Module ediacara.reports
None
None
View Source
from datetime import datetime
import os
import matplotlib.pyplot as plt
from pdf_reports import (
add_css_class,
dataframe_to_html,
pug_to_html,
style_table_rows,
write_report,
)
import pdf_reports.tools as pdf_tools
from .version import __version__
from .Comparator import result_keywords
THIS_PATH = os.path.dirname(os.path.realpath(__file__))
ASSETS_PATH = os.path.join(THIS_PATH, "report_assets")
SEQUENCINGGROUP_REPORT_TEMPLATE = os.path.join(ASSETS_PATH, "run_simulation_report.pug")
ASSEMBLY_ANALYSIS_REPORT_TEMPLATE = os.path.join(ASSETS_PATH, "assembly_report.pug")
STYLESHEET = os.path.join(ASSETS_PATH, "report_style.css")
def end_pug_to_html(template, **context):
now = datetime.now().strftime("%Y-%m-%d")
defaults = {
"sidebar_text": "Generated on %s by Ediacara (version %s)" % (now, __version__),
"ediacara_logo_url": os.path.join(ASSETS_PATH, "imgs", "logo.png"),
}
for k in defaults:
if k not in context:
context[k] = defaults[k]
return pug_to_html(template, **context)
def write_assembly_analysis_report(target, assemblybatch):
"""Write a sequencing run report with a PDF summary.
**Parameters**
**target**
> Path for PDF file.
**assemblybatch**
> `AssemblyBatch` instance.
"""
for assembly in assemblybatch.assemblies:
assembly.assembly_figure_data = pdf_tools.figure_data(
assembly.assembly_figure, fmt="svg"
)
assembly.report_table = dataframe_to_html(
assembly.subset_paf(), extra_classes=("definition",)
)
html = end_pug_to_html(
ASSEMBLY_ANALYSIS_REPORT_TEMPLATE, assemblybatch=assemblybatch
)
write_report(html, target, extra_stylesheets=(STYLESHEET,))
def write_sequencinggroup_report(target, sequencinggroup):
"""Write a sequencing run report with a PDF summary.
**Parameters**
**target**
> Path for PDF file.
**sequencinggroup**
> `SequencingGroup` instance.
"""
def tr_modifier(tr):
tds = list(tr.find_all("td"))
if len(tds) == 0:
return
result = tds[1] # second element of list is the result symbol
if result.text == result_keywords["good"]:
add_css_class(tr, "positive")
elif result.text == result_keywords["error"]:
add_css_class(tr, "negative")
if not sequencinggroup.comparisons_performed:
return "Run perform_all_comparisons_in_sequencinggroup()!"
for comparatorgroup in sequencinggroup.comparatorgroups:
comparatorgroup.report_table = dataframe_to_html(
comparatorgroup.summary_table, extra_classes=("definition",)
)
# This colours the summary table:
comparatorgroup.report_table = style_table_rows(
comparatorgroup.report_table, tr_modifier
)
# Histogram of reads in the report summary
histogram_height = comparatorgroup.fastq_plot.get_size_inches()[1]
comparatorgroup.fastq_figure_data = pdf_tools.figure_data(
comparatorgroup.fastq_plot, fmt="svg", size=[8, histogram_height]
)
for comparator in comparatorgroup.comparators:
comparator.figure_data = pdf_tools.figure_data(comparator.fig, fmt="svg")
# Keep first few only:
if comparator.vcf_table.shape[0] > sequencinggroup.vcf_cutoff: # 0 for rows
vcf_table = comparator.vcf_table[: sequencinggroup.vcf_cutoff]
comparator.vcf_table_message = True
else:
vcf_table = comparator.vcf_table
comparator.vcf_table_message = False
# This column has lists, does not look good in print:
vcf_table["ALT"] = vcf_table["ALT"].apply(lambda x: ", ".join(x))
# Convert to string then truncate too long entries and add three dots:
columnwidth = 15 # wider columns don't display well in PDF
vcf_table = vcf_table.apply(
lambda x: x.astype(str).apply(
lambda y: y[:columnwidth] + "..." if len(y) > columnwidth else y
)
)
comparator.vcf_table_html = dataframe_to_html(
vcf_table, extra_classes=("definition",)
)
if hasattr(comparator, "is_comparison_successful"):
if comparator.is_comparison_successful:
height = comparator.comparison_figure.figure.get_size_inches()[1]
if height > 10:
height = 10 # to fit on one page
comparator.comparison_figure_data = pdf_tools.figure_data(
comparator.comparison_figure, fmt="svg", size=[7, height]
)
else:
comparator.comparison_figure_data = None
if comparator.has_consensus:
comparator.has_comparison_error = True
if comparator.geneblocks_outcome == "none":
comparator.geneblocks_text = (
"Missing consensus file for comparison!"
