Oncodrive3D 1.0.4__py3-none-any.whl

scripts/plotting/utils.py

@@ -0,0 +1,594 @@
+import logging
+import os
+
+import daiquiri
+import subprocess
+import click
+import sys
+import numpy as np
+import pandas as pd
+import json
+
+from scripts import __logger_name__
+
+logger = daiquiri.getLogger(__logger_name__ + ".plotting.utils")
+
+logging.getLogger('urllib3.connectionpool').setLevel(logging.WARNING)
+
+
+
+def get_species(species):
+    """
+    Simply change species name to accepted format.
+    """
+    
+    if species.capitalize() == "Human" or species.capitalize() == "Homo sapiens":
+        species = "Homo sapiens"
+    elif species.capitalize() == "Mouse" or species.capitalize() == "Mus musculus": 
+        species = "Mus musculus"
+    else:
+        raise RuntimeError(f"Failed to recognize '{species}' as species. Currently accepted ones are 'Homo sapiens' and 'Mus musculus'. Exiting...")
+
+    return species
+
+
+def clean_annotations_dir(path: str, loc: str) -> None:
+    """
+    Clean the annotations directory by removing specific files 
+    and subdirectories.
+
+    Args:
+        path (str): Path to the directory to be cleaned.
+    """
+
+    if loc == "d":
+
+        clean_files = f"rm -rf {os.path.join(path, '*.csv')} {os.path.join(path, '*.tsv')} {os.path.join(path, '*.json')} {os.path.join(path, '.*.txt')}"
+        clean_ddg = ["rm", "-rf", os.path.join(path, "stability_change")]
+        clean_pdbtool = ["rm", "-rf", os.path.join(path, "pdb_tool")]
+        #clean_log = ["rm", "-rf", os.path.join(path, "log")]
+
+        logger.debug(clean_files)
+        subprocess.run(clean_files, shell=True)
+
+        logger.debug(' '.join(clean_ddg))
+        subprocess.run(clean_ddg)
+        
+        logger.debug(' '.join(clean_pdbtool))
+        subprocess.run(clean_pdbtool)
+
+        # logger.debug(' '.join(clean_log))
+        # subprocess.run(clean_log)
+
+    elif loc == "r":
+        # TODO: implement cleaning function for output
+        pass
+
+
+def clean_annot_dir(path: str, loc: str = 'd') -> None:
+    """
+    Clean it upon request if it already exists.
+
+    Args:
+        path (str): Path to the directory to be created or cleaned.
+    """
+
+    if os.listdir(path) != ['log']:
+        logger.warning(f"Directory {path} already exists and is not empty.")
+
+        overwrite = "y" if click.get_current_context().params['yes'] else input("Clean existing directory? (y/n): ")
+        while overwrite.lower() not in ["y", "yes", "n", "no"]:
+            print("Please choose yes or no")
+            overwrite = input("Clean existing directory? (y/n): ")
+
+        if overwrite.lower() in ["y", "yes"]:
+            clean_annotations_dir(path, loc)
+            logger.info(f"Dataset files in {path} have been removed.")
+        else:
+            logger.warning(f"Dataset files in {path} have not been removed.")
+    else:
+        pass
+    
+    
+def get_broad_consequence(list_of_annotations):
+    """
+    Group variants into broader consequence types.
