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Split not_in_panel into two filters #222

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Merged
FerriolCalvet merged 1 commit into from
Jan 13, 2025
Merged

Split not_in_panel into two filters #222

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3 changes: 2 additions & 1 deletion bin/panels_computedna2protein.py
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,8 @@ def get_normal_maf(path_maf):
print("Initial shape of MAF DataFrame:", maf_df.shape)

maf_df_filtered = maf_df.loc[
(~maf_df["FILTER.not_in_panel"]) &
(~maf_df["FILTER.not_in_exons"]) &
(~maf_df["FILTER.not_covered"]) &
(maf_df["TYPE"].isin(["SNV", "INSERTION", "DELETION"]))
].reset_index(drop=True)

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18 changes: 6 additions & 12 deletions bin/plot_selectionfeatures.py
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Expand Up @@ -745,19 +745,13 @@ def preprocess_maf(maf_df):

maf_df["CLEAN_SAMPLE_ID"] = maf_df["SAMPLE_ID"].apply(lambda x: "_".join(x.split("_")[1:3]))

# Reduce the number of samples and the number of mutations
samples_histo_findings = ['P19_0017_BDO_01', 'P19_0017_BTR_01',
'P19_0032_BDO_01', 'P19_0032_BTR_01',
'P19_0044_BDO_01', 'P19_0044_BTR_01']
maf_df_f = maf_df.loc[(maf_df["VAF"] <= 0.35) &
# (maf_df["FILTER.repetitive_variant"] == False) & # filter not well defined yet; may hide hotspots
(~maf_df["FILTER.not_in_panel"]) &
(~maf_df["FILTER.no_pileup_support"]) & # avoid variants w/o VAF recomputed
(~maf_df["FILTER.n_rich"]) &
(~maf_df["FILTER.low_mappability"]) &
(~maf_df["FILTER.other_sample_SNP"]) &
(~maf_df["SAMPLE_ID"].isin(samples_histo_findings))
].reset_index(drop = True)
(~maf_df["FILTER.not_in_exons"]) &
(~maf_df["FILTER.not_covered"]) &
(~maf_df["FILTER.no_pileup_support"]) & # avoid variants w/o VAF recomputed
(~maf_df["FILTER.n_rich"]) &
(~maf_df["FILTER.low_mappability"])
].reset_index(drop = True)

# SNV
snvs_maf = maf_df_f[(maf_df_f["TYPE"] == 'SNV') &
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7 changes: 7 additions & 0 deletions conf/modules.config
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Expand Up @@ -168,6 +168,13 @@ process {
]
}

withName: 'FILTEREXONS' {
ext.filtername = 'not_in_exons'
}

withName: 'FILTERPANEL' {
ext.filtername = 'not_covered'
}

withName: 'SUBSETDEPTHS' {
ext.prefix = { "${meta.id}.subset_depths" }
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4 changes: 2 additions & 2 deletions conf/test.config
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Expand Up @@ -50,8 +50,8 @@ params {

mutated_epithelium = false
mutated_epithelium_vaf = false
expected_mutation_rate = true
dnds = true
expected_mutation_rate = false
dnds = false

indels = false

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5 changes: 2 additions & 3 deletions modules/local/filterbed/main.nf
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Expand Up @@ -26,10 +26,9 @@ process FILTERBED {
task.ext.when == null || task.ext.when

script:
def args = task.ext.args ?: ""
def prefix = task.ext.prefix ?: "${meta.id}"
def filtername = task.ext.filtername ?: "covered"
"""
filterbed.py ${maf} ${bedfile} not_in_panel;
filterbed.py ${maf} ${bedfile} ${filtername};

cat <<-END_VERSIONS > versions.yml
"${task.process}":
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7 changes: 6 additions & 1 deletion subworkflows/local/mutationpreprocessing/main.nf
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Expand Up @@ -5,6 +5,7 @@ include { VCF_ANNOTATE_ENSEMBLVEP as VCFANNOTATE } from '../../nf-core/vc
include { SUMMARIZE_ANNOTATION as SUMANNOTATION } from '../../../modules/local/summarize_annotation/main'
include { VCF2MAF as VCF2MAF } from '../../../modules/local/vcf2maf/main'
include { FILTERBED as FILTERPANEL } from '../../../modules/local/filterbed/main'
include { FILTERBED as FILTEREXONS } from '../../../modules/local/filterbed/main'
include { MERGE_BATCH as MERGEBATCH } from '../../../modules/local/mergemafs/main'
include { FILTER_BATCH as FILTERBATCH } from '../../../modules/local/filtermaf/main'
include { WRITE_MAFS as WRITEMAF } from '../../../modules/local/writemaf/main'
Expand All @@ -20,6 +21,7 @@ workflow MUTATION_PREPROCESSING {
vep_cache
vep_extra_files
bedfile
bedfile_exons
groups
sequence_information_df

Expand All @@ -46,7 +48,10 @@ workflow MUTATION_PREPROCESSING {
VCF2MAF(vcfs, SUMANNOTATION.out.tab)
ch_versions = ch_versions.mix(VCF2MAF.out.versions.first())

FILTERPANEL(VCF2MAF.out.maf, bedfile)
FILTEREXONS(VCF2MAF.out.maf, bedfile_exons)
ch_versions = ch_versions.mix(FILTEREXONS.out.versions.first())

FILTERPANEL(FILTEREXONS.out.maf, bedfile)
ch_versions = ch_versions.mix(FILTERPANEL.out.versions.first())

// Join all samples' MAFs and put them in a channel to be merged
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22 changes: 12 additions & 10 deletions workflows/deepcsa.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -169,17 +169,17 @@ workflow DEEPCSA{
//
// Separate input BAMs and VCFs
//
INPUT_CHECK.out.mutations.
map{ it -> [it[0], it[1]]}.
set{ meta_vcfs_alone }
INPUT_CHECK.out.mutations
.map{ it -> [it[0], it[1]]}
.set{ meta_vcfs_alone }

INPUT_CHECK.out.mutations.
map{ it -> [it[0], it[2]]}.
set{ meta_bams_alone }
INPUT_CHECK.out.mutations
.map{ it -> [it[0], it[2]]}
.set{ meta_bams_alone }

INPUT_CHECK.out.mutations.
map{ it -> [it[0], it[3], it[4]]}.
set{ meta_pileupbamindex_alone }
INPUT_CHECK.out.mutations
.map{ it -> [it[0], it[3], it[4]]}
.set{ meta_pileupbamindex_alone }



Expand Down Expand Up @@ -221,7 +221,9 @@ workflow DEEPCSA{
}

// Mutation preprocessing
MUT_PREPROCESSING(meta_vcfs_alone, vep_cache, vep_extra_files, CREATEPANELS.out.exons_consensus_bed,
MUT_PREPROCESSING(meta_vcfs_alone, vep_cache, vep_extra_files,
CREATEPANELS.out.all_consensus_bed,
CREATEPANELS.out.exons_bed,
TABLE2GROUP.out.json_allgroups, seqinfo_df)
ch_versions = ch_versions.mix(MUT_PREPROCESSING.out.versions)
positive_selection_results = MUT_PREPROCESSING.out.somatic_mafs
Expand Down