#!/usr/bin/env python2.7
# This file is part of pyGenClean.
#
# pyGenClean is free software: you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
# Foundation, either version 3 of the License, or (at your option) any later
# version.
#
# pyGenClean is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
# A PARTICULAR PURPOSE. See the GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License along with
# pyGenClean. If not, see <http://www.gnu.org/licenses/>.
import os
import re
from datetime import datetime
from . import utils as latex
from ..pipeline_error import ProgramError
from .. import __version__ as pygenclean_version
[docs]def create_report(outdirname, report_filename, **kwargs):
"""Creates a LaTeX report.
:param report_filename: the name of the file.
:param outdirname: the name of the output directory.
:type report_filename: str
:type outdirname: str
"""
# Checking the required variables
if "steps" in kwargs:
assert "descriptions" in kwargs
assert "long_descriptions" in kwargs
assert "steps_filename" not in kwargs
else:
assert "steps_filename" in kwargs
assert "descriptions" not in kwargs
assert "long_descriptions" not in kwargs
assert "summaries" in kwargs
assert "background" in kwargs
assert "project_name" in kwargs
assert "summary_fn" in kwargs
assert "report_title" in kwargs
assert "report_author" in kwargs
assert "initial_files" in kwargs
assert "final_nb_markers" in kwargs
assert "final_nb_samples" in kwargs
assert "final_files" in kwargs
assert "plink_version" in kwargs
assert "graphic_paths_fn" in kwargs
# Formatting the background section
background_section = _format_background(kwargs["background"])
# Writing the method steps to a separate file (for access later)
steps_filename = None
if "steps_filename" in kwargs:
steps_filename = kwargs["steps_filename"]
else:
steps_filename = os.path.join(outdirname, "steps_summary.tex")
with open(steps_filename, "w") as o_file:
zipped = zip(kwargs["steps"], kwargs["descriptions"],
kwargs["long_descriptions"])
for step, desc, long_desc in zipped:
if desc.endswith("."):
desc = desc[:-1]
step = step.replace("_", r"\_")
to_print = latex.item(desc)
to_print += " [{}].".format(latex.texttt(step))
if long_desc is not None:
to_print += " " + long_desc
print >>o_file, latex.wrap_lines(to_print) + "\n"
# Adding the content of the results section
result_summaries = []
for name in kwargs["summaries"]:
full_path = os.path.abspath(name)
if os.path.isfile(full_path):
rel_path = os.path.relpath(full_path, outdirname)
result_summaries.append(re.sub(r"\\", "/", rel_path))
# Reading the initial_files file
initial_files = None
with open(kwargs["initial_files"], "r") as i_file:
initial_files = i_file.read().splitlines()
# Reading the final_files file
final_files = None
with open(kwargs["final_files"], "r") as i_file:
final_files = [i.split("\t")[0] for i in i_file.read().splitlines()]
# Adding the bibliography content
biblio_entry = latex.bib_entry(
name="pyGenClean",
authors="Lemieux Perreault LP, Provost S, Legault MA, Barhdadi A, "
r"Dub\'e MP",
title="pyGenClean: efficient tool for genetic data clean up before "
"association testing",
journal="Bioinformatics",
year="2013",
volume="29",
number="13",
pages="1704--1705",
) + "\n" * 2 + latex.bib_entry(
name="plink",
authors="Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, "
"Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, Sham PC",
title="PLINK: a tool set for whole-genome association and "
"population-based linkage analyses",
journal="American Journal of Human Genetics",
year="2007",
volume="81",
number="3",
pages="559--575",
) + "\n" * 2 + latex.bib_entry(
name="bafRegress",
authors=r"Goo J, Matthew F, Kurt NH, Jane MR, Kimberly FD, "
r"Gon{\c{c}}alo RA, Michael B, Hyun Min K",
title="Detecting and estimating contamination of human DNA samples in "
"sequencing and array-based genotype data",
journal="The American Journal of Human Genetics",
year="2012",
volume="91",
number="5",
pages="839--848",
)