)
elif comparator.geneblocks_outcome == "incorrect_length":
comparator.geneblocks_text = (
"Incorrect length! " + comparator.incorrect_length_msg
)
elif comparator.geneblocks_outcome == "too_many_differences":
comparator.geneblocks_text = (
"Plot not created. "
+ "Too many differences between consensus and reference."
)
elif comparator.geneblocks_outcome == "geneblocks_error":
comparator.geneblocks_text = (
"GeneBlocks comparison of consensus and reference failed."
)
elif comparator.geneblocks_outcome == "swapped_diffblocks":
comparator.geneblocks_text = (
"Note: plotting the reference against the consensus failed."
+ " Instead, this plot compares the consensus to the reference "
+ comparator.name
+ " , therefore there are no annotations."
)
comparator.has_comparison_error = False
elif comparator.geneblocks_outcome == "all_good":
comparator.geneblocks_text = (
"<b>"
+ comparator.name
+ "</b> reference vs consensus of reads:"
)
comparator.has_comparison_error = False
# plt.close("all")
html = end_pug_to_html(
SEQUENCINGGROUP_REPORT_TEMPLATE, sequencinggroup=sequencinggroup
)
write_report(html, target, extra_stylesheets=(STYLESHEET,))
Variables
ASSEMBLY_ANALYSIS_REPORT_TEMPLATE
ASSETS_PATH
SEQUENCINGGROUP_REPORT_TEMPLATE
STYLESHEET
THIS_PATH
result_keywords
Functions
end_pug_to_html
def end_pug_to_html(
template,
**context
)
View Source
def end_pug_to_html(template, **context):
now = datetime.now().strftime("%Y-%m-%d")
defaults = {
"sidebar_text": "Generated on %s by Ediacara (version %s)" % (now, __version__),
"ediacara_logo_url": os.path.join(ASSETS_PATH, "imgs", "logo.png"),
}
for k in defaults:
if k not in context:
context[k] = defaults[k]
return pug_to_html(template, **context)
write_assembly_analysis_report
def write_assembly_analysis_report(
target,
assemblybatch
)
Write a sequencing run report with a PDF summary.
Parameters
target
Path for PDF file.
assemblybatch
AssemblyBatchinstance.
View Source
def write_assembly_analysis_report(target, assemblybatch):
"""Write a sequencing run report with a PDF summary.
**Parameters**
**target**
> Path for PDF file.
**assemblybatch**
> `AssemblyBatch` instance.
"""
for assembly in assemblybatch.assemblies:
assembly.assembly_figure_data = pdf_tools.figure_data(
assembly.assembly_figure, fmt="svg"
)
assembly.report_table = dataframe_to_html(
assembly.subset_paf(), extra_classes=("definition",)
)
html = end_pug_to_html(
ASSEMBLY_ANALYSIS_REPORT_TEMPLATE, assemblybatch=assemblybatch
)
write_report(html, target, extra_stylesheets=(STYLESHEET,))
write_sequencinggroup_report
def write_sequencinggroup_report(
target,
sequencinggroup
)
Write a sequencing run report with a PDF summary.
Parameters
target
Path for PDF file.
sequencinggroup
SequencingGroupinstance.
View Source
def write_sequencinggroup_report(target, sequencinggroup):
"""Write a sequencing run report with a PDF summary.
