"""Misc. plotting and reporting methods, some of which are really arbitrary.
Here is a typical example of use:
>>> import dnachisel.reports.constraint_reports as cr
>>> dataframe = cr.constraints_breaches_dataframe(constraints, sequences)
>>> dataframe.to_excel("output_breaches.xlsx")
>>> records = cr.records_from_breaches_dataframe(dataframe, sequences)
>>> cr.breaches_records_to_pdf(records, 'output_breaches_plots.pdf')
"""
from copy import deepcopy
import re
from io import BytesIO
import proglog
from ...biotools import sequence_to_biopython_record, annotate_record
from ...builtin_specifications import (
EnforceGCContent,
AvoidPattern,
AvoidHairpins,
)
from ..colors_cycle import colors_cycle
from .GraphicTranslator import GraphicTranslator
try:
import matplotlib.pyplot as plt
from matplotlib.backends.backend_pdf import PdfPages
MPL_AVAILABLE = True
except ImportError:
MPL_AVAILABLE = False
def _sequences_to_new_records(sequences):
"""Turn acceptable sequences input into a records list.
Acceptable formats are
- ('name', 'sequence')
- {'name': 'sequence'}
- [records] (will be deepcopied)
"""
if isinstance(sequences, dict):
sequences = list(sequences.items())
records = []
for seq in sequences:
if hasattr(seq, "id"):
records.append(deepcopy(seq))
else:
name, seq = seq
records.append(
sequence_to_biopython_record(seq, id=name, name=name)
)
return records
def _parse_location(location_string):
"""Parses locations like 235-350(+)"""
location_regex = r"(\d+)-(\d+)(\(+\)|\(-\)|)"
match = re.match(location_regex, location_string.strip())
start, end, strand = match.groups()
return int(start), int(end), -1 if strand == "(-)" else 1
[docs]def records_from_breaches_dataframe(dataframe, sequences):
"""Generate records with annotations indicating constraints breaches.
Parameters
----------
dataframe
A breaches dataframe returned by ``constraints_breaches_dataframe``
sequences
Either a list [("name", "sequence")...] or a dict {"name": "sequence"}
or a list of biopython records whole id is the sequence name.
"""
records = _sequences_to_new_records(sequences)
for record in records:
record.features = [
f
for f in record.features
if not f.qualifiers.get("is_a_breach", False)
]
colors_cycle_iterator = colors_cycle()
columns_colors = {
c: next(colors_cycle_iterator) for c in dataframe.columns
}
for rec, (i, row) in zip(records, dataframe.iterrows()):
for column in dataframe.columns:
locations = row[column]
if not locations:
continue
for location in locations.split(","):
annotate_record(
rec,
location=_parse_location(location),
label=column,
color=columns_colors[column],
ApEinfo_fwdcolor=columns_colors[column],
ApEinfo_revcolor=columns_colors[column],
is_a_breach=True,
)
return records
def plot_breaches_record(record, ax=None, figure_width=10):
translator = GraphicTranslator()
graphic_record = translator.translate_record(record)
ax, _ = graphic_record.plot(
ax=ax, figure_width=figure_width, strand_in_label_threshold=7
)
ax.set_title(record.id, loc="left", fontweight="bold")
ax.set_ylim(top=ax.get_ylim()[1] + 1)
return ax
[docs]def breaches_records_to_pdf(
breaches_records, pdf_path=None, figure_width=10, logger="bar"
):
"""Plots figures of the breaches annotated in the records into a PDF file.
Parameters
----------
breaches_records
A least of records annotated with breaches, as returned by the
pdf_path
Either the path to a PDF, or a file handle (open in wb mode) or None
for this method to return binary PDF data.
logger
Either "bar" for a progress bar, None for no logging, or any Proglog
logger. The bar name is "sequence".
"""
pdf_io = BytesIO() if pdf_path is None else pdf_path
logger = proglog.default_bar_logger(logger, min_time_interval=0.2)
with PdfPages(pdf_io) as pdf:
for record in logger.iter_bar(sequence=breaches_records):
ax = plot_breaches_record(record, figure_width=figure_width)
pdf.savefig(ax.figure, bbox_inches="tight")
plt.close(ax.figure)
if pdf_path is None:
return pdf_io.getvalue()
EXAMPLE_MANUFACTURING_CONSTRAINTS = [
AvoidPattern("BsaI_site"),
AvoidPattern("BsmBI_site"),
AvoidPattern("BbsI_site"),
AvoidPattern("SapI_site"),
AvoidPattern("9xA"),
AvoidPattern("9xT"),
AvoidPattern("6xG"),
AvoidPattern("6xC"),
AvoidPattern("5x3mer"),
AvoidPattern("9x2mer"),
AvoidHairpins(stem_size=20, hairpin_window=200),
EnforceGCContent(mini=0.3, maxi=0.7, window=100),
]
