Add some fixes: chromosomes and genes not mandatory

src/generate_panel.py

@@ -69,8 +69,8 @@ def parse_gtf(gtf_file, source=None, chromosomes=False, chunksize=5000):
  chunk = chunk[chunk['source'].apply(
  lambda sources_gtf: common_member(sources_gtf, source))]
 
- chunk = chunk[chunk['chrom'].isin(chromosomes)]
  if chromosomes:
+ chunk = chunk[chunk['chrom'].isin(chromosomes)]
  # chunk = chunk[chunk['chrom'].isin([])]
  chunk.loc[:, "chrom"] = chunk["chrom"].map(chromosomes)
 
@@ -259,13 +259,16 @@ def main(args):
  if args.verbose:
  print("Mode verbose activé")
 
- chr_df = pd.read_table(args.chromosomes, sep='\t')
- if args.without_chr:
- chr_df['UCSC style name'] = chr_df['UCSC style name'].apply(
- lambda x: str(x).replace("chr", ''))
- chr_df = chr_df[chr_df['UCSC style name'].isin(args.usable_chromosomes)]
- chr_names = ["RefSeq seq accession", "UCSC style name"]
- chromosomes = dict(chr_df[chr_names].to_dict('split')['data'])
+ if args.chromosomes:
+ chr_df = pd.read_table(args.chromosomes, sep='\t')
+ if args.without_chr:
+ chr_df['UCSC style name'] = chr_df['UCSC style name'].apply(
+ lambda x: str(x).replace("chr", ''))
+ chr_df = chr_df[chr_df['UCSC style name'].isin(args.usable_chromosomes)]
+ chr_names = ["RefSeq seq accession", "UCSC style name"]
+ chromosomes = dict(chr_df[chr_names].to_dict('split')['data'])
+ else:
+ chromosomes = False
 
  genes = []
  if args.gene:
@@ -275,10 +278,13 @@ def main(args):
  genes = sorted(set(sum(genes, [])))
 
  gtf_df = parse_gtf(args.gtf, args.source, chromosomes)
+
  missing_genes = set(genes).difference(set(gtf_df["gene"]))
  keep_genes = set(genes).difference(missing_genes)
-
- filtered_df = gtf_df[(gtf_df['gene'].isin(genes)) & (gtf_df['type'].isin(args.type))]
+ if genes:
+ filtered_df = gtf_df[(gtf_df['gene'].isin(genes)) & (gtf_df['type'].isin(args.type))]
+ else:
+ filtered_df = gtf_df[(gtf_df['type'].isin(args.type))]
  df_selected = get_bed(filtered_df, args.type, args.padding, chromosomes)
  df_selected.to_csv(
  f'{args.output}.selected.bed',
@@ -287,7 +293,10 @@ def main(args):
  missing_type = keep_genes.difference(set(filtered_df["gene"]))
  bed_selected = pybedtools.BedTool.from_dataframe(df_selected)
 
- filtered_gene_df = gtf_df[(gtf_df['gene'].isin(genes)) & (gtf_df['type'].isin(["gene"]))]
+ if genes:
+ filtered_gene_df = gtf_df[(gtf_df['gene'].isin(genes)) & (gtf_df['type'].isin(["gene"]))]
+ else:
+ filtered_gene_df = gtf_df[(gtf_df['type'].isin(["gene"]))]
  filtered_gene_df = get_bed(
  filtered_gene_df, ["gene"],
  args.padding, chromosomes)
@@ -436,8 +445,8 @@ def script():
  # Argument parsing
  args = parser.parse_args()
 
- if not (args.gene or args.genes_list):
- parser.error('No genes provided, add --gene (-g) or --genes-list')
+ # if not (args.gene or args.genes_list):
+ #  parser.error('No genes provided, add --gene (-g) or --genes-list')
 
  # Execution of the main function
  main(args)