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Merged
FerriolCalvet merged 1 commit into from
Apr 8, 2025
Merged

Write all versions of mutational profiles #271

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33 changes: 24 additions & 9 deletions bin/mut_profile.py
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Original file line number Diff line number Diff line change
Expand Up @@ -98,7 +98,7 @@ def compute_mutation_matrix(sample_name, mutations_file, mutation_matrix, method
sep = "\t")


def compute_mutation_profile(sample_name, mutation_matrix_file, trinucleotide_counts_file, json_output, plot,
def compute_mutation_profile(sample_name, mutation_matrix_file, trinucleotide_counts_file, plot,
wgs = False, wgs_trinucleotide_counts = False, sigprofiler = False):
"""
Compute mutational profile from the input data
Expand All @@ -115,6 +115,14 @@ def compute_mutation_profile(sample_name, mutation_matrix_file, trinucleotide_co
mutation_matrix = mutation_matrix.set_index("CONTEXT_MUT")
total_mutations = np.sum(mutation_matrix[sample_name])

# proportion of SBS mutations per trinucleotide in panel
mutation_matrix[sample_name] = mutation_matrix[sample_name] / total_mutations
mutation_matrix.to_csv(f"{sample_name}.proportion_mutations.tsv",
header = True,
index = True,
sep = "\t")


# Load the trinucleotide counts
trinucleotide_counts = pd.read_csv(trinucleotide_counts_file, sep = "\t", header = 0)
trinucleotide_counts = trinucleotide_counts.set_index("CONTEXT")
Expand Down Expand Up @@ -149,7 +157,7 @@ def compute_mutation_profile(sample_name, mutation_matrix_file, trinucleotide_co
mut_probability.index.name = "CONTEXT_MUT"
mut_probability = mut_probability.reset_index()

mut_probability.to_csv(json_output,
mut_probability.to_csv(f"{sample_name}.profile.tsv",
header = True,
index = False,
sep = "\t")
Expand All @@ -163,7 +171,7 @@ def compute_mutation_profile(sample_name, mutation_matrix_file, trinucleotide_co
output_f = f'{sample_name}.profile.pdf')

# plot the profile as a percentage of SBS mutations seen in our sequenced panel
plot_profile(dict(zip(mutation_matrix.index, [x[0].item() for x in (mutation_matrix / mutation_matrix.sum()).values])),
plot_profile(dict(zip(mutation_matrix.index, mutation_matrix[sample_name])),
title=f'{sample_name} ({round(total_mutations)} muts)',
output_f = f'{sample_name}.profile.percentage.pdf')

Expand All @@ -185,22 +193,30 @@ def compute_mutation_profile(sample_name, mutation_matrix_file, trinucleotide_co
profile_trinuc_clean = profile_trinuc_clean.reindex(contexts_formatted)
profile_trinuc_clean.columns = [sample_name]

profile_trinuc_clean.to_csv(f"{json_output}.matrix.WGS",
profile_trinuc_clean.to_csv(f"{sample_name}.matrix.WGS.tsv",
header = True,
index = True,
sep = "\t")

profile_trinuc_clean_proportion = profile_trinuc_clean.copy()
profile_trinuc_clean_proportion[sample_name] = profile_trinuc_clean_proportion[sample_name] / profile_trinuc_clean_proportion[sample_name].sum()
profile_trinuc_clean_proportion.to_csv(f"{sample_name}.proportion_mutations.WGS.tsv",
header = True,
index = True,
sep = "\t")


# plot the profile as a percentage of SBS mutations seen after sequencing one WGS
# if mutations were occuring with the same probabilities as they occur in our sequenced panel
plot_profile(dict(zip(profile_trinuc_clean.index.values, (profile_trinuc_clean[sample_name] / profile_trinuc_clean[sample_name].sum()).values)),
plot_profile(dict(zip(profile_trinuc_clean_proportion.index.values, profile_trinuc_clean_proportion[sample_name].values)),
title=f'{sample_name} ({round(total_mutations)} muts)',
output_f = f'{sample_name}.profile.percentage_WGS.pdf')

if sigprofiler:
profile_trinuc_clean.index = contexts_formatted_sigprofiler
profile_trinuc_clean.index.name = "CONTEXT_MUT"
profile_trinuc_clean = profile_trinuc_clean.reset_index().sort_values(by = "CONTEXT_MUT")
profile_trinuc_clean.to_csv(f"{json_output}.matrix.WGS.sigprofiler",
profile_trinuc_clean.to_csv(f"{sample_name}.matrix.WGS.sigprofiler.tsv",
header = True,
index = False,
sep = "\t")
Expand All @@ -220,7 +236,6 @@ def compute_mutation_profile(sample_name, mutation_matrix_file, trinucleotide_co

