Merge pull request #86 from zifornd/71-suppa-cluster-events-error

suppa fix attempt 1

bin/suppa_groups.py

@@ -0,0 +1,48 @@
+#!/usr/bin/env python3
+# Author: Zifo Bioinformatics
+# Email: [email protected]
+# License: MIT
+
+import argparse
+import itertools
+
+
+def main(args):
+    # Open file
+    handle = open(args.file, "r")
+
+    # Read header only
+    header = handle.readline()
+
+    # Split header by delimiter (e.g., transcript_GBR_1)
+    samples = header.split("\t")
+
+    # Trim replicate number (e.g., transcript_GBR_1 -> transcript_GBR)
+    conditions = [sample.rsplit("_", 1)[0] for sample in samples]
+
+    # Close file
+    handle.close()
+
+    # Create list of consecutive condition indices (e.g., [[1,2], [3,4]])
+    last_index = 0
+    out = []
+    for v, g in itertools.groupby(enumerate(conditions), lambda k: k[1]):
+        l = [*g]
+        out.append([last_index + 1, l[-1][0] + 1])
+        last_index += len(l)
+
+    # Assert that condition indices are consecutive
+    assert len(out) == 2, "Column numbers have to be continuous, with no overlapping or missing columns between them."
+
+    # Format ranges for printing
+    groups = ",".join([f"{start}-{end}" for start, end in out])
+
+    # Print to stdout without newline
+    print(groups, end="")
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument("file")
+    args = parser.parse_args()
+    main(args)

modules/local/suppa_clusterevents.nf

@@ -11,7 +11,7 @@ process CLUSTEREVENTS {
     input:
     tuple val(cond1), val(cond2), path(dpsi)
     tuple val(cond1), val(cond2), path(psivec)
-    val cluster_ranges // e.g. 1-3,4-6
+    val group_ranges // e.g. 1-3,4-6
     val prefix
     val clusterevents_dpsithreshold    // val params.clusterevents_dpsithreshold
     val clusterevents_eps              // val params.clusterevents_eps
@@ -43,7 +43,7 @@ process CLUSTEREVENTS {
         --eps $clusterevents_eps \\
         --metric $clusterevents_metric \\
         --min-pts $clusterevents_min_pts \\
-        --groups $cluster_ranges \\
+        --groups $group_ranges \\
         --clustering $clusterevents_method \\
         $clusterevents_sigthreshold $clusterevents_separation -o ${cond1}-${cond2}_${prefix}_cluster
 

modules/local/suppa_clustergroups.nf

@@ -0,0 +1,24 @@
+process CLUSTERGROUPS {
+    tag "${cond1}-${cond2}"
+    label 'process_single'
+
+    conda "conda-forge::python=3.9.5"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/python:3.9--1' :
+        'biocontainers/python:3.9--1' }"
+
+    input:
+    tuple val(cond1), val(cond2), path(psivec)
+
+    output:
+    stdout
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    """
+    suppa_groups.py $psivec
+    """
+
+}

subworkflows/local/suppa.nf

@@ -15,6 +15,9 @@ include { SPLIT_FILES as SPLIT_FILES_IOI } from '../../modules/local/suppa_split
 include { DIFFSPLICE as DIFFSPLICE_IOE } from '../../modules/local/suppa_diffsplice.nf'
 include { DIFFSPLICE as DIFFSPLICE_IOI } from '../../modules/local/suppa_diffsplice.nf'
 
+include { CLUSTERGROUPS as CLUSTERGROUPS_IOE } from '../../modules/local/suppa_clustergroups.nf'
+include { CLUSTERGROUPS as CLUSTERGROUPS_IOI } from '../../modules/local/suppa_clustergroups.nf'
+
 include { CLUSTEREVENTS as CLUSTEREVENTS_IOE } from '../../modules/local/suppa_clusterevents.nf'
 include { CLUSTEREVENTS as CLUSTEREVENTS_IOI } from '../../modules/local/suppa_clusterevents.nf'
 
@@ -85,7 +88,7 @@ workflow SUPPA {
     ch_dpsi_local             = Channel.empty()
     ch_psivec_local           = Channel.empty()
 
-    ch_ranges_ioe             = Channel.empty()
+    ch_groups_ioe             = Channel.empty()
     ch_cluster_vec_local      = Channel.empty()
     ch_cluster_log_local      = Channel.empty()
 
@@ -149,13 +152,13 @@ workflow SUPPA {
 
             ch_suppa_local_contrasts = ch_suppa_local_contrasts
                 .map { it -> [it['treatment'], it] }
-                .cross ( ch_suppa_tpm_conditions )
-                .map { it -> it[0][1] + ['tpm1': it[1][1]] }
+                .combine ( ch_suppa_tpm_conditions, by: 0 )
+                .map { it -> it[1] + ['tpm1': it[2]] }
 
             ch_suppa_local_contrasts = ch_suppa_local_contrasts
                 .map { it -> [it['control'], it] }
-                .cross ( ch_suppa_tpm_conditions )
-                .map { it -> it[0][1] + ['tpm2': it[1][1]] }
+                .combine ( ch_suppa_tpm_conditions, by: 0 )
+                .map { it -> it[1] + ['tpm2': it[2]] }
 
