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v0.9.0 release #38

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merged 6 commits into from
Oct 6, 2024
Merged

v0.9.0 release #38

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f4d9504
Add grid functionality
alexsweeten Oct 6, 2024
a08a2ec
Merge branch 'main' of https://github.com/marbl/ModDotPlot into develop
alexsweeten Oct 6, 2024
363ed50
Update grid functionality
alexsweeten Oct 6, 2024
9563b4a
lint with black
alexsweeten Oct 6, 2024
f5f10d9
bump version
alexsweeten Oct 6, 2024
50ecda4
remove debug artifact
alexsweeten Oct 6, 2024
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2 changes: 1 addition & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"

[project]
name = "ModDotPlot"
version = "0.8.8"
version = "0.9.0"
requires-python = ">= 3.7"
dependencies = [
"pysam",
Expand Down
2 changes: 1 addition & 1 deletion src/moddotplot/const.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
VERSION = "0.8.8"
VERSION = "0.9.0"
COLS = [
"#query_name",
"query_start",
Expand Down
172 changes: 123 additions & 49 deletions src/moddotplot/moddotplot.py
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@

import argparse
import math
from moddotplot.static_plots import read_df_from_file, create_plots
from moddotplot.static_plots import read_df_from_file, create_plots, create_grid
import json
import numpy as np
import pickle
Expand Down Expand Up @@ -342,6 +342,12 @@ def get_parser():
help="Plot comparative plots in an NxN grid like format.",
)

static_parser.add_argument(
"--grid-only",
action="store_true",
help="Plot comparative plots in an NxN grid like format, skipping individual plots",
)

# TODO: Implement static mode logging options

return parser
Expand Down Expand Up @@ -428,6 +434,13 @@ def main():
args.bin_freq = config.get("bin_freq", args.bin_freq)

# TODO: Include logging options here
# Check if conflicitng command line args
if args.grid or args.grid_only:
if not (args.compare or args.compare_only) and not args.bed:
print(
f"Option --grid was selected, but no comparative plots will be produced. Please rerun ModDotPlot with the `--compare` or `--compare-only` option.\n"
)
sys.exit(10)

# -----------INPUT COMMAND VALIDATION-----------
# TODO: More tests!
Expand All @@ -447,65 +460,100 @@ def main():

# -----------BEDFILE INPUT FOR STATIC MODE-----------
if hasattr(args, "bed") and args.bed:
if args.grid or args.grid_only:
single_vals = []
double_vals = []
single_val_name = []
double_val_name = []
try:
for bed in args.bed:
# If args.bed is provided as input, run static mode directly from the bed file. Skip counting input k-mers.
df = read_df_from_file(bed)

unique_query_names = df["#query_name"].unique()
unique_reference_names = df["reference_name"].unique()
assert len(unique_query_names) == len(unique_reference_names)
# TODO: Change this to allow for multiple seqs in bed file
assert len(unique_reference_names) == 1
self_id_scores = df[df["#query_name"] == df["reference_name"]]
pairwise_id_scores = df[df["#query_name"] != df["reference_name"]]
print(
f"Input bed file {bed} read successfully! Creating plots... \n"
)
if not args.grid_only:
print(
f"Input bed file {bed} read successfully! Creating plots... \n"
)
# Create directory
if not args.output_dir:
args.output_dir = os.getcwd()
if not os.path.exists(args.output_dir):
os.makedirs(args.output_dir)
if len(self_id_scores) > 1:
create_plots(
sdf=None,
directory=args.output_dir if args.output_dir else ".",
name_x=unique_query_names[0],
name_y=unique_query_names[0],
palette=args.palette,
palette_orientation=args.palette_orientation,
no_hist=args.no_hist,
width=args.width,
dpi=args.dpi,
is_freq=args.bin_freq,
xlim=args.axes_limits,
custom_colors=args.colors,
custom_breakpoints=args.breakpoints,
from_file=df,
is_pairwise=False,
axes_labels=args.axes_ticks,
)
if not args.grid_only:
create_plots(
sdf=None,
directory=args.output_dir if args.output_dir else ".",
name_x=unique_query_names[0],
name_y=unique_query_names[0],
palette=args.palette,
palette_orientation=args.palette_orientation,
no_hist=args.no_hist,
width=args.width,
dpi=args.dpi,
is_freq=args.bin_freq,
xlim=args.axes_limits,
custom_colors=args.colors,
custom_breakpoints=args.breakpoints,
from_file=df,
is_pairwise=False,
axes_labels=args.axes_ticks,
)
if args.grid or args.grid_only:
single_vals.append(df)
single_val_name.append(unique_query_names[0])
# Case 2: Pairwise bed file
if len(pairwise_id_scores) > 1:
create_plots(
sdf=None,
directory=args.output_dir if args.output_dir else ".",
name_x=unique_query_names[0],
name_y=unique_reference_names[0],
palette=args.palette,
palette_orientation=args.palette_orientation,
no_hist=args.no_hist,
width=args.width,
dpi=args.dpi,
is_freq=args.bin_freq,
xlim=args.axes_limits, # TODO: Get xlim working
custom_colors=args.colors,
custom_breakpoints=args.breakpoints,
from_file=df,
is_pairwise=True,
axes_labels=args.axes_ticks,
)
if not args.grid_only:
create_plots(
sdf=None,
directory=args.output_dir if args.output_dir else ".",
name_x=unique_query_names[0],
name_y=unique_reference_names[0],
palette=args.palette,
palette_orientation=args.palette_orientation,
no_hist=args.no_hist,
width=args.width,
dpi=args.dpi,
is_freq=args.bin_freq,
xlim=args.axes_limits,
custom_colors=args.colors,
custom_breakpoints=args.axes_ticks,
from_file=df,
is_pairwise=True,
axes_labels=args.axes_ticks,
)
if args.grid or args.grid_only:
double_vals.append(df)
double_val_name.append(
[unique_query_names[0], unique_reference_names[0]]
)
# Exit once all bed files have been iterated through
if args.grid or args.grid_only:
print(f"Creating a {len(sequences)}x{len(sequences)} grid.\n")
create_grid(
singles=single_vals,
doubles=double_vals,
directory=args.output_dir if args.output_dir else ".",
palette=args.palette,
palette_orientation=args.palette_orientation,
no_hist=args.no_hist,
single_names=single_val_name,
double_names=double_val_name,
is_freq=args.bin_freq,
xlim=args.axes_limits,
custom_colors=args.colors,
custom_breakpoints=args.axes_ticks,
axes_label=args.axes_ticks,
is_bed=True,
)
sys.exit(0)
except Exception as e:
# Exit code 7: Error getting info from bed file:
Expand All @@ -531,7 +579,6 @@ def main():
for i in args.fasta:
kmer_list.append(readKmersFromFile(i, args.kmer, False))
k_list = [item for sublist in kmer_list for item in sublist]

