diff --git a/metaprof_utils/__init__.py b/metaprof_utils/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..a00bb4c12558e6e9ccc03906a73edbe35b78022a
--- /dev/null
+++ b/metaprof_utils/__init__.py
@@ -0,0 +1,5 @@
+__copyright__ = "Copyright (C) 2020-2021 Blaise Li"
+__licence__ = "GNU GPLv3"
+from .metaprof_utils import (
+ DEFAULT_PARAMETERS,
+ compute_matrix)
diff --git a/metaprof_utils/metaprof_utils.py b/metaprof_utils/metaprof_utils.py
new file mode 100644
index 0000000000000000000000000000000000000000..5f1f9d336be144a0186d7c6acb04b01681b9adf8
--- /dev/null
+++ b/metaprof_utils/metaprof_utils.py
@@ -0,0 +1,99 @@
+# Copyright (C) 2020-2021 Blaise Li
+#
+# This program 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.
+#
+# This program 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 this program. If not, see <https://www.gnu.org/licenses/>.
+"""
+Module containing metaprofile creation utilities based on deeptools.
+"""
+from copy import deepcopy
+from deeptools import heatmapper
+from deeptools.plotProfile import Profile
+from cytoolz import keyfilter
+
+
+DEFAULT_PARAMETERS = {
+ "upstream": 0,
+ "downstream": 0,
+ # TODO: change to 2000 ?
+ "body": 500,
+ "bin size": 10,
+ "ref point": None,
+ "verbose": False,
+ "bin avg type": "mean",
+ "missing data as zero": False,
+ "min threshold": None,
+ "max threshold": None,
+ "scale": 1,
+ "skip zeros": False,
+ "nan after end": False,
+ "proc number": 4,
+ "sort regions": "keep",
+ "sort using": "mean",
+ "unscaled 5 prime": 0,
+ "unscaled 3 prime": 0,
+ "start_label": "start",
+ "end_label": "end",
+ "label_rotation": 90,
+}
+
+
+def is_prof_param(key):
+ """Determine if *key* corresponds to a valid parameter for a *Profile*."""
+ return key in {
+ "plot_title", "y_axis_label", "y_min", "y_max", "averagetype",
+ "reference_point_label", "start_label", "end_label",
+ "plot_height", "plot_width", "per_group",
+ "plot_type", "image_format", "color_list",
+ "legend_location", "plots_per_row", "label_rotation", "dpi"}
+
+
+def compute_matrix(bigwig_filenames,
+ bed_filename,
+ plot_filename=None,
+ **extra_parameters):
+ """Combine information from bigwig files *bigwig_filenames* and bed file
+ *bed_filename*.
+
+ If *plot_filename* is set, write the corresponding meta profile
+ in this file.
+ """
+ parameters = deepcopy(DEFAULT_PARAMETERS)
+ parameters.update(extra_parameters)
+ heatm = heatmapper.heatmapper()
+ heatm.computeMatrix(bigwig_filenames, bed_filename, parameters)
+ if "sample_labels" in parameters:
+ heatm.matrix.set_sample_labels(parameters["sample_labels"])
+ if "group_labels" in parameters:
+ heatm.matrix.set_group_labels(parameters["group_labels"])
+ # Fixing parameters (as in heatmapper.read_matrix_file
+ # and heatmapper.save_matrix)
+ nb_samples = len(heatm.matrix.sample_labels)
+ hm_params = dict()
+ for (key, val) in heatm.parameters.items():
+ if isinstance(val, list) and not val:
+ val = None
+ if key in heatm.special_params and not isinstance(val, list):
+ val = [val] * nb_samples
+ if not val:
+ val = [None] * nb_samples
+ hm_params[key] = val
+ heatm.parameters = hm_params
+
+ if plot_filename is not None:
+ print(f"plotting profile to {plot_filename}")
+ prof_params = keyfilter(is_prof_param, parameters)
+ prof_params["per_group"] = True
+ prof = Profile(
+ heatm, plot_filename,
+ **prof_params)
+ prof.plot_profile()
diff --git a/scripts/create_metagene_profile.py b/scripts/create_metagene_profile.py
index 3b185a4c5e0ed53d1e1ea7bd84e1a73d201c2a39..6e95ce41d61690b3f449e0e6d15faec0c56084ea 100755
--- a/scripts/create_metagene_profile.py
+++ b/scripts/create_metagene_profile.py
@@ -1,5 +1,5 @@
#!/usr/bin/env python3
-# Copyright (C) 2020 Blaise Li
+# Copyright (C) 2020-2021 Blaise Li
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
@@ -70,7 +70,7 @@ import argparse
import os
import sys
import warnings
-from copy import deepcopy
+# from copy import deepcopy
from pathlib import Path
from shutil import copyfile
from tempfile import NamedTemporaryFile
@@ -80,9 +80,14 @@ from sqlite3 import OperationalError
from yaml import load as yload
# https://pythonhosted.org/gffutils/
from gffutils import FeatureDB, create_db
-from deeptools import heatmapper
-from deeptools.plotProfile import Profile
-from cytoolz import keyfilter, valmap
+# from deeptools import heatmapper
+# from deeptools.plotProfile import Profile
+# from cytoolz import keyfilter, valmap
+from cytoolz import valmap
+
+from metaprof_utils import (
+ DEFAULT_PARAMETERS,
+ compute_matrix)
def formatwarning(message, category, filename, lineno, line):
@@ -206,83 +211,83 @@ def fix_none(param_value):
return param_value
-DEFAULT_PARAMETERS = {
- "upstream": 0,
- "downstream": 0,
- # TODO: change to 2000 ?