             // Add PSI files to contrasts channel
 
@@ -165,13 +168,13 @@ workflow SUPPA {
 
             ch_suppa_local_contrasts = ch_suppa_local_contrasts
                 .map { it -> [it['treatment'], it] }
-                .cross ( ch_suppa_psi_conditions )
-                .map { it -> it[0][1] + ['psi1': it[1][1]] }
+                .combine ( ch_suppa_psi_conditions, by: 0 )
+                .map { it -> it[1] + ['psi1': it[2]] }
 
             ch_suppa_local_contrasts = ch_suppa_local_contrasts
                 .map { it -> [it['control'], it] }
-                .cross ( ch_suppa_psi_conditions )
-                .map { it -> it[0][1] + ['psi2': it[1][1]] }
+                .combine ( ch_suppa_psi_conditions, by: 0 )
+                .map { it -> it[1] + ['psi2': it[2]] }
 
             // Create input channels to diffsplice process
 
@@ -202,16 +205,16 @@ workflow SUPPA {
 
                 // Get ranges for cluster analysis
 
-                ch_ranges_ioe = SPLIT_FILES_IOE.out.ranges
-                    .splitText( by: 1 ) { it.trim() }
-                    .first()
+                CLUSTERGROUPS_IOE ( ch_psivec_local )
+
+                ch_groups_ioe = CLUSTERGROUPS_IOE.out
 
                 // Run Clustering
 
                 CLUSTEREVENTS_IOE(
                     ch_dpsi_local,
                     ch_psivec_local,
-                    ch_ranges_ioe,
+                    ch_groups_ioe,
                     prefix,
                     clusterevents_dpsithreshold,
                     clusterevents_eps,
@@ -237,7 +240,7 @@ workflow SUPPA {
     ch_dpsi_isoform            = Channel.empty()
     ch_psivec_isoform          = Channel.empty()
 
-    ch_ranges_ioi              = Channel.empty()
+    ch_groups_ioi              = Channel.empty()
     ch_cluster_vec_isoform     = Channel.empty()
     ch_cluster_log_isoform     = Channel.empty()
 
@@ -300,13 +303,13 @@ workflow SUPPA {
 
             ch_suppa_isoform_contrasts = ch_suppa_isoform_contrasts
                 .map { it -> [it['treatment'], it] }
-                .cross ( ch_suppa_tpm_conditions )
-                .map { it -> it[0][1] + ['tpm1': it[1][1]] }
+                .combine ( ch_suppa_tpm_conditions, by: 0)
+                .map { it -> it[1] + ['tpm1': it[2]] }
 
             ch_suppa_isoform_contrasts = ch_suppa_isoform_contrasts
                 .map { it -> [it['control'], it] }
-                .cross ( ch_suppa_tpm_conditions )
-                .map { it -> it[0][1] + ['tpm2': it[1][1]] }
+                .combine ( ch_suppa_tpm_conditions, by: 0)
+                .map { it -> it[1] + ['tpm2': it[2]] }
 
             // Add PSI files to contrasts channel
 
@@ -316,13 +319,13 @@ workflow SUPPA {
 
             ch_suppa_isoform_contrasts = ch_suppa_isoform_contrasts
                 .map { it -> [it['treatment'], it] }
-                .cross ( ch_suppa_psi_conditions )
-                .map { it -> it[0][1] + ['psi1': it[1][1]] }
+                .combine ( ch_suppa_psi_conditions, by: 0 )
+                .map { it -> it[1] + ['psi1': it[2]] }
 
             ch_suppa_isoform_contrasts = ch_suppa_isoform_contrasts
                 .map { it -> [it['control'], it] }
-                .cross ( ch_suppa_psi_conditions )
-                .map { it -> it[0][1] + ['psi2': it[1][1]] }
+                .combine ( ch_suppa_psi_conditions, by: 0 )
+                .map { it -> it[1] + ['psi2': it[2]] }
 
             // Create input channels to diffsplice process
 
@@ -353,16 +356,16 @@ workflow SUPPA {
 
                 // Get ranges for cluster analysis
 
-                ch_ranges_ioi = SPLIT_FILES_IOI.out.ranges
-                    .splitText( by: 1 ) { it.trim() }
-                    .first()
+                CLUSTERGROUPS_IOI ( ch_psivec_isoform )
+
+                ch_groups_ioi = CLUSTERGROUPS_IOI.out
 
                 // Run Clustering
 
                 CLUSTEREVENTS_IOI(
                     ch_dpsi_isoform,
                     ch_psivec_isoform,
-                    ch_ranges_ioi,
+                    ch_groups_ioi,
                     prefix,
                     clusterevents_dpsithreshold,
                     clusterevents_eps,
@@ -375,6 +378,7 @@ workflow SUPPA {
 
                 ch_cluster_vec_isoform = CLUSTEREVENTS_IOI.out.clustvec
                 ch_cluster_log_isoform = CLUSTEREVENTS_IOI.out.cluster_log
+
             }
         }
     }

subworkflows/local/tx2gene_tximport.nf

@@ -34,7 +34,6 @@ workflow TX2GENE_TXIMPORT {
     .set{ salmon_results }
     UNTAR ( salmon_results.tar )
     salmon_results = salmon_results.dir.mix(UNTAR.out.untar)
-    salmon_results.view()
 
     //
     // Quantify and merge counts across samples