**Parameters**
**target**
> Path for PDF file.
**sequencinggroup**
> `SequencingGroup` instance.
"""
def tr_modifier(tr):
tds = list(tr.find_all("td"))
if len(tds) == 0:
return
result = tds[1] # second element of list is the result symbol
if result.text == result_keywords["good"]:
add_css_class(tr, "positive")
elif result.text == result_keywords["error"]:
add_css_class(tr, "negative")
if not sequencinggroup.comparisons_performed:
return "Run perform_all_comparisons_in_sequencinggroup()!"
for comparatorgroup in sequencinggroup.comparatorgroups:
comparatorgroup.report_table = dataframe_to_html(
comparatorgroup.summary_table, extra_classes=("definition",)
)
# This colours the summary table:
comparatorgroup.report_table = style_table_rows(
comparatorgroup.report_table, tr_modifier
)
# Histogram of reads in the report summary
histogram_height = comparatorgroup.fastq_plot.get_size_inches()[1]
comparatorgroup.fastq_figure_data = pdf_tools.figure_data(
comparatorgroup.fastq_plot, fmt="svg", size=[8, histogram_height]
)
for comparator in comparatorgroup.comparators:
comparator.figure_data = pdf_tools.figure_data(comparator.fig, fmt="svg")
# Keep first few only:
if comparator.vcf_table.shape[0] > sequencinggroup.vcf_cutoff: # 0 for rows
vcf_table = comparator.vcf_table[: sequencinggroup.vcf_cutoff]
comparator.vcf_table_message = True
else:
vcf_table = comparator.vcf_table
comparator.vcf_table_message = False
# This column has lists, does not look good in print:
vcf_table["ALT"] = vcf_table["ALT"].apply(lambda x: ", ".join(x))
# Convert to string then truncate too long entries and add three dots:
columnwidth = 15 # wider columns don't display well in PDF
vcf_table = vcf_table.apply(
lambda x: x.astype(str).apply(
lambda y: y[:columnwidth] + "..." if len(y) > columnwidth else y
)
)
comparator.vcf_table_html = dataframe_to_html(
vcf_table, extra_classes=("definition",)
)
if hasattr(comparator, "is_comparison_successful"):
if comparator.is_comparison_successful:
height = comparator.comparison_figure.figure.get_size_inches()[1]
if height > 10:
height = 10 # to fit on one page
comparator.comparison_figure_data = pdf_tools.figure_data(
comparator.comparison_figure, fmt="svg", size=[7, height]
)
else:
comparator.comparison_figure_data = None
if comparator.has_consensus:
comparator.has_comparison_error = True
if comparator.geneblocks_outcome == "none":
comparator.geneblocks_text = (
"Missing consensus file for comparison!"
)
elif comparator.geneblocks_outcome == "incorrect_length":
comparator.geneblocks_text = (
"Incorrect length! " + comparator.incorrect_length_msg
)
elif comparator.geneblocks_outcome == "too_many_differences":
comparator.geneblocks_text = (
"Plot not created. "
+ "Too many differences between consensus and reference."
)
elif comparator.geneblocks_outcome == "geneblocks_error":
comparator.geneblocks_text = (
"GeneBlocks comparison of consensus and reference failed."
)
elif comparator.geneblocks_outcome == "swapped_diffblocks":
comparator.geneblocks_text = (
"Note: plotting the reference against the consensus failed."
+ " Instead, this plot compares the consensus to the reference "
+ comparator.name
+ " , therefore there are no annotations."
)
comparator.has_comparison_error = False
elif comparator.geneblocks_outcome == "all_good":
comparator.geneblocks_text = (
"<b>"
+ comparator.name
+ "</b> reference vs consensus of reads:"
)
comparator.has_comparison_error = False
# plt.close("all")
html = end_pug_to_html(
SEQUENCINGGROUP_REPORT_TEMPLATE, sequencinggroup=sequencinggroup
)
write_report(html, target, extra_stylesheets=(STYLESHEET,))