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Merge branch 'v2.3.0-release' of https://github.com/eastgenomics/eggd…
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…_generate_variant_workbook into v2.3.0-release
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@jethror1
jethror1 committed Jan 5, 2023
2 parents 3f3b887 + cf54ede commit 6bd0ec3
Showing 1 changed file with 100 additions and 62 deletions.
162 changes: 100 additions & 62 deletions resources/home/dnanexus/generate_workbook/utils/excel.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@
import re
from string import ascii_uppercase as uppercase
from timeit import default_timer as timer
from typing import Union

from colour import Color
import Levenshtein as levenshtein
Expand Down Expand Up @@ -95,6 +96,74 @@ def write_summary(self) -> None:
self.dias_summary()


def summary_sheet_cell_colour_key(self, row_count, to_bold) -> Union[int, list]:
"""
Write conditions and colours of colouring applied to cells to
the summary sheet if --colour specified
Parameters
----------
row_count : int
counter of current row to write to in sheet
to_bold : list
list of cells to set to bold
Returns
-------
int
counter of current row to write to in sheet
list
list of cells to set to bold
"""
# build a dict of each column and all its colour conditions
cols_to_colours = defaultdict(dict)
for i in self.args.colour:
column, condition, colour = i.split(':')
cols_to_colours[column][condition] = colour

self.summary.cell(row_count, 1).value = "Cell colouring applied:"
to_bold.append(f"A{row_count}")
self.summary[f"A{row_count}"].font = Font(
bold=True, name=DEFAULT_FONT.name
)

colour_col = 2
max_colour_rows_written = 0

# write colouring applied to each field as seperate column in summary
for column, conditions in cols_to_colours.items():
colour_row = row_count + 1
column_letter = get_column_letter(colour_col)

self.summary.cell(row_count, colour_col).value = column
to_bold.append(f"{column_letter}{row_count}")

for condition, colour in conditions.items():
condition = condition.replace('&', ' & ').replace('|', ' | ')
self.summary.cell(colour_row, colour_col).value = condition
self.summary.cell(colour_row, colour_col).data_type = 's'

colour = self.convert_colour(colour)

self.summary[f"{column_letter}{colour_row}"].fill = PatternFill(
patternType="solid",
start_color=colour
)
colour_row += 1

# set width to wider than max value in cell
width = max([len(x) for x in conditions.keys()])
width = 10 if width < 13 else width
self.summary.column_dimensions[column_letter].width = width + 3

colour_col += 2

if colour_row > max_colour_rows_written:
max_colour_rows_written = colour_row

return max_colour_rows_written, to_bold


def basic_summary(self) -> None:
"""
Writes basic summary sheet with metrics such as variant records
Expand Down Expand Up @@ -130,17 +199,7 @@ def basic_summary(self) -> None:
to_bold.append(f"B{row_count}")
row_count += 1

row_count += 2
self.summary.cell(row_count, 1).value = "Workflow:"
self.summary.cell(row_count + 1, 1).value = "Workflow ID:"
self.summary.cell(row_count + 2, 1).value = "Report Job ID:"
to_bold.extend([f"A{row_count + x}" for x in range(0, 3)])

self.summary.cell(row_count, 2).value = self.args.workflow[0]
self.summary.cell(row_count + 1, 2).value = self.args.workflow[1]
self.summary.cell(row_count + 2, 2).value = self.args.job_id

row_count += 6
row_count += 4

if self.args.human_filter:
self.summary.cell(row_count, 1).value = "Filters applied:"
Expand All @@ -161,46 +220,18 @@ def basic_summary(self) -> None:
row_count += 2

if self.args.colour:
# build a dict of each column and all its colour conditions
cols_to_colours = defaultdict(dict)
for i in self.args.colour:
column, condition, colour = i.split(':')
cols_to_colours[column][condition] = colour

self.summary.cell(row_count, 1).value = "Cell colouring applied:"
to_bold.append(f"A{row_count}")
self.summary[f"A{row_count}"].font = Font(
bold=True, name=DEFAULT_FONT.name
)

colour_col = 2
for column, conditions in cols_to_colours.items():
colour_row = row_count + 1

column_letter = get_column_letter(colour_col)

self.summary.cell(row_count, colour_col).value = column
to_bold.append(f"{column_letter}{row_count}")

for condition, colour in conditions.items():
condition = condition.replace('&', ' & ').replace('|', ' | ')
self.summary.cell(colour_row, colour_col).value = condition
self.summary.cell(colour_row, colour_col).data_type = 's'
row_count, to_bold = self.summary_sheet_cell_colour_key(
row_count, to_bold)

colour = self.convert_colour(colour)

self.summary[f"{column_letter}{colour_row}"].fill = PatternFill(
patternType="solid",
start_color=colour
)
colour_row+=1

