Skip to content

Commit

Permalink
Merge pull request #38 from marbl/develop
Browse files Browse the repository at this point in the history 
v0.9.0 release
  • Loading branch information
@alexsweeten
alexsweeten authored Oct 6, 2024
2 parents 2d0adb3 + 50ecda4 commit 02b55f9
Show file tree
Hide file tree
Showing 4 changed files with 668 additions and 62 deletions.
2 changes: 1 addition & 1 deletion pyproject.toml
View file
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
View file
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
View file
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
Loading

0 comments on commit 02b55f9

Please sign in to comment.