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Web updates refactoring done
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@Snicker7
Snicker7 committed Sep 13, 2022
1 parent 99c8e22 commit 08fcd4e
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Showing 6 changed files with 609 additions and 73 deletions.
113 changes: 64 additions & 49 deletions CRISPRessoReport.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,39 +25,37 @@ def make_report_from_folder(crispresso_report_file, crispresso_folder, _ROOT):
make_report(run_data, crispresso_report_file, crispresso_folder, _ROOT)


def make_report(run_data, crispresso_report_file, crispresso_folder, _ROOT):
# dicts for each amplicon fig_names[amp_name] = [list of fig names]
# fig_locs[amp_name][fig_name] = figure location
# print('crispresso_report file: ' + crispresso_report_file + ' crispresso_folder : ' + crispresso_folder + ' root: ' + _ROOT)
figures = {'names': {}, 'locs': {}, 'titles': {}, 'captions': {}, 'datas': {}, 'htmls': {}, 'sgRNA_based_names': {}}

def add_fig_if_exists(fig_name, fig_root, fig_title, fig_caption, fig_data,
amplicon_fig_names, amplicon_figures):
def add_fig_if_exists(fig_name, fig_root, fig_title, fig_caption, fig_data,
amplicon_fig_names, amplicon_figures, crispresso_folder):
"""
Helper function to add figure if the file exists
if fig at filename exists,
amplicon_figs[figname] is set to that file
"""
Helper function to add figure if the file exists
if fig at filename exists,
amplicon_figs[figname] is set to that file
"""
# fullpath=os.path.join(crispresso_folder,fig_root+'.png')
pngfullpath = os.path.join(crispresso_folder, fig_root + '.png')
htmlfullpath = os.path.join(crispresso_folder, fig_root + '.html')
# print('adding file ' + fig_root + ' at ' + fullpath)
if os.path.exists(pngfullpath) or os.path.exists(htmlfullpath):
amplicon_fig_names.append(fig_name)
# amplicon_fig_locs[fig_name]=os.path.basename(fig_root+'.png')
amplicon_figures['locs'][fig_name] = os.path.basename(fig_root)
amplicon_figures['titles'][fig_name] = fig_title
amplicon_figures['captions'][fig_name] = fig_caption
amplicon_figures['datas'][fig_name] = []
for (data_caption, data_file) in fig_data:
if os.path.exists(os.path.join(crispresso_folder, data_file)):
amplicon_figures['datas'][fig_name].append((data_caption, data_file))
if os.path.exists(htmlfullpath):
with open(htmlfullpath) as html:
html_string = "<div align='center'>"
html_string += html.read()
html_string += "</div>"
amplicon_figures['htmls'][fig_name] = html_string
# fullpath=os.path.join(crispresso_folder,fig_root+'.png')
pngfullpath = os.path.join(crispresso_folder, fig_root + '.png')
htmlfullpath = os.path.join(crispresso_folder, fig_root + '.html')
# print('adding file ' + fig_root + ' at ' + fullpath)
if os.path.exists(pngfullpath) or os.path.exists(htmlfullpath):
amplicon_fig_names.append(fig_name)
# amplicon_fig_locs[fig_name]=os.path.basename(fig_root+'.png')
amplicon_figures['locs'][fig_name] = os.path.basename(fig_root)
amplicon_figures['titles'][fig_name] = fig_title
amplicon_figures['captions'][fig_name] = fig_caption
amplicon_figures['datas'][fig_name] = []
for (data_caption, data_file) in fig_data:
if os.path.exists(os.path.join(crispresso_folder, data_file)):
amplicon_figures['datas'][fig_name].append((data_caption, data_file))
if os.path.exists(htmlfullpath):
with open(htmlfullpath) as html:
html_string = "<div align='center'>"
html_string += html.read()
html_string += "</div>"
amplicon_figures['htmls'][fig_name] = html_string


def assemble_figs(run_data, crispresso_folder):
figures = {'names': {}, 'locs': {}, 'titles': {}, 'captions': {}, 'datas': {}, 'htmls': {}, 'sgRNA_based_names': {}}