+    """
+        
+    CONSEQUENCES_LIST = [
+        'transcript_ablation',
+        'splice_acceptor_variant',
+        'splice_donor_variant',
+        'stop_gained',
+        'frameshift_variant',
+        'stop_lost',
+        'start_lost',
+        'transcript_amplification',
+        'inframe_insertion',
+        'inframe_deletion',
+        'missense_variant',
+        'protein_altering_variant',
+        'splice_region_variant',
+        'splice_donor_5th_base_variant',
+        'splice_donor_region_variant',
+        'splice_polypyrimidine_tract_variant',
+        'incomplete_terminal_codon_variant',
+        'start_retained_variant',
+        'stop_retained_variant',
+        'synonymous_variant',
+        'coding_sequence_variant',
+        'mature_miRNA_variant',
+        '5_prime_UTR_variant',
+        '3_prime_UTR_variant',
+        'non_coding_transcript_exon_variant',
+        'intron_variant',
+        'NMD_transcript_variant',
+        'non_coding_transcript_variant',
+        'upstream_gene_variant',
+        'downstream_gene_variant',
+        'TFBS_ablation',
+        'TFBS_amplification',
+        'TF_binding_site_variant',
+        'regulatory_region_ablation',
+        'regulatory_region_amplification',
+        'feature_elongation',
+        'regulatory_region_variant',
+        'feature_truncation',
+        'intergenic_variant'
+    ]
+    
+    GROUPING_DICT = {
+        'transcript_ablation': 'nonsense',
+        'splice_acceptor_variant': 'nonsense',
+        'splice_donor_variant': 'nonsense',
+        'stop_gained': 'nonsense',
+        'frameshift_variant': 'nonsense',
+        'stop_lost': 'nonsense',
+        'start_lost': 'nonsense',
+        'missense_variant': 'missense',
+        'inframe_insertion': 'indel',
+        'inframe_deletion': 'indel',
+        'splice_donor_variant': 'splicing',
+        'splice_acceptor_variant': 'splicing',
+        'splice_region_variant': 'splicing',
+        'splice_donor_5th_base_variant': 'splicing',
+        'splice_donor_region_variant': 'splicing',
+        'splice_polypyrimidine_tract_variant': 'splicing',
+        'synonymous_variant': 'synonymous',
+        'incomplete_terminal_codon_variant': 'synonymous',
+        'start_retained_variant': 'synonymous',
+        'stop_retained_variant': 'synonymous',
+        'protein_altering_variant' : 'protein_altering_variant',
+        'transcript_amplification' : 'transcript_amplification', 
+        'coding_sequence_variant': 'coding_sequence_variant', 
+        'mature_miRNA_variant': 'non_coding_exon_region',
+        '5_prime_UTR_variant': 'non_coding_exon_region',
+        '3_prime_UTR_variant': 'non_coding_exon_region',
+        'non_coding_transcript_exon_variant': 'non_coding_exon_region',
+        'NMD_transcript_variant': 'non_coding_exon_region',
+        'intron_variant': 'intron_variant',
+        'non_coding_transcript_variant' : 'non_coding_transcript_variant',
+        'upstream_gene_variant': 'non_genic_variant',
+        'downstream_gene_variant': 'non_genic_variant',
+        'TFBS_ablation': 'non_genic_variant',
+        'TFBS_amplification': 'non_genic_variant',
+        'TF_binding_site_variant': 'non_genic_variant',
+        'regulatory_region_ablation': 'non_genic_variant',
+        'regulatory_region_amplification': 'non_genic_variant',
+        'feature_elongation': 'non_genic_variant',
+        'regulatory_region_variant': 'non_genic_variant',
+        'feature_truncation': 'non_genic_variant',
+        'intergenic_variant': 'non_genic_variant',
+        '-'  : '-'
+    }
+    
+    consequence_rank_dict = { consequence : rank for rank, consequence in enumerate(CONSEQUENCES_LIST) }
+    rank_consequence_dict = { rank : consequence for rank, consequence in enumerate(CONSEQUENCES_LIST) }
+    
+    list_of_single_annotations = []
+    list_of_broad_annotations = []
+    for x in list_of_annotations:
+        all_consequences = x.split(",")
+        all_consequences_ranks = map(lambda x: consequence_rank_dict[x], all_consequences)
+        single_consequence = rank_consequence_dict[min(all_consequences_ranks)]
+        list_of_single_annotations.append(single_consequence)
+        if single_consequence in GROUPING_DICT:
+            list_of_broad_annotations.append(GROUPING_DICT[single_consequence])
+        else:
+            list_of_broad_annotations.append(single_consequence)
+
+    return list_of_broad_annotations
+
+
+def init_plot_pars(summary_fsize_x=0.4,    # It will be moltiplied for the number of genes
+                   summary_fsize_y=8,
+                   gene_fsize_x=24, 
+                   gene_fsize_y=12, 
+                   volcano_fsize_x=15,
+                   volcano_fsize_y=10,
+                   volcano_subplots_fsize_x=4,
+                   volcano_subplots_fsize_y=2,
+                   log_odds_fsize_x=20,
+                   log_odds_fsize_y=4,
+                   s_lw=0.2, 
+                   sse_fill_width=0.43, 
+                   dist_thr=0.1, 
+                   summary_alpha=0.3,
+                   lst_summary_tracks=None,
+                   lst_summary_hratios=None,
+                   lst_gene_annot=None, 
+                   lst_gene_hratios=None,
+                   volcano_top_n=15):
+    """
+    Initialize plotting parameters.