# set width to wider than max value in cell
width = max([len(x) for x in conditions.keys()])
width = 10 if width < 13 else width
self.summary.column_dimensions[column_letter].width = width + 3
row_count += 4
self.summary.cell(row_count, 1).value = "Workflow:"
self.summary.cell(row_count + 1, 1).value = "Workflow ID:"
self.summary.cell(row_count + 2, 1).value = "Report Job ID:"
to_bold.extend([f"A{row_count + x}" for x in range(0, 3)])

colour_col += 2
self.summary.cell(row_count, 2).value = self.args.workflow[0]
self.summary.cell(row_count + 1, 2).value = self.args.workflow[1]
self.summary.cell(row_count + 2, 2).value = self.args.job_id

for cell in to_bold:
self.summary[cell].font = Font(bold=True, name=DEFAULT_FONT.name)
Expand Down Expand Up @@ -235,12 +266,13 @@ def dias_summary(self) -> None:
# write total rows in each sheet
count = 34

# cells to make bold
to_bold = []

for sheet, vcf in zip(self.args.sheets, self.vcfs):
self.summary.cell(count, 2).value = sheet
self.summary.cell(count, 3).value = len(vcf.index)
self.summary[f"A{count}"].font = Font(
bold=True, name=DEFAULT_FONT.name
)
to_bold.append(f"A{count}")
count += 1

count += 5
Expand All @@ -259,28 +291,33 @@ def dias_summary(self) -> None:

if self.args.human_filter:
self.summary.cell(count, 1).value = "Filters applied:"
self.summary[f"A{count}"].font = Font(
bold=True, name=DEFAULT_FONT.name)
self.summary.cell(count, 2).value = self.args.human_filter
to_bold.append(f"A{count}")

count += 2

# write args passed to script to generate report
self.summary.cell(count, 1).value = "Filter command:"
self.summary[f"A{count}"].font = Font(bold=True, name=DEFAULT_FONT.name)
to_bold.append(f"A{count}")
if self.args.filter:
self.summary.cell(count, 2).value = self.args.filter
else:
self.summary.cell(count, 2).value = "None"

count += 2

if self.args.colour:
count, to_bold = self.summary_sheet_cell_colour_key(
count, to_bold)

count += 2

self.summary.cell(count, 1).value = "Workflow:"
self.summary.cell(count + 1, 1).value = "Workflow ID:"
self.summary.cell(count + 2, 1).value = "Report Job ID:"
self.summary[f"A{count}"].font = Font(bold=True, name=DEFAULT_FONT.name)
self.summary[f"A{count + 1}"].font = Font(bold=True, name=DEFAULT_FONT.name)
self.summary[f"A{count + 2}"].font = Font(bold=True, name=DEFAULT_FONT.name)
to_bold.append(f"A{count}")
to_bold.append(f"A{count + 1}")
to_bold.append(f"A{count + 2}")

self.summary.cell(count, 2).value = self.args.workflow[0]
self.summary.cell(count + 1, 2).value = self.args.workflow[1]
Expand Down Expand Up @@ -328,18 +365,19 @@ def dias_summary(self) -> None:
self.summary.merge_cells(
start_row=28, end_row=28, start_column=4, end_column=6)

# set titles to bold
title_cells = [
# titles to set to bold
to_bold += [
"A1", "A34", "A35", "A36","A38", "B1",
"B9", "B16", "B21", "B22", "B28", "B34", "B35", "B36", "B37",
"C16", "C22", "D16", "D22", "D28", "E1", "E2", "E22",
"F16", "F22", "G16", "G22", "H16", "H22", "I16"
]
for cell in title_cells:

for cell in to_bold:
self.summary[cell].font = Font(bold=True, name=DEFAULT_FONT.name)

# set column widths for readability
self.summary.column_dimensions['A'].width = 18
self.summary.column_dimensions['A'].width = 22 if self.args.colour else 18
self.summary.column_dimensions['B'].width = 13
self.summary.column_dimensions['C'].width = 13
self.summary.column_dimensions['D'].width = 13
Expand Down

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