From c20987eae442f568ed949528c1faf75349dfabcc Mon Sep 17 00:00:00 2001
From: msbentsen <mette.bentsen@mpi-bn.mpg.de>
Date: Mon, 29 Apr 2019 12:36:14 +0200
Subject: [PATCH] Getting ready for 0.4.0
---
CHANGES | 7 ++++-
setup.py | 5 ++-
tobias/TOBIAS.py | 27 +++++++++-------
tobias/__init__.py | 2 +-
tobias/footprinting/ATACorrect.py | 2 +-
tobias/footprinting/BINDetect.py | 23 ++++++--------
tobias/footprinting/BINDetect_functions.py | 4 +--
.../{footprint_scores.py => scorebigwig.py} | 31 ++++++++++---------
8 files changed, 55 insertions(+), 46 deletions(-)
rename tobias/footprinting/{footprint_scores.py => scorebigwig.py} (86%)
diff --git a/CHANGES b/CHANGES
index 806cd70..86297b9 100644
--- a/CHANGES
+++ b/CHANGES
@@ -1,5 +1,10 @@
-## 0.3.2 (2019-04-26)
+## 0.4.0 (2019-04-26)
- Added --add_region_columns to TFBScan
+- Renamed FootprintScores to ScoreBigwig
+- Added normalization of input score distributions in BINDetect
+- Added general warning for --cores > max number of processors when running multiprocessing
+- Updated PlotChanges to also plot mean_score and percent_bound as well as overview per motif cluster
+- Added MOODS-python as dependency through pip
## 0.3.1 (2019-04-10)
- Split motif ids between name/motif_id/output_prefix
\ No newline at end of file
diff --git a/setup.py b/setup.py
index 210fb09..6d2574f 100644
--- a/setup.py
+++ b/setup.py
@@ -1,7 +1,7 @@
import os
import sys
import re
-from setuptools import setup, Extension, dist
+from setuptools import setup, Extension, dist, find_packages
#Test if numpy is installed
try:
@@ -56,7 +56,7 @@ def readme():
author='Mette Bentsen',
author_email='mette.bentsen@mpi-bn.mpg.de',
license='MIT',
- packages=['tobias', 'tobias.footprinting', 'tobias.plotting', 'tobias.motifs', 'tobias.misc', 'tobias.utils'],
+ packages=find_packages(), #"tobias"), #['tobias', 'tobias.footprinting', 'tobias.plotting', 'tobias.motifs', 'tobias.misc', 'tobias.utils'],
entry_points={
'console_scripts': ['TOBIAS=tobias.TOBIAS:main']
},
@@ -77,7 +77,6 @@ def readme():
'pyBigWig',
'MOODS-python',
],
- scripts = ["tobias/utils/filter_important_factors.py"],
classifiers=[
'License :: OSI Approved :: MIT License',
'Intended Audience :: Science/Research',
diff --git a/tobias/TOBIAS.py b/tobias/TOBIAS.py
index 35e1dd9..b2fa07b 100644
--- a/tobias/TOBIAS.py
+++ b/tobias/TOBIAS.py
@@ -28,9 +28,9 @@
from argparse import SUPPRESS
import textwrap
-from tobias.footprinting.ATACorrect import *
-from tobias.footprinting.footprint_scores import *
-from tobias.footprinting.BINDetect import *
+from tobias.footprinting.atacorrect import *
+from tobias.footprinting.scorebigwig import *
+from tobias.footprinting.bindetect import *
from tobias.plotting.plot_aggregate import *
from tobias.plotting.plot_heatmap import *
@@ -44,7 +44,7 @@
from tobias.misc.subsample_bam import *
from tobias.misc.merge_pdfs import *
from tobias.misc.maxpos import *
-from tobias.misc.create_network import *
+#from tobias.misc.create_network import *
from tobias.misc.log2table import *
from tobias import __version__ as TOBIAS_VERSION
@@ -56,7 +56,7 @@ def main():
all_parser_info = {"Tools for footprinting analysis":
{
"ATACorrect":{"help":"Correct reads with regards to Tn5 sequence bias", "add_arguments": add_atacorrect_arguments, "function":run_atacorrect},
- "FootprintScores":{"help":"Calculate footprint scores from cutsites", "add_arguments": add_footprint_arguments, "function":run_footprinting, "space":"\t"},
+ "ScoreBigwig":{"help":"Calculate scores such as footprints from cutsites", "add_arguments": add_scorebigwig_arguments, "function":run_scorebigwig, "replaces":"FootprintScores"},
"BINDetect":{"help":"Detect TF binding from footprints and motifs", "add_arguments": add_bindetect_arguments, "function":run_bindetect},
},
@@ -80,7 +80,7 @@ def main():