global_fig_names = []
for fig in ['1a', '1b', '1c', '1d', '5a', '6a', '8a', '11c']:
Expand All @@ -66,7 +64,7 @@ def add_fig_if_exists(fig_name, fig_root, fig_title, fig_caption, fig_data,
add_fig_if_exists(fig_name, run_data['results']['general_plots'][fig_name + '_root'], 'Figure ' + fig,
run_data['results']['general_plots'][fig_name + '_caption'],
run_data['results']['general_plots'][fig_name + '_data'],
global_fig_names, figures)
global_fig_names, figures, crispresso_folder)

amplicons = []
for amplicon_name in run_data['results']['ref_names']:
Expand All @@ -81,7 +79,7 @@ def add_fig_if_exists(fig_name, fig_root, fig_title, fig_caption, fig_data,
'Figure ' + fig_name,
run_data['results']['refs'][amplicon_name][fig_name + '_caption'],
run_data['results']['refs'][amplicon_name][fig_name + '_data'],
global_fig_names, amplicon_figures)
global_fig_names, amplicon_figures, crispresso_folder)

this_sgRNA_based_fig_names = {}
for fig in ['2b', '9', '10d', '10e', '10f', '10g', '11b']:
Expand All @@ -93,7 +91,7 @@ def add_fig_if_exists(fig_name, fig_root, fig_title, fig_caption, fig_data,
add_fig_if_exists(fig_name, plot_root, 'Figure ' + fig_name + ' sgRNA ' + str(idx + 1),
run_data['results']['refs'][amplicon_name]['plot_' + fig + '_captions'][idx],
run_data['results']['refs'][amplicon_name]['plot_' + fig + '_datas'][idx],
this_fig_names, amplicon_figures)
this_fig_names, amplicon_figures, crispresso_folder)
this_sgRNA_based_fig_names[fig] = this_fig_names

figures['names'][amplicon_name] = amplicon_figures['names']
Expand All @@ -103,6 +101,15 @@ def add_fig_if_exists(fig_name, fig_root, fig_title, fig_caption, fig_data,
figures['titles'][amplicon_name] = amplicon_figures['titles']
figures['captions'][amplicon_name] = amplicon_figures['captions']
figures['datas'][amplicon_name] = amplicon_figures['datas']
data = {'amplicons': amplicons, 'figures': figures}
return data


def make_report(run_data, crispresso_report_file, crispresso_folder, _ROOT, web_version=False):
# dicts for each amplicon fig_names[amp_name] = [list of fig names]
# fig_locs[amp_name][fig_name] = figure location
# print('crispresso_report file: ' + crispresso_report_file + ' crispresso_folder : ' + crispresso_folder + ' root: ' + _ROOT)
data = assemble_figs(run_data, crispresso_folder)

report_display_name = ""
if run_data['running_info']['args'].name != "":
Expand All @@ -116,8 +123,8 @@ def add_fig_if_exists(fig_name, fig_root, fig_title, fig_caption, fig_data,
crispresso_data_path += "/"

report_data = {
'amplicons': amplicons,
'figures': figures,
'amplicons': data['amplicons'],
'figures': data['figures'],
'run_data': run_data,
'report_display_name': report_display_name,
'crispresso_data_path': crispresso_data_path,
Expand Down Expand Up @@ -247,6 +254,7 @@ def make_batch_report_from_folder(crispressoBatch_report_file, crispresso2_info,
batch_folder,
_ROOT,
output_title,
'batch',
summary_plots={
'names': summary_plot_names,
'titles': summary_plot_titles,
Expand All @@ -267,15 +275,15 @@ def make_pooled_report_from_folder(crispresso_report_file, crispresso2_info, fol
output_title = 'CRISPResso Pooled Output'
if crispresso2_info['running_info']['args'].name != '':
output_title += '<br/>{0}'.format(crispresso2_info['running_info']['args'].name)
make_multi_report_from_folder(crispresso2_info, names_arr, output_title, crispresso_report_file, folder, _ROOT)
make_multi_report_from_folder(crispresso2_info, names_arr, output_title, crispresso_report_file, folder, _ROOT, 'pooled')