# Getting the template
main_template = latex.jinja2_env.get_template("main_document.tex")
# Getting the data
today = datetime.today()
# Reading the graphics path
graphic_paths = []
if kwargs["graphic_paths_fn"] is not None:
with open(kwargs["graphic_paths_fn"], "r") as i_file:
graphic_paths = [
re.sub(r"\\", "/", path) + ("" if path.endswith("/") else "/")
for path in i_file.read().splitlines()
]
try:
with open(report_filename, "w") as i_file:
# Rendering the template
print >>i_file, main_template.render(
project_name=latex.sanitize_tex(kwargs["project_name"]),
month=today.strftime("%B"),
day=today.day,
year=today.year,
background_content=background_section,
result_summaries=result_summaries,
bibliography_content=biblio_entry,
pygenclean_version=pygenclean_version,
plink_version=kwargs["plink_version"],
steps_filename=os.path.basename(steps_filename),
final_results=_create_summary_table(
kwargs["summary_fn"],
latex.jinja2_env.get_template("summary_table.tex"),
nb_samples=kwargs["final_nb_samples"],
nb_markers=kwargs["final_nb_markers"],
),
report_title=latex.sanitize_tex(kwargs["report_title"]),
report_author=latex.sanitize_tex(kwargs["report_author"]),
initial_files=initial_files,
final_files=final_files,
final_nb_samples=kwargs["final_nb_samples"],
final_nb_markers=kwargs["final_nb_markers"],
graphic_paths=graphic_paths,
)
except IOError:
msg = "{}: could not create report".format(report_filename)
raise ProgramError(msg)
def _format_background(background):
"""Formats the background section
:param background: the background content or file.
:type background: str or file
:returns: the background content.
:rtype: str
"""
# Getting the background
if os.path.isfile(background):
with open(background, "r") as i_file:
background = i_file.read().splitlines()
else:
background = background.splitlines()
# Formatting
final_background = ""
for line in background:
if line == "":
final_background += r"\\" + "\n\n"
continue
final_background += latex.wrap_lines(latex.sanitize_tex(line))
return final_background
def _create_summary_table(fn, template, nb_samples, nb_markers):
"""Creates the final table.
:param fn: the name of the file containing the summary.
:param template: the Jinja2 template.
:param nb_samples: the final number of samples.
:param nb_markers: the final number of markers.
:type fn: str
:type template: Jinja2.template
:type nb_samples: str
:type nb_markers: str
"""
# The final data
table_data = []
# Reading the summary file
with open(fn, "r") as i_file:
data = None
line = i_file.readline()
while line != "":
if line.startswith("#"):
# If there is data, this isn't the first line, so we save
if data:
table_data.append(data)
# This is the 'header' of a section (hence a new section)
data = dict(
header=line.rstrip("\r\n").split(" ")[1],
data=[],
)
# Changing to next line
line = i_file.readline()
continue
# If the line starts with '---', then it's a horizontal line
if line.startswith("---"):
data["data"].append(dict(hline=True))
# Changing to next line
line = i_file.readline()
continue
# If the line starts with ' -', then it's a sub section
if line.startswith(" -"):
tmp = line[4:].rstrip("\r\n").split("\t")
if data["header"].endswith("/subset"):
if tmp[0].startswith("_file_path:"):
tmp[0] = r"\path{" + tmp[0][11:] + "}"
elif data["header"].endswith("/flag_hw"):
tmp[0] = latex.format_numbers(tmp[0], prefix="p < ")
else:
tmp = map(latex.sanitize_tex, tmp)
if tmp[0].startswith("x"):
tmp[0] = latex.inline_math(r"\times " + tmp[0][1:])
data["data"].append(dict(
hline=False,
multicol=False,
row_data=tmp,
))
# Changing to next line
line = i_file.readline()
continue
# This is a regular line
data["data"].append(dict(
hline=False,
multicol=True,
row_data=map(
latex.sanitize_tex,
line.rstrip("\r\n").split("\t"),
),
))
# Skipping to next line
line = i_file.readline()
# We add the last entry
table_data.append(data)
# Rendering
return template.render(table_data=table_data, final_nb_markers=nb_markers,
final_nb_samples=nb_samples)