"MergePDF": {"help": "Merge pdf files to one", "add_arguments":add_mergepdf_arguments, "function":run_mergepdf},
"MaxPos": {"help": "Get .bed-positions of highest bigwig signal within .bed-regions", "add_arguments": add_maxpos_arguments, "function": run_maxpos},
"SubsampleBam": {"help": "Subsample a .bam-file using samtools", "add_arguments": add_subsample_arguments, "function": run_subsampling},
- "CreateNetwork": {"help": "Create TF-gene network from annotated TFBS", "add_arguments": add_network_arguments, "function": run_network, "space":"\t"},
+ #"CreateNetwork": {"help": "Create TF-gene network from annotated TFBS", "add_arguments": add_network_arguments, "function": run_network, "space":"\t"},
"Log2Table": {"help": "Convert logs from PlotAggregate to tab-delimitered tables of footprint stats", "add_arguments": add_log2table_arguments, "function": run_log2table}
}
}
@@ -116,16 +116,21 @@ def main():
subparser = info[tool]["add_arguments"](subparser)
subparser.set_defaults(func=info[tool]["function"])
all_tool_parsers[tool.lower()] = subparser
-
+
+ #Add version to subparser
+ subparser.add_argument("--version", action='version', version=TOBIAS_VERSION)
+
+ #Add parser for old tool names
+ if "replaces" in info[tool]:
+ all_tool_parsers[info[tool]["replaces"].lower()] = subparser
+
parser.description += "\n"
parser.description += "For help on each tool, please run: TOBIAS <TOOLNAME> --help\n"
-
- #Add version number to upper TOBIAS parser and all subparsers
+
+ #Add version number to upper TOBIAS parser
parser.description += "For version number: TOBIAS --version"
parser.add_argument("--version", action='version', version=TOBIAS_VERSION)
- for name in all_tool_parsers:
- all_tool_parsers[name].add_argument("--version", action='version', version=TOBIAS_VERSION)
#If no args, print help for top-level TOBIAS
if len(sys.argv[1:]) == 0:
diff --git a/tobias/__init__.py b/tobias/__init__.py
index 39a2139..6a9beea 100644
--- a/tobias/__init__.py
+++ b/tobias/__init__.py
@@ -1 +1 @@
-__version__ = "0.3.2"
+__version__ = "0.4.0"
diff --git a/tobias/footprinting/ATACorrect.py b/tobias/footprinting/ATACorrect.py
index d01b70e..89ae7da 100644
--- a/tobias/footprinting/ATACorrect.py
+++ b/tobias/footprinting/ATACorrect.py
@@ -37,7 +37,7 @@
import pysam
#Internal functions and classes
-from tobias.footprinting.ATACorrect_functions import *
+from tobias.footprinting.atacorrect_functions import *
from tobias.utils.utilities import *
from tobias.utils.regions import *
from tobias.utils.sequences import *
diff --git a/tobias/footprinting/BINDetect.py b/tobias/footprinting/BINDetect.py
index ee6acfc..cf93e11 100644
--- a/tobias/footprinting/BINDetect.py
+++ b/tobias/footprinting/BINDetect.py
@@ -36,7 +36,7 @@
import pysam
#Internal functions and classes
-from tobias.footprinting.BINDetect_functions import *
+from tobias.footprinting.bindetect_functions import *
from tobias.utils.utilities import *
from tobias.utils.regions import *
from tobias.utils.sequences import *
@@ -177,10 +177,9 @@ def run_bindetect(args):
#output and order
titles = []
+ titles.append("Raw score distributions")
+ titles.append("Normalized score distributions")
if args.debug:
-
- titles.append("Raw score distributions")
- titles.append("Normalized score distributions")
for (cond1, cond2) in comparisons:
titles.append("Background log2FCs ({0} / {1})".format(cond1, cond2))
@@ -361,10 +360,9 @@ def run_bindetect(args):
logger.comment("")
logger.info("Estimating score distribution per condition")
- if args.debug == True:
- fig = plot_score_distribution([background["signal"][bigwig] for bigwig in args.cond_names], labels=args.cond_names, title="Raw scores per condition")
- figure_pdf.savefig(fig, bbox_inches='tight')
- plt.close()
+ fig = plot_score_distribution([background["signal"][bigwig] for bigwig in args.cond_names], labels=args.cond_names, title="Raw scores per condition")