+    """
+        
+    plot_pars = {}
+
+    plot_pars["summary_figsize"] = summary_fsize_x, summary_fsize_y
+    plot_pars["figsize"] = gene_fsize_x, gene_fsize_y
+    plot_pars["s_lw"] = s_lw
+    plot_pars["sse_fill_width"] = sse_fill_width
+    plot_pars["dist_thr"] = dist_thr
+    plot_pars["summary_alpha"] = summary_alpha
+
+    
+    # Summary-plot
+    # ============
+    
+    # Default values
+    plot_pars["summary_h_ratios"] = {"score"         : 0.3,
+                                     "miss_count"    : 0.2,
+                                     "res_count"     : 0.2,
+                                     "res_clust_mut" : 0.2,
+                                     "clusters"      : 0.2}
+    
+    # Custom values
+    if not lst_summary_tracks:
+        lst_summary_tracks = plot_pars["summary_h_ratios"].keys()
+    if lst_summary_hratios:
+        plot_pars["summary_h_ratios"] = {lst_summary_tracks[i] : h_ratio for i, h_ratio in enumerate(lst_summary_hratios)}
+    else:
+        plot_pars["summary_h_ratios"] = {annot : plot_pars["summary_h_ratios"][annot] for annot in lst_summary_tracks}
+    plot_pars["summary_h_ratios"] = {k:v/sum(plot_pars["summary_h_ratios"].values()) for k,v in plot_pars["summary_h_ratios"].items()}
+        
+    
+    # Gene-plots
+    # ==========
+    
+    # Default values
+    plot_pars["h_ratios"] = {"nonmiss_count" : 0.13,
+                             "miss_count"    : 0.13,
+                             "miss_prob"     : 0.13,
+                             "score"         : 0.13,
+                             "pae"           : 0.1,
+                             "disorder"      : 0.1,
+                             "pacc"          : 0.1,
+                             "ddg"           : 0.1,
+                             "ptm"           : 0.022,
+                             "site"          : 0.022,
+                             "clusters"      : 0.04,
+                             "sse"           : 0.065,
+                             "pfam"          : 0.04,
+                             "prosite"       : 0.04,
+                             "membrane"      : 0.04,
+                             "motif"         : 0.04}
+    
+    plot_pars["color_cnsq"] = {"splicing" : "C2",
+                               "missense" : "C5",
+                               "synonymous" : "C9",
+                               "coding_sequence_variant" : "C1",
+                               "nonsense" : "C6",
+                               "intron_variant" : "C7",
+                               "indel" : "C8",
+                               "protein_altering_variant" : "C3"}
+
+    # Custom values
+    if not lst_gene_annot:
+        lst_gene_annot = plot_pars["h_ratios"].keys()
+    if lst_gene_hratios:
+        plot_pars["h_ratios"] = {lst_gene_annot[i] : h_ratio for i, h_ratio in enumerate(lst_gene_hratios)}
+    else:
+        plot_pars["h_ratios"] = {annot : plot_pars["h_ratios"][annot] for annot in lst_gene_annot}
+        
+    
+    # Associations-plots
+    # ==================
+    
+    plot_pars["volcano_fsize_x"] = volcano_fsize_x
+    plot_pars["volcano_fsize_y"] =volcano_fsize_y
+    plot_pars["volcano_subplots_fsize_x"] = volcano_subplots_fsize_x
+    plot_pars["volcano_subplots_fsize_y"] = volcano_subplots_fsize_y
+    plot_pars["log_odds_fsize_x"] = log_odds_fsize_x
+    plot_pars["log_odds_fsize_y"] = log_odds_fsize_y
+    plot_pars["volcano_top_n"] = volcano_top_n
+    
+    return plot_pars
+
+
+def init_comp_plot_pars(fsize_x=24, 
+                        fsize_y=12, 
+                        s_lw=0.2, 
+                        sse_fill_width=0.43, 
+                        dist_thr=0.1, 
+                        lst_tracks=None,
+                        lst_hratios=None,
+                        count_mirror=False, 
+                        score_mirror=False,
+                        prob_mirror=False):
+    """
+    Initialize plotting parameters.