- "body": 500,
- "bin size": 10,
- "ref point": None,
- "verbose": False,
- "bin avg type": "mean",
- "missing data as zero": False,
- "min threshold": None,
- "max threshold": None,
- "scale": 1,
- "skip zeros": False,
- "nan after end": False,
- "proc number": 4,
- "sort regions": "keep",
- "sort using": "mean",
- "unscaled 5 prime": 0,
- "unscaled 3 prime": 0,
- "start_label": "start",
- "end_label": "end",
- "label_rotation": 90,
-}
+# DEFAULT_PARAMETERS = {
+# "upstream": 0,
+# "downstream": 0,
+# # TODO: change to 2000 ?
+# "body": 500,
+# "bin size": 10,
+# "ref point": None,
+# "verbose": False,
+# "bin avg type": "mean",
+# "missing data as zero": False,
+# "min threshold": None,
+# "max threshold": None,
+# "scale": 1,
+# "skip zeros": False,
+# "nan after end": False,
+# "proc number": 4,
+# "sort regions": "keep",
+# "sort using": "mean",
+# "unscaled 5 prime": 0,
+# "unscaled 3 prime": 0,
+# "start_label": "start",
+# "end_label": "end",
+# "label_rotation": 90,
+# }
PARAMETER_INFO = "\n".join(DEFAULT_PARAMETERS.keys())
-def is_prof_param(key):
- """Determine if *key* corresponds to a valid parameter for a *Profile*."""
- return key in {
- "plot_title", "y_axis_label", "y_min", "y_max", "averagetype",
- "reference_point_label", "start_label", "end_label",
- "plot_height", "plot_width", "per_group",
- "plot_type", "image_format", "color_list",
- "legend_location", "plots_per_row", "label_rotation", "dpi"}
-
-
-def compute_matrix(bigwig_filenames,
- bed_filename,
- plot_filename=None,
- **extra_parameters):
- """Combine information from bigwig files *bigwig_filenames* and bed file
- *bed_filename*.
-
- If *plot_filename* is set, write the corresponding meta profile
- in this file.
- """
- parameters = deepcopy(DEFAULT_PARAMETERS)
- parameters.update(extra_parameters)
- heatm = heatmapper.heatmapper()
- heatm.computeMatrix(bigwig_filenames, bed_filename, parameters)
- if "sample_labels" in parameters:
- heatm.matrix.set_sample_labels(parameters["sample_labels"])
- if "group_labels" in parameters:
- heatm.matrix.set_group_labels(parameters["group_labels"])
- # Fixing parameters (as in heatmapper.read_matrix_file
- # and heatmapper.save_matrix)
- nb_samples = len(heatm.matrix.sample_labels)
- hm_params = dict()
- for (key, val) in heatm.parameters.items():
- if isinstance(val, list) and not val:
- val = None
- if key in heatm.special_params and not isinstance(val, list):
- val = [val] * nb_samples
- if not val:
- val = [None] * nb_samples
- hm_params[key] = val
- heatm.parameters = hm_params
-
- if plot_filename is not None:
- print(f"plotting profile to {plot_filename}")
- prof_params = keyfilter(is_prof_param, parameters)
- prof_params["per_group"] = True
- prof = Profile(
- heatm, plot_filename,
- **prof_params)
- prof.plot_profile()
+# def is_prof_param(key):
+# """Determine if *key* corresponds to a valid parameter for a *Profile*."""
+# return key in {
+# "plot_title", "y_axis_label", "y_min", "y_max", "averagetype",
+# "reference_point_label", "start_label", "end_label",
+# "plot_height", "plot_width", "per_group",
+# "plot_type", "image_format", "color_list",
+# "legend_location", "plots_per_row", "label_rotation", "dpi"}
+
+
+# def compute_matrix(bigwig_filenames,
+# bed_filename,
+# plot_filename=None,
+# **extra_parameters):
+# """Combine information from bigwig files *bigwig_filenames* and bed file
+# *bed_filename*.
+#
+# If *plot_filename* is set, write the corresponding meta profile
+# in this file.
+# """
+# parameters = deepcopy(DEFAULT_PARAMETERS)
+# parameters.update(extra_parameters)
+# heatm = heatmapper.heatmapper()
+# heatm.computeMatrix(bigwig_filenames, bed_filename, parameters)
+# if "sample_labels" in parameters:
+# heatm.matrix.set_sample_labels(parameters["sample_labels"])
+# if "group_labels" in parameters:
+# heatm.matrix.set_group_labels(parameters["group_labels"])
+# # Fixing parameters (as in heatmapper.read_matrix_file
+# # and heatmapper.save_matrix)
+# nb_samples = len(heatm.matrix.sample_labels)
+# hm_params = dict()
+# for (key, val) in heatm.parameters.items():
+# if isinstance(val, list) and not val:
+# val = None
+# if key in heatm.special_params and not isinstance(val, list):
+# val = [val] * nb_samples
+# if not val:
+# val = [None] * nb_samples
+# hm_params[key] = val
+# heatm.parameters = hm_params
+#
+# if plot_filename is not None:
+# print(f"plotting profile to {plot_filename}")
+# prof_params = keyfilter(is_prof_param, parameters)
+# prof_params["per_group"] = True
+# prof = Profile(
+# heatm, plot_filename,
+# **prof_params)
+# prof.plot_profile()
# def get_transcript_structure(fdb, transcript):
diff --git a/setup.py b/setup.py
index 4e2acc3fb2300ff965dfe56819123498e8825fae..2df66a2058764b23e4506c7e3aa1cec2c5aa4503 100644
--- a/setup.py
+++ b/setup.py
@@ -17,7 +17,7 @@ from setuptools import setup, find_packages
name = "plotting_scripts"
-__version__ = "0.1"
+__version__ = "0.2"
setup(