+ figure_pdf.savefig(fig, bbox_inches='tight')
+ plt.close()
logger.info("Normalizing scores")
list_of_vals = [background["signal"][bigwig] for bigwig in args.cond_names]
@@ -374,10 +372,9 @@ def run_bindetect(args):
for bigwig in args.cond_names:
background["signal"][bigwig] = args.norm_objects[bigwig].normalize(background["signal"][bigwig])
- if args.debug == True:
- fig = plot_score_distribution([background["signal"][bigwig] for bigwig in args.cond_names], labels=args.cond_names, title="Normalized scores per condition")
- figure_pdf.savefig(fig, bbox_inches='tight')
- plt.close()
+ fig = plot_score_distribution([background["signal"][bigwig] for bigwig in args.cond_names], labels=args.cond_names, title="Normalized scores per condition")
+ figure_pdf.savefig(fig, bbox_inches='tight')
+ plt.close()
###########################################################
logger.info("Estimating bound/unbound threshold")
@@ -413,7 +410,7 @@ def run_bindetect(args):
mode = scipy.optimize.fmin(lambda x: -scipy.stats.lognorm.pdf(x, *log_params), 0, disp=False)[0]
logger.debug("- Mode estimated at: {0}".format(mode))
pseudo = mode / 2.0 #pseudo is half the mode
- args.pseudo = pseudo #. append(pseudo)
+ args.pseudo = pseudo
logger.debug("Pseudocount estimated at: {0}".format(round(args.pseudo, 5)))
# Estimate theoretical normal for threshold
diff --git a/tobias/footprinting/BINDetect_functions.py b/tobias/footprinting/BINDetect_functions.py
index 8f265f1..a9a8c32 100644
--- a/tobias/footprinting/BINDetect_functions.py
+++ b/tobias/footprinting/BINDetect_functions.py
@@ -617,8 +617,8 @@ def plot_bindetect(motifs, cluster_obj, conditions, args):
#print(txts)
#Plot custom legend for colors
- legend_elements = [Line2D([0],[0], marker='o', color='w', markerfacecolor="red", label="More bound in {0}".format(conditions[0])),
- Line2D([0],[0], marker='o', color='w', markerfacecolor="blue", label="More bound in {0}".format(conditions[1]))]
+ legend_elements = [Line2D([0],[0], marker='o', color='w', markerfacecolor="red", label="Higher scores in {0}".format(conditions[0])),
+ Line2D([0],[0], marker='o', color='w', markerfacecolor="blue", label="Higher scores in {0}".format(conditions[1]))]
ax1.legend(handles=legend_elements, bbox_to_anchor=(1.05, 1), loc='upper left')
return(fig)
diff --git a/tobias/footprinting/footprint_scores.py b/tobias/footprinting/scorebigwig.py
similarity index 86%
rename from tobias/footprinting/footprint_scores.py
rename to tobias/footprinting/scorebigwig.py
index 8f521f0..356970a 100644
--- a/tobias/footprinting/footprint_scores.py
+++ b/tobias/footprinting/scorebigwig.py
@@ -31,12 +31,12 @@
from tobias.utils.logger import *
#-----------------------------------------------------------------#
-def add_footprint_arguments(parser):
+def add_scorebigwig_arguments(parser):
parser.formatter_class = lambda prog: argparse.RawDescriptionHelpFormatter(prog, max_help_position=40, width=90)
- description = "FootprintScores calculates footprint scores from ATAC-seq cutsites (.bigwig format) calculated using the ATACorrect tool.\n\n"
- description += "Usage: FootprintScores --signal <cutsites.bw> --output <output.bw>\n\n"
- description += "Output:\n- <footprint_scores.bigwig>"
+ description = "ScoreBigwig calculates scores (such as footprint-scores) from bigwig files (such as ATAC-seq cutsites calculated using the ATACorrect tool).\n\n"
+ description += "Usage: ScoreBigwig --signal <cutsites.bw> --regions <regions.bed> --output <output.bw>\n\n"
+ description += "Output:\n- <output.bw>"
parser.description = format_help_description("FootprintScores", description)
parser._action_groups.pop() #pop -h
@@ -48,20 +48,22 @@ def add_footprint_arguments(parser):
required.add_argument('-r', '--regions', metavar="<bed>", help="Genomic regions to run footprinting within")
optargs = parser.add_argument_group('Optional arguments')