+    """
+    
+    plot_pars = {}
+ 
+    plot_pars["figsize"] = fsize_x, fsize_y
+    plot_pars["s_lw"] = s_lw
+    plot_pars["sse_fill_width"] = sse_fill_width
+    plot_pars["dist_thr"] = dist_thr
+    plot_pars["count_mirror"] = count_mirror
+    plot_pars["score_mirror"] = score_mirror
+    plot_pars["prob_mirror"] = prob_mirror
+        
+    # Default values
+    plot_pars["h_ratios"] = {"nonmiss_count" : 0.13,
+                             "miss_count"    : 0.13,
+                             "miss_prob"     : 0.13,
+                             "score"         : 0.13,
+                             "clusters"      : 0.04,
+                             "pae"           : 0.1,
+                             "disorder"      : 0.1,
+                             "pacc"          : 0.1,
+                             "ddg"           : 0.1,
+                             "ptm"           : 0.022,
+                             "site"          : 0.022,
+                             "sse"           : 0.065,
+                             "pfam"          : 0.04,
+                             "prosite"       : 0.04,
+                             "membrane"      : 0.04,
+                             "motif"         : 0.04}
+    
+    plot_pars["color_cnsq"] = {"splicing" : "C2",
+                               "missense" : "C5",
+                               "synonymous" : "C9",
+                               "coding_sequence_variant" : "C1",
+                               "nonsense" : "C6",
+                               "intron_variant" : "C7",
+                               "indel" : "C8",
+                               "protein_altering_variant" : "C3"}
+
+    # Custom values
+    if not lst_tracks:
+        lst_tracks = list(plot_pars["h_ratios"].keys())
+    
+    if not count_mirror and "nonmiss_count" in lst_tracks:    
+        ix = lst_tracks.index("nonmiss_count")
+        lst_tracks.insert(ix+1, "nonmiss_count_2")
+        plot_pars["h_ratios"]["nonmiss_count_2"] = plot_pars["h_ratios"]["nonmiss_count"] 
+        
+    if not count_mirror and "miss_count" in lst_tracks:    
+        ix = lst_tracks.index("miss_count")
+        lst_tracks.insert(ix+1, "miss_count_2")
+        plot_pars["h_ratios"]["miss_count_2"] = plot_pars["h_ratios"]["miss_count"]
+        
+    if not score_mirror and "score" in lst_tracks:    
+        ix = lst_tracks.index("score")
+        lst_tracks.insert(ix+1, "score_2")
+        plot_pars["h_ratios"]["score_2"] = plot_pars["h_ratios"]["score"]
+        
+    if "clusters" in lst_tracks:
+        ix = lst_tracks.index("clusters")
+        lst_tracks.insert(ix+1, "clusters_2")
+        plot_pars["h_ratios"]["clusters_2"] = plot_pars["h_ratios"]["clusters"]
+        
+    if "ddg" in lst_tracks:
+        ix = lst_tracks.index("ddg")
+        lst_tracks.insert(ix+1, "ddg_2")
+        plot_pars["h_ratios"]["ddg_2"] = plot_pars["h_ratios"]["ddg"]
+
+    if lst_hratios:
+        plot_pars["h_ratios"] = {lst_tracks[i] : h_ratio for i, h_ratio in enumerate(lst_hratios)}
+    else:
+        plot_pars["h_ratios"] = {annot : plot_pars["h_ratios"][annot] for annot in lst_tracks}   
+        
+    plot_pars["h_ratios"] = {k:v/sum(plot_pars["h_ratios"].values()) for k,v in plot_pars["h_ratios"].items()}
+    
+    return plot_pars
+
+
+def load_o3d_result(o3d_result_path, cohort):
+    """
+    Load all files generated by 3D clustering analysis of Oncodrive3D.
