:2],
nucleotide_percentage_summary_df.iloc[:, 2:].apply(
pd.to_numeric)
],
axis=1)
nucleotide_percentage_summary_filename = _jp(
amplicon_plot_name + 'Nucleotide_percentage_summary.txt')
nucleotide_percentage_summary_df.to_csv(
nucleotide_percentage_summary_filename,
sep='\t',
index=None)
colnames = ['Batch', 'Modification']
colnames.extend(list(consensus_sequence))
modification_frequency_summary_df = pd.DataFrame(
modification_frequency_summary, columns=colnames)
modification_frequency_summary_df = pd.concat([
modification_frequency_summary_df.iloc[:, 0:2],
modification_frequency_summary_df.iloc[:, 2:].apply(
pd.to_numeric)
],
axis=1)
modification_frequency_summary_filename = _jp(
amplicon_plot_name + 'MODIFICATION_FREQUENCY_SUMMARY.txt')
modification_frequency_summary_df.to_csv(
modification_frequency_summary_filename,
sep='\t',
index=None)
modification_percentage_summary_df = pd.DataFrame(
modification_percentage_summary, columns=colnames)
modification_percentage_summary_df = pd.concat([
modification_percentage_summary_df.iloc[:, 0:2],
modification_percentage_summary_df.iloc[:, 2:].apply(
pd.to_numeric)
],
axis=1)
modification_percentage_summary_filename = _jp(
amplicon_plot_name + 'MODIFICATION_PERCENTAGE_SUMMARY.txt')
modification_percentage_summary_df.to_csv(
modification_percentage_summary_filename,
sep='\t',
index=None)
crispresso2_info[
'nucleotide_frequency_summary_filename'] = os.path.basename(
nucleotide_frequency_summary_filename)
crispresso2_info[
'nucleotide_percentage_summary_filename'] = os.path.basename(
nucleotide_percentage_summary_filename)
crispresso2_info[
'modification_frequency_summary_filename'] = os.path.basename(
modification_frequency_summary_filename)
crispresso2_info[
'modification_percentage_summary_filename'] = os.path.basename(
modification_percentage_summary_filename)
crispresso2_info['summary_plot_titles'] = {}
crispresso2_info['summary_plot_labels'] = {}
crispresso2_info['summary_plot_datas'] = {}
#if guides are all the same, merge substitutions and perform base editor comparison at guide quantification window
if guides_all_same and consensus_guides != []:
info(
"All guides are equal. Performing comparison of batches for amplicon '%s'"
% amplicon_name)
include_idxs = consensus_include_idxs #include indexes are the same for all guides
for idx, sgRNA in enumerate(consensus_guides):
sgRNA_intervals = consensus_sgRNA_intervals[idx]
sgRNA_plot_idxs = consensus_sgRNA_plot_idxs[idx]
plot_idxs_flat = [0, 1] # guide, nucleotide
plot_idxs_flat.extend(
[plot_idx + 2 for plot_idx in sgRNA_plot_idxs])
sub_nucleotide_frequency_summary_df = nucleotide_frequency_summary_df.iloc[:,
plot_idxs_flat]
sub_nucleotide_percentage_summary_df = nucleotide_percentage_summary_df.iloc[:,
plot_idxs_flat]
sub_modification_percentage_summary_df = modification_percentage_summary_df.iloc[:,
plot_idxs_flat]
#show all sgRNA's on the plot
sub_sgRNA_intervals = []
for sgRNA_interval in consensus_sgRNA_intervals:
newstart = None
newend = None
for idx, i in enumerate(sgRNA_plot_idxs):
if i <= sgRNA_interval[0]:
newstart = idx
if newend is None and i >= sgRNA_interval[1]:
newend = idx
#if guide doesn't overlap with plot idxs
if newend == 0 or newstart == len(sgRNA_plot_idxs):
continue
#otherwise, correct partial overlaps
elif newstart == None and newend == None:
newstart = 0
newend = len(include_idxs) - 1
elif newstart == None:
newstart = 0
elif newend == None:
newend = len(include_idxs) - 1
#and add it to the list
sub_sgRNA_intervals.append((newstart, newend))
if not args.suppress_plots:
#plot for each guide
this_window_nuc_pct_quilt_plot_name = _jp(
amplicon_plot_name +
'Nucleotide_percentage_quilt_around_sgRNA_' +
sgRNA)
CRISPRessoPlot.plot_nucleotide_quilt(
sub_nucleotide_percentage_summary_df,
sub_modification_percentage_summary_df,
this_window_nuc_pct_quilt_plot_name,
save_png,
sgRNA_intervals=sub_sgRNA_intervals,
quantification_window_idxs=include_idxs)
plot_name = os.path.basename(
this_window_nuc_pct_quilt_plot_name)
window_nuc_pct_quilt_plot_names.append(plot_name)
crispresso2_info['summary_plot_titles'][
plot_name] = 'sgRNA: ' + sgRNA + ' Amplicon: ' + amplicon_name
if len(consensus_guides) == 1:
crispresso2_info['summary_plot_titles'][
plot_name] = ''
crispresso2_info['summary_plot_labels'][
plot_name] = 'Composition of each base around the guide ' + sgRNA + ' for the amplicon ' + amplicon_name
crispresso2_info['summary_plot_datas'][plot_name] = [
('Nucleotide frequencies',
os.path.basename(
nucleotide_frequency_summary_filename)),
('Modification frequencies',
os.path.basename(
modification_frequency_summary_filename))
]
sub_nucleotide_frequency_summary_df = pd.concat(
[
sub_nucleotide_frequency_summary_df.
