Merge pull request #219 from labgem/RGPBorderOutFix

Fix writing starter gene insted of start coordinate
labgem · May 16, 2024 · e19a6b2 · e19a6b2
2 parents ab9799e + 0bbf7b3
commit e19a6b2
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/ppanggolin/formats/writeFlatPangenome.py b/ppanggolin/formats/writeFlatPangenome.py
@@ -840,8 +840,8 @@ def write_rgp_table(regions: Set[Region],
                 "region": region.name,
                 "genome": region.organism,
                 "contig": region.contig,
-                "start": region.starter,
-                "stop": region.stopper,
+                "start": region.start,
+                "stop": region.stop,
                 "genes": len(region),
                 "contigBorder": region.is_contig_border,
                 "wholeContig": region.is_whole_contig

diff --git a/ppanggolin/formats/writeSequences.py b/ppanggolin/formats/writeSequences.py
@@ -337,7 +337,7 @@ def write_regions_sequences(pangenome: Pangenome, output: Path, regions: str, fa
                 genome_sequence = read_genome_file(org_dict[organism.name], organism)
             fasta.write(f">{region.name}\n")
             fasta.write(
-                write_spaced_fasta(genome_sequence[region.contig.name][region.starter.start:region.stopper.stop], 60))
+                write_spaced_fasta(genome_sequence[region.contig.name][region.start:region.stop], 60))
     logging.getLogger("PPanGGOLiN").info(f"Done writing the regions nucleotide sequences: '{outname}'")