def make_compare_report_from_folder(crispresso_report_file, crispresso2_info, folder, _ROOT):
names_arr = []
output_title = 'CRISPResso Compare Output'
if crispresso2_info['running_info']['args'].name != '':
output_title += '<br/>{0}'.format(crispresso2_info['running_info']['args'].name)
make_multi_report_from_folder(crispresso2_info, names_arr, output_title, crispresso_report_file, folder, _ROOT)
make_multi_report_from_folder(crispresso2_info, names_arr, output_title, crispresso_report_file, folder, _ROOT, 'compare')


def make_meta_report_from_folder(crispresso_report_file, crispresso2_info, folder, _ROOT):
Expand All @@ -284,7 +292,7 @@ def make_meta_report_from_folder(crispresso_report_file, crispresso2_info, folde
output_title = 'CRISPresso Meta Output'
if crispresso2_info['running_info']['args'].name != '':
output_title += '<br/>{0}'.format(crispresso2_info['running_info']['args'].name)
make_multi_report_from_folder(crispresso2_info, names_arr, output_title, crispresso_report_file, folder, _ROOT,
make_multi_report_from_folder(crispresso2_info, names_arr, output_title, crispresso_report_file, folder, _ROOT, 'meta',
display_names=input_names)


Expand All @@ -293,10 +301,10 @@ def make_wgs_report_from_folder(crispresso_report_file, crispresso2_info, folder
output_title = 'CRISPResso WGS Output'
if crispresso2_info['running_info']['args'].name != '':
output_title += '<br/>{0}'.format(crispresso2_info['running_info']['args'].name)
make_multi_report_from_folder(crispresso2_info, names_arr, output_title, crispresso_report_file, folder, _ROOT)
make_multi_report_from_folder(crispresso2_info, names_arr, output_title, crispresso_report_file, folder, _ROOT, 'wgs')


def make_multi_report_from_folder(crispresso2_info, names_arr, report_name, crispresso_report_file, folder, _ROOT,
def make_multi_report_from_folder(crispresso2_info, names_arr, report_name, crispresso_report_file, folder, _ROOT, crispresso_tool,
display_names=None):
"""
Prepares information to make a report of multiple CRISPResso runs - like CRISPRessoWGS or CRISPRessoPooled
Expand Down Expand Up @@ -369,6 +377,7 @@ def make_multi_report_from_folder(crispresso2_info, names_arr, report_name, cris
folder,
_ROOT,
report_name,
crispresso_tool,
summary_plots={
'names': summary_plot_names,
'titles': summary_plot_titles,
Expand All @@ -385,6 +394,7 @@ def make_multi_report(
crispresso_folder,
_ROOT,
report_name,
crispresso_tool,
window_nuc_pct_quilts=[],
nuc_pct_quilts=[],
window_nuc_conv_plots=[],
Expand All @@ -409,12 +419,7 @@ def make_multi_report(
report_name (string): description of report type to be shown at top of report
crispresso_folder (string): absolute path to the crispresso output
_ROOT (string): absolute path to the crispresso executable
<<<<<<< HEAD
summary_plot (dict): a dict with the following keys:
=======
summary_plots (dict): a dict with the following keys:
>>>>>>> origin/master
names (list): list of plot names - keys for following dicts
titles (dict): dict of plot_name->plot_title
labels (dict): dict of plot_name->plot_label
Expand All @@ -439,7 +444,14 @@ def fill_default(dictionary, key, default_type=list):
loader=FileSystemLoader(os.path.join(_ROOT, 'templates')),
)
j2_env.filters['dirname'] = dirname
template = j2_env.get_template('multiReport.html')
if crispresso_tool == 'batch':
template = j2_env.get_template('batchReport.html')
elif crispresso_tool == 'pooled':
template = j2_env.get_template('pooledReport.html')
elif crispresso_tool == 'wgs':
template = j2_env.get_template('wgsReport.html')
else:
template = j2_env.get_template('multiReport.html')

crispresso_data_path = os.path.relpath(
crispresso_folder, os.path.dirname(crispresso_multi_report_file),
Expand All @@ -466,7 +478,10 @@ def fill_default(dictionary, key, default_type=list):
key,
default_type,
)

web = False
if not web:
for html in sub_html_files:
sub_html_files[html] = crispresso_data_path + sub_html_files[html]
with open(crispresso_multi_report_file, 'w') as outfile:
outfile.write(template.render(
window_nuc_pct_quilts=window_nuc_pct_quilts,
Expand Down
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