iloc[:, 0:2],
sub_nucleotide_frequency_summary_df.
iloc[:, 2:].apply(pd.to_numeric)
],
axis=1)
sub_nucleotide_frequency_summary_filename = _jp(
amplicon_plot_name +
'Nucleotide_frequency_summary_around_sgRNA_' +
sgRNA + '.txt')
sub_nucleotide_frequency_summary_df.to_csv(
sub_nucleotide_frequency_summary_filename,
sep='\t',
index=None)
sub_nucleotide_percentage_summary_df = pd.concat(
[
sub_nucleotide_percentage_summary_df.
iloc[:, 0:2],
sub_nucleotide_percentage_summary_df.
iloc[:, 2:].apply(pd.to_numeric)
],
axis=1)
sub_nucleotide_percentage_summary_filename = _jp(
amplicon_plot_name +
'Nucleotide_percentage_summary_around_sgRNA_' +
sgRNA + '.txt')
sub_nucleotide_percentage_summary_df.to_csv(
sub_nucleotide_percentage_summary_filename,
sep='\t',
index=None)
if args.base_editor_output:
this_window_nuc_conv_plot_name = _jp(
amplicon_plot_name +
'Nucleotide_conversion_map_around_sgRNA_' +
sgRNA)
CRISPRessoPlot.plot_conversion_map(
sub_nucleotide_percentage_summary_df,
this_window_nuc_conv_plot_name,
args.conversion_nuc_from,
args.conversion_nuc_to,
save_png,
sgRNA_intervals=sub_sgRNA_intervals,
quantification_window_idxs=include_idxs)
plot_name = os.path.basename(
this_window_nuc_conv_plot_name)
window_nuc_conv_plot_names.append(plot_name)
crispresso2_info['summary_plot_titles'][
plot_name] = 'sgRNA: ' + sgRNA + ' Amplicon: ' + amplicon_name
if len(consensus_guides) == 1:
crispresso2_info['summary_plot_titles'][
plot_name] = ''
crispresso2_info['summary_plot_labels'][
plot_name] = args.conversion_nuc_from + '->' + args.conversion_nuc_to + ' conversion rates around the guide ' + sgRNA + ' for the amplicon ' + amplicon_name
crispresso2_info['summary_plot_datas'][
plot_name] = [
('Nucleotide frequencies around sgRNA',
os.path.basename(
sub_nucleotide_frequency_summary_filename
)),
('Nucleotide percentages around sgRNA',
os.path.basename(
sub_nucleotide_percentage_summary_filename
))
]
if not args.suppress_plots: # plot the whole region
this_nuc_pct_quilt_plot_name = _jp(
amplicon_plot_name + 'Nucleotide_percentage_quilt')
CRISPRessoPlot.plot_nucleotide_quilt(
nucleotide_percentage_summary_df,
modification_percentage_summary_df,
this_nuc_pct_quilt_plot_name,
save_png,
sgRNA_intervals=consensus_sgRNA_intervals,
quantification_window_idxs=include_idxs)
plot_name = os.path.basename(
this_nuc_pct_quilt_plot_name)
nuc_pct_quilt_plot_names.append(plot_name)
crispresso2_info['summary_plot_titles'][
plot_name] = 'Amplicon: ' + amplicon_name
if len(amplicon_names) == 1:
crispresso2_info['summary_plot_titles'][
plot_name] = ''
crispresso2_info['summary_plot_labels'][
plot_name] = 'Composition of each base for the amplicon ' + amplicon_name
crispresso2_info['summary_plot_datas'][plot_name] = [
('Nucleotide frequencies',
os.path.basename(
nucleotide_frequency_summary_filename)),
('Modification frequencies',
os.path.basename(
modification_frequency_summary_filename))
]
if args.base_editor_output:
this_nuc_conv_plot_name = _jp(
amplicon_plot_name +
'Nucleotide_conversion_map')
CRISPRessoPlot.plot_conversion_map(
nucleotide_percentage_summary_df,
this_nuc_conv_plot_name,
args.conversion_nuc_from,
args.conversion_nuc_to,
save_png,
sgRNA_intervals=consensus_sgRNA_intervals,
quantification_window_idxs=include_idxs)
plot_name = os.path.basename(
this_nuc_conv_plot_name)
nuc_conv_plot_names.append(plot_name)
crispresso2_info['summary_plot_titles'][
plot_name] = 'Amplicon: ' + amplicon_name
if len(amplicon_names) == 1:
crispresso2_info['summary_plot_titles'][
plot_name] = ''
crispresso2_info['summary_plot_titles'][
plot_name] = ''
crispresso2_info['summary_plot_labels'][
plot_name] = args.conversion_nuc_from + '->' + args.conversion_nuc_to + ' conversion rates for the amplicon ' + amplicon_name
crispresso2_info['summary_plot_datas'][plot_name] = [
('Nucleotide frequencies',
os.path.basename(
nucleotide_frequency_summary_filename)),
('Modification frequencies',
os.path.basename(