- optargs.add_argument('--score', metavar="<score>", choices=["footprint", "sum", "FOS"], help="Type of scoring to perform on cutsites (footprint/sum/FOS) (default: footprint)", default="footprint")
+ optargs.add_argument('--score', metavar="<score>", choices=["footprint", "sum"], help="Type of scoring to perform on cutsites (footprint/sum) (default: footprint)", default="footprint")
+ #mean
+ #abs convert bigwig signal to absolute scores before calculating score
optargs.add_argument('--extend', metavar="<int>", type=int, help="Extend input regions with bp (default: 100)", default=100)
optargs.add_argument('--smooth', metavar="<int>", type=int, help="Smooth output signal by mean in <bp> windows (default: no smoothing)", default=1)
- optargs.add_argument('--min_limit', metavar="<float>", type=float, help="Limit input bigwig score range (default: no lower limit)") #default none
- optargs.add_argument('--max_limit', metavar="<float>", type=float, help="Limit input bigwig score range (default: no upper limit)") #default none
+ optargs.add_argument('--min-limit', metavar="<float>", type=float, help="Limit input bigwig score range (default: no lower limit)") #default none
+ optargs.add_argument('--max-limit', metavar="<float>", type=float, help="Limit input bigwig score range (default: no upper limit)") #default none
footprintargs = parser.add_argument_group('Parameters for score == footprint')
- optargs.add_argument('--fp_min', metavar="<int>", type=int, help="Minimum footprint width (default: 20)", default=20)
- optargs.add_argument('--fp_max', metavar="<int>", type=int, help="Maximum footprint width (default: 50)", default=50)
- optargs.add_argument('--flank_min', metavar="<int>", type=int, help="Minimum range of flanking regions (default: 10)", default=10)
- optargs.add_argument('--flank_max', metavar="<int>", type=int, help="Maximum range of flanking regions (default: 30)", default=30)
+ optargs.add_argument('--fp-min', metavar="<int>", type=int, help="Minimum footprint width (default: 20)", default=20)
+ optargs.add_argument('--fp-max', metavar="<int>", type=int, help="Maximum footprint width (default: 50)", default=50)
+ optargs.add_argument('--flank-min', metavar="<int>", type=int, help="Minimum range of flanking regions (default: 10)", default=10)
+ optargs.add_argument('--flank-max', metavar="<int>", type=int, help="Maximum range of flanking regions (default: 30)", default=30)
sumargs = parser.add_argument_group('Parameters for score == sum')
- optargs.add_argument('--window', metavar="<int>", type=int, help="The window for calculation of sum (default: 100)", default=100)
+ sumargs.add_argument('--window', metavar="<int>", type=int, help="The window for calculation of sum (default: 100)", default=100)
runargs = parser.add_argument_group('Run arguments')
runargs.add_argument('--cores', metavar="<int>", type=int, help="Number of cores to use for computation (default: 1)", default=1)
@@ -91,6 +93,7 @@ def calculate_scores(regions, args):
signal = region.get_signal(pybw_signal)
signal = np.nan_to_num(signal).astype("float64")
+ #
if args.min_limit != None:
signal[signal < args.min_limit] = args.min_limit
if args.max_limit != None:
@@ -125,7 +128,7 @@ def calculate_scores(regions, args):
#------------------------------------------------------------------------------------------#
-def run_footprinting(args):
+def run_scorebigwig(args):
check_required(args, ["signal", "output", "regions"])
check_files([args.signal, args.regions], "r")
@@ -135,7 +138,7 @@ def run_footprinting(args):
# Create logger and write info to log
#---------------------------------------------------------------------------------------#
- logger = TobiasLogger("FootprintScores", args.verbosity)
+ logger = TobiasLogger("ScoreBigwig", args.verbosity)
logger.begin()
parser = add_footprint_arguments(argparse.ArgumentParser())