+    """
+    
+    gene_result_path = f"{o3d_result_path}/{cohort}/{cohort}.3d_clustering_genes.csv"
+    pos_result_path = f"{o3d_result_path}/{cohort}/{cohort}.3d_clustering_pos.csv"
+    maf_path = f"{o3d_result_path}/{cohort}/{cohort}.mutations.processed.tsv"
+    miss_prob_dict_path = f"{o3d_result_path}/{cohort}/{cohort}.miss_prob.processed.json"
+    gene_result = pd.read_csv(gene_result_path)
+    pos_result = pd.read_csv(pos_result_path)
+    maf = pd.read_csv(maf_path, sep="\t")
+    miss_prob_dict = json.load(open(miss_prob_dict_path))  
+    
+    return gene_result, pos_result, maf, miss_prob_dict
+
+
+def subset_genes_and_ids(genes, 
+                         uni_ids, 
+                         seq_df, 
+                         disorder, 
+                         pdb_tool, 
+                         uniprot_feat):
+    """
+    Subset each dataframe by keeping only selected genes and proteins IDs.
+    """
+
+    seq_df = seq_df.copy()
+    disorder = disorder.copy()
+    pdb_tool = pdb_tool.copy()
+    uniprot_feat = uniprot_feat.copy()
+    # Filter genes in the other df
+    seq_df = seq_df[seq_df["Gene"].isin(genes)]
+    disorder = disorder[disorder["Uniprot_ID"].isin(uni_ids)].reset_index(drop=True) 
+    pdb_tool = pdb_tool[pdb_tool["Uniprot_ID"].isin(uni_ids)].reset_index(drop=True)
+    uniprot_feat = uniprot_feat[uniprot_feat["Gene"].isin(genes)]
+    
+    return seq_df, disorder, pdb_tool, uniprot_feat
+
+
+def filter_o3d_result(gene_result, pos_result, n_genes=None, lst_genes=None):
+    """
+    Subset gene-level and position-level Oncodrive3D result.
+    """
+
+    if isinstance(lst_genes, str):
+        lst_genes = lst_genes.replace(" ", "")
+        lst_genes = lst_genes.split(",")
+        gene_result = gene_result[gene_result["Gene"].isin(lst_genes)]    
+    gene_result = gene_result[gene_result["Status"] == "Processed"]
+    if n_genes:
+        gene_result = gene_result[:n_genes]                                     
+    uni_ids = gene_result.Uniprot_ID.values
+    genes = gene_result.Gene.values   
+    pos_result = pos_result[pos_result["Gene"].isin(genes)]   
+    
+    return gene_result, pos_result, genes, uni_ids
+
+
+def get_enriched_result(pos_result_gene, 
+                        disorder_gene, 
+                        pdb_tool_gene, 
+                        seq_df):
+    """
+    Add annotations to Oncodrive3D result to return an annotated tsv. 
+    """
+
+    pos_result_gene = pos_result_gene.copy()
+
+    # DDG
+    pos_result_gene.loc[pos_result_gene["Mut_in_res"] == 0, "DDG"] = np.nan
+
+    # Disorder
+    pos_result_gene = pos_result_gene.merge(disorder_gene, how="left", on=["Pos"])
+    pos_result_gene = pos_result_gene.rename(columns={"Confidence" : "pLDDT_res"})
+
+    # PDB_Tool
+    pos_result_gene = pos_result_gene.rename(columns={"AF_F" : "F"}).merge(
+            pdb_tool_gene.drop(columns="F"), on=["Res", "Uniprot_ID", "Pos"], how="left")
+
+    # Transcript and gene IDs
+    pos_result_gene = pos_result_gene.merge(
+        seq_df[["Gene", "Uniprot_ID", "Ens_Gene_ID", "Ens_Transcr_ID"]], 
+        how="left", on=["Uniprot_ID"])
+
+    return pos_result_gene
+
+
+def reorganize_df_to_save(pos_result_df):
+    
+    pos_result_df = pos_result_df.rename(columns={"Res" : "WT_res"})
+    cols = ['Gene', 'Ens_Gene_ID', 'Ens_Transcr_ID', 'Uniprot_ID', 'F', 'Pos', "WT_res",
+            'Mut_in_gene', 'Mut_in_res', 'Mut_in_vol',
+            'Score', 'Score_obs_sim', 'pval', 'C', 'C_ext', 'Cluster', 'Rank',
+            'Tot_samples', 'Samples_in_vol', 'Samples_in_cl_vol', 'Mut_in_cl_vol', 'Res_in_cl', 
+            'PAE_vol', 'pLDDT_res', 'pLDDT_vol', 'pLDDT_cl_vol', 
+            'Cancer', 'Cohort', 
+            'SSE', 'pACC', 'DDG', "Domain", "Ptm", "Membrane", "Site"]
+    
+    return pos_result_df[[col for col in cols if col in pos_result_df.columns]]
+    
+    
+def save_annotated_result(pos_result, 
+                          annot_pos_result, 
+                          uni_feat_processed, 
+                          output_dir, 
+                          run_name, 
+                          output_all_pos=False):
+    """
+    Save the annotated pos-level result.