modification_frequency_summary_filename))
]
else: #guides are not the same
if not args.suppress_plots:
this_nuc_pct_quilt_plot_name = _jp(
amplicon_plot_name + 'Nucleotide_percentage_quilt')
CRISPRessoPlot.plot_nucleotide_quilt(
nucleotide_percentage_summary_df,
modification_percentage_summary_df,
this_nuc_pct_quilt_plot_name, save_png)
plot_name = os.path.basename(
this_nuc_pct_quilt_plot_name)
nuc_pct_quilt_plot_names.append(plot_name)
crispresso2_info['summary_plot_labels'][
plot_name] = 'Composition of each base for the amplicon ' + amplicon_name
crispresso2_info['summary_plot_datas'][plot_name] = [
('Nucleotide frequencies',
os.path.basename(
nucleotide_frequency_summary_filename)),
('Modification frequencies',
os.path.basename(
modification_frequency_summary_filename))
]
if args.base_editor_output:
this_nuc_conv_plot_name = _jp(
amplicon_plot_name +
'Nucleotide_percentage_quilt')
CRISPRessoPlot.plot_conversion_map(
nucleotide_percentage_summary_df,
this_nuc_conv_plot_name,
args.conversion_nuc_from,
args.conversion_nuc_to, save_png)
plot_name = os.path.basename(
this_nuc_conv_plot_name)
nuc_conv_plot_names.append(plot_name)
crispresso2_info['summary_plot_labels'][
plot_name] = args.conversion_nuc_from + '->' + args.conversion_nuc_to + ' conversion rates for the amplicon ' + amplicon_name
crispresso2_info['summary_plot_datas'][plot_name] = [
('Nucleotide frequencies',
os.path.basename(
nucleotide_frequency_summary_filename)),
('Modification frequencies',
os.path.basename(
modification_frequency_summary_filename))
]
crispresso2_info[
'window_nuc_pct_quilt_plot_names'] = window_nuc_pct_quilt_plot_names
crispresso2_info['nuc_pct_quilt_plot_names'] = nuc_pct_quilt_plot_names
crispresso2_info[
'window_nuc_conv_plot_names'] = window_nuc_conv_plot_names
crispresso2_info['nuc_conv_plot_names'] = nuc_conv_plot_names
#summarize amplicon modifications
with open(
_jp('CRISPRessoBatch_quantification_of_editing_frequency.txt'),
'w') as outfile:
wrote_header = False
for idx, row in batch_params.iterrows():
batchName = CRISPRessoShared.slugify(row["name"])
file_prefix = row['file_prefix']
folder_name = os.path.join(OUTPUT_DIRECTORY,
'CRISPResso_on_%s' % batchName)
run_data = run_datas[idx]
if run_data is None:
continue
amplicon_modification_file = os.path.join(
folder_name, run_data['quant_of_editing_freq_filename'])
with open(amplicon_modification_file, 'r') as infile:
file_head = infile.readline()
if not wrote_header:
outfile.write('Batch\t' + file_head)
wrote_header = True
for line in infile:
outfile.write(batchName + "\t" + line)
#summarize alignment
with open(_jp('CRISPRessoBatch_mapping_statistics.txt'),
'w') as outfile:
wrote_header = False
for idx, row in batch_params.iterrows():
batchName = CRISPRessoShared.slugify(row["name"])
folder_name = os.path.join(OUTPUT_DIRECTORY,
'CRISPResso_on_%s' % batchName)
run_data = run_datas[idx]
if run_data is None:
continue
amplicon_modification_file = os.path.join(
folder_name, run_data['mapping_stats_filename'])
with open(amplicon_modification_file, 'r') as infile:
file_head = infile.readline()
if not wrote_header:
outfile.write('Batch\t' + file_head)
wrote_header = True
for line in infile:
outfile.write(batchName + "\t" + line)
if not args.suppress_report:
if (args.place_report_in_output_folder):
report_name = _jp("CRISPResso2Batch_report.html")
else:
report_name = OUTPUT_DIRECTORY + '.html'
CRISPRessoReport.make_batch_report_from_folder(
report_name, crispresso2_info, OUTPUT_DIRECTORY, _ROOT)
crispresso2_info['report_location'] = report_name
crispresso2_info['report_filename'] = os.path.basename(report_name)
cp.dump(crispresso2_info, open(crispresso2Batch_info_file, 'wb'))
info('Analysis Complete!')
print(CRISPRessoShared.get_crispresso_footer())
sys.exit(0)
except Exception as e:
debug_flag = False
if 'args' in vars() and 'debug' in args:
debug_flag = args.debug
if debug_flag:
traceback.print_exc(file=sys.stdout)
error('\n\nERROR: %s' % e)
sys.exit(-1)