# Throw error if compare only selected with one sequence.
if len(k_list) < 2 and args.compare_only:
print(
Expand Down Expand Up @@ -817,8 +864,12 @@ def main():
# -----------SETUP STATIC MODE-----------
elif args.command == "static":
# -----------SET SPARSITY VALUE-----------
# TODO: this is not sorting correctly
if args.grid or args.grid_only:
grid_val_singles = []
grid_val_single_names = []
sequences = list(zip(seq_list, k_list))
if len(sequences) > 6 and (args.grid or args.grid_only):
print("Too many sequences to create a grid. Skipping. \n")

# Create output directory, if doesn't exist:
if (args.output_dir) and not os.path.exists(args.output_dir):
Expand Down Expand Up @@ -884,6 +935,9 @@ def main():
bed = convertMatrixToBed(
self_mat, win, args.identity, seq_list[i], seq_list[i], True
)
if args.grid or args.grid_only:
grid_val_singles.append(bed)
grid_val_single_names.append(sequences[i][0])

if not args.no_bed:
# Log saving bed file
Expand Down Expand Up @@ -923,8 +977,9 @@ def main():
if (args.compare or args.compare_only) and len(sequences) > 1:
# Set window size to args.window. Otherwise, set it to n/resolution

if args.grid:
grid_vals = []
if args.grid or args.grid_only:
grid_val_doubles = []
grid_val_double_names = []

for i in range(len(sequences)):
for j in range(i + 1, len(sequences)):
Expand Down Expand Up @@ -987,7 +1042,7 @@ def main():
expectation,
)
# Throw error if the matrix is empty
if np.all(pair_mat == 0):
if np.all(pair_mat == 0) and (not (args.grid or args.grid_only)):
print(
f"The pairwise identity matrix for {sequences[i][0]} and {sequences[j][0]} is empty. Skipping.\n"
)
Expand All @@ -1000,8 +1055,11 @@ def main():
seq_list[j],
False,
)
if args.grid:
grid_vals.append(bed)
if args.grid or args.grid_only:
grid_val_doubles.append(bed)
grid_val_double_names.append(
[larger_seq_name, smaller_seq_name]
)

if not args.no_bed:
# Log saving bed file
Expand Down Expand Up @@ -1045,8 +1103,24 @@ def main():
axes_labels=args.axes_ticks,
)

"""if args.grid:
print(grid_vals)"""
if args.grid or args.grid_only:
print(f"Creating a {len(sequences)}x{len(sequences)} grid.\n")
create_grid(
singles=grid_val_singles,
doubles=grid_val_doubles,
directory=args.output_dir if args.output_dir else ".",
palette=args.palette,
palette_orientation=args.palette_orientation,
no_hist=args.no_hist,
single_names=grid_val_single_names,
double_names=grid_val_double_names,
is_freq=args.bin_freq,
xlim=args.axes_limits,
custom_colors=args.colors,
custom_breakpoints=args.axes_ticks,
axes_label=args.axes_ticks,
is_bed=False,
)


if __name__ == "__main__":
Expand Down
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