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Merged
grexor merged 2 commits into from
Oct 8, 2025
Merged

Dev #108

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3c9d656
Merge pull request #107 from bedapub/main
grexor Oct 7, 2025
2a09de2
removed platform
grexor Oct 8, 2025
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2 changes: 1 addition & 1 deletion Snakefile
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
import os
import fireducks.pandas as pd
import pandas as pd
import splicekit

DEFAULT_CORES = config["defaults"]["cores"]
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73 changes: 4 additions & 69 deletions splicekit/core/annotation.py
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Expand Up @@ -134,23 +134,7 @@ def make_comparisons():
annotation.samples = [str(el) for el in annotation.samples]

def write_comparisons():
if splicekit.config.platform == 'SLURM':
job_rmats="""
#!/bin/bash
#SBATCH --job-name={job_name} # Job name
#SBATCH --ntasks=1 # Number of tasks
#SBATCH --mem=8G # Allocate memory
#SBATCH --nodes=1 # All tasks on one node
#SBATCH --partition=short # Select queue
#SBATCH --output=logs/rmats/{comparison_name}.out # Output file
#SBATCH --error=logs/rmats/{comparison_name}.err # Error file

{container} run_rmats --b1 results/rmats/{comparison_name}_test.tab --b2 results/rmats/{comparison_name}_control.tab --gtf {gtf_path} -t paired --readLength 150 --variable-read-length --allow-clipping --nthread 4 --od results/rmats/{comparison_name}_results --tmp results/rmats/{comparison_name}_temp
"""

else:

job_rmats="""
job_rmats="""
#!/bin/bash
#BSUB -J {job_name} # job name
#BSUB -n 1 # number of tasks
Expand Down Expand Up @@ -213,23 +197,7 @@ def write_comparisons():
write_mds_job()

def write_edgeR_jobs():
if splicekit.config.platform == 'SLURM':
job_edgeR="""
#!/bin/bash
#SBATCH --job-name={job_name} # Job name
#SBATCH --ntasks=1 # Number of tasks
#SBATCH --nodes=1 # All tasks on one node
#SBATCH --mem=8G # Allocate memory
#SBATCH --partition=short # Select queue
#SBATCH --output=logs/edgeR/{atype}/{comparison_name}.out # Output file
#SBATCH --error=logs/edgeR/{atype}/{comparison_name}.err # Error file

module load R
{container} R --no-save --args {input_folder} {atype} {control_name} {test_name} {comparison_name} {sample_membership} {filter_low} < {core_path}/comps_edgeR.R
"""

else:
job_edgeR="""
job_edgeR="""
#!/bin/bash
#BSUB -J {job_name} # job name
#BSUB -n 1 # number of tasks
Expand Down Expand Up @@ -332,23 +300,7 @@ def write_edgeR_jobs():
fsh_acceptor_anchors.close()

def write_dexseq_jobs():
if splicekit.config.platform == 'SLURM':
job_dexseq="""
#!/bin/bash
#SBATCH --job-name={job_name} # Job name
#SBATCH --ntasks=1 # Number of tasks
#SBATCH --nodes=1 # All tasks on one node
#SBATCH --mem=8G # Allocate memory
#SBATCH --partition=short # Select queue
#SBATCH --output=logs/dexseq/{atype}/{comparison_name}.out # Output file
#SBATCH --error=logs/dexseq/{atype}/{comparison_name}.err # Error file

module load R
{container} R --no-save --args {input_folder} {atype} {control_name} {test_name} {comparison_name} {sample_membership} {samples} < {core_path}/comps_dexseq.R
"""

else:
job_dexseq="""
job_dexseq="""
#!/bin/bash
#BSUB -J {job_name} # job name
#BSUB -n 1 # number of tasks
Expand Down Expand Up @@ -392,24 +344,7 @@ def write_dexseq_jobs():
fsh_exons.close()

def write_mds_job():
if splicekit.config.platform == 'SLURM':
job_mds="""
#!/bin/bash
#SBATCH --job-name=edgeR_mds # Job name
#SBATCH --ntasks=1 # Number of tasks
#SBATCH --nodes=1 # All tasks on one node
#SBATCH --mem=8G # Allocate memory
#SBATCH --partition=short # Select queue
#SBATCH --output=logs/edgeR/mds/mds.out # Output file
#SBATCH --error=logs/edgeR/mds/mds.err # Error file

module load R
{container} R --no-save --args {input_folder} {sample_membership} {filter_low} < {core_path}/comps_edgeR_mds.R
"""

else:

job_mds="""
job_mds="""
#!/bin/bash
#BSUB -J mds # job name
#BSUB -n 1 # number of tasks
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2 changes: 1 addition & 1 deletion splicekit/judge/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
import sys
import seaborn as sns
import matplotlib.pyplot as plt
import fireducks.pandas as pd
import pandas as pd
from scipy.stats.stats import pearsonr
import glob
import math
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