@click.option('--mutation_matrix', type=click.Path(exists=True), help='Mutation matrix file (for profile mode)')
@click.option('--trinucleotide_counts', type=click.Path(exists=True), help='Trinucleotide counts file (for profile mode)')
@click.option('--out_profile', type=click.Path(), help='JSON output file (for profile mode)')
@click.option('--plot', is_flag=True, help='Generate plot and save as PDF')
@click.option('--wgs', is_flag=True, help='Store matrix of mutation counts at WGS level')
@click.option('--wgs_trinucleotide_counts', type=click.Path(exists=True), help='Trinucleotide counts file of the WGS (for profile mode if WGS active)')
Expand All @@ -229,7 +244,7 @@ def compute_mutation_profile(sample_name, mutation_matrix_file, trinucleotide_co
@click.option('--sigprofiler', is_flag=True, help='Store the index column using the SigProfiler format')

def main(mode, sample_name, mut_file, out_matrix, method, pseud, sigprofiler, per_sample, mutation_matrix,
trinucleotide_counts, out_profile, plot, wgs, wgs_trinucleotide_counts):
trinucleotide_counts, plot, wgs, wgs_trinucleotide_counts):

if mode == 'matrix':
click.echo(f"Running in matrix mode...")
Expand All @@ -239,7 +254,7 @@ def main(mode, sample_name, mut_file, out_matrix, method, pseud, sigprofiler, pe

elif mode == 'profile':
click.echo(f"Running in profile mode...")
compute_mutation_profile(sample_name, mutation_matrix, trinucleotide_counts, out_profile, plot, wgs, wgs_trinucleotide_counts, sigprofiler)
compute_mutation_profile(sample_name, mutation_matrix, trinucleotide_counts, plot, wgs, wgs_trinucleotide_counts, sigprofiler)
click.echo("Profile computation completed.")

else:
Expand Down
16 changes: 9 additions & 7 deletions modules/local/compute_profile/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -11,26 +11,28 @@ process COMPUTE_PROFILE {
path( wgs_trinucleotides )

output:
tuple val(meta), path("*.profile.tsv") , emit: profile
tuple val(meta), path("*.pdf") , optional:true , emit: plots
tuple val(meta), path("*.matrix.WGS") , optional:true , emit: wgs
tuple val(meta), path("*.matrix.WGS.sigprofiler") , optional:true , emit: wgs_sigprofiler
path "versions.yml" , topic: versions
tuple val(meta), path("*.profile.tsv") , emit: profile
tuple val(meta), path("*.proportion_mutations.tsv") , optional:true , emit: panel_proportions
tuple val(meta), path("*.proportion_mutations.WGS.tsv") , optional:true , emit: wgs_proportions
tuple val(meta), path("*.matrix.WGS.tsv") , optional:true , emit: wgs
tuple val(meta), path("*.matrix.WGS.sigprofiler.tsv") , optional:true , emit: wgs_sigprofiler

tuple val(meta), path("*.pdf") , optional:true , emit: plots

path "versions.yml" , topic: versions

when:
task.ext.when == null || task.ext.when

script:
def args = task.ext.args ?: ""
def prefix = task.ext.prefix ?: "${meta.id}"
def filters = task.ext.filters ?: ""
def wgs_trinuc = wgs_trinucleotides ? "--wgs --wgs_trinucleotide_counts ${wgs_trinucleotides}" : ""
"""
mut_profile.py profile \\
--sample_name ${prefix} \\
--mutation_matrix ${matrix} \\
--trinucleotide_counts ${trinucleotide} \\
--out_profile ${prefix}.profile.tsv \\
${wgs_trinuc} \\
${args}
cat <<-END_VERSIONS > versions.yml
Expand Down