+    """
+    
+    # Do not include non-mutated positions (default)
+    if output_all_pos == False:
+        annot_pos_result = annot_pos_result[annot_pos_result["Mut_in_res"] > 0].reset_index(drop=True)
+    
+    # Merge with 'original' one to retrieve dropped cols
+    output_pos_result = os.path.join(output_dir, f"{run_name}.3d_clustering_pos.annotated.csv")
+    output_uniprot_feat = os.path.join(output_dir, f"{run_name}.uniprot_feat.tsv")
+    cols = ["Gene", "Uniprot_ID", "F", "Ens_Gene_ID", "Ens_Transcr_ID", 
+            "Pos", "Res", "pLDDT_res", "SSE", "pACC", "DDG",
+            "Domain", "Ptm", "Membrane", "Site"]
+    annot_pos_result = pos_result.drop(columns=["F", "pLDDT_res"]).merge(
+        annot_pos_result[[col for col in cols if col in annot_pos_result.columns]],
+        how="right", on=["Gene", "Uniprot_ID", "Pos"])
+    annot_pos_result = annot_pos_result.sort_values(["Gene", "Pos"])
+    
+    # Fill the NA of the non-mutated positions in features
+    for col in ["Cancer", "Cohort"]:
+        if annot_pos_result[col].isnull().all():
+            annot_pos_result[col] = np.nan
+        else:
+            annot_pos_result[col] = annot_pos_result[col].dropna().unique()[0]
+    annot_pos_result["Mut_in_res"] = annot_pos_result["Mut_in_res"].fillna(0)
+    for gene in annot_pos_result.Gene.unique():
+        mut_in_gene = annot_pos_result.loc[annot_pos_result["Gene"] == gene, "Mut_in_gene"].dropna().unique()[0]
+        annot_pos_result.loc[annot_pos_result["Gene"] == gene, "Mut_in_gene"] = mut_in_gene
+        if "Tot_samples" in annot_pos_result.columns:
+            tot_samples = annot_pos_result.loc[annot_pos_result["Gene"] == gene, "Tot_samples"].dropna().unique()
+            if tot_samples: 
+                tot_samples = tot_samples[0]
+            else:
+                tot_samples = np.nan
+            annot_pos_result.loc[annot_pos_result["Gene"] == gene, "Tot_samples"] = tot_samples
+
+    # Save
+    annot_pos_result = reorganize_df_to_save(annot_pos_result)
+    annot_pos_result.to_csv(output_pos_result, index=False)
+    logger.info(f"Saved annotated position-level result to {output_pos_result}")
+    uni_feat_processed.to_csv(output_uniprot_feat, sep="\t", index=False)
+    logger.info(f"Saved Uniprot features annotations to {output_uniprot_feat}")
+    
+    
+def parse_lst_tracks(lst, plot_type):
+    """
+    Parse the list of tracks from click arg.
+    """
+    
+    summary_tracks = ["score",
+                      "miss_count",
+                      "res_count",
+                      "res_clust_mut",
+                      "clusters"]
+    
+    gene_tracks = ["nonmiss_count",
+                  "miss_count",
+                  "miss_prob",
+                  "score",
+                  "pae",
+                  "disorder",
+                  "pacc",
+                  "ddg",
+                  "ptm",
+                  "site",
+                  "clusters",
+                  "sse",
+                  "pfam",
+                  "prosite",
+                  "membrane",
+                  "motif"]
+
+    if plot_type == "summary":
+        available_tracks = summary_tracks
+    elif plot_type == "gene":
+        available_tracks = gene_tracks
+    lst = lst.split(",")
+    
+    is_valid = np.array([track not in available_tracks for track in lst])
+    if is_valid.any():
+        invalid_tracks = list(np.array(lst)[np.where(is_valid)])
+        logger.error(f"One or more track names for {plot_type} plot are not accepted: {invalid_tracks}")
+        logger.error(f"Available track names are: {available_tracks}")
+        logger.error(f"Exiting..")
+        sys.exit(1)
+        
+    return lst