fix writing the whole genome msa without gene ids in aln files

labgem · Feb 23, 2021 · 8c1cd38 · 8c1cd38
1 parent 25cd3df
commit 8c1cd38
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Showing 2 changed files with 7 additions and 4 deletions.
diff --git a/VERSION b/VERSION
@@ -1 +1 @@
-1.1.134
+1.1.135
diff --git a/ppanggolin/formats/writeMSA.py b/ppanggolin/formats/writeMSA.py
@@ -127,7 +127,7 @@ def computeMSA(families, output, cpu, tmpdir, source, use_gene_id, code, show_ba
 
     msa_total = msa_total + (time.time() - start_msa)
 
-def writeWholeGenomeMSA(pangenome, families, phylo_name, outname, show_bar=True):
+def writeWholeGenomeMSA(pangenome, families, phylo_name, outname, use_gene_id = False, show_bar=True):
     phyloDict = {}
     for org in pangenome.organisms:
         phyloDict[org.name]=""
@@ -151,7 +151,10 @@ def writeWholeGenomeMSA(pangenome, families, phylo_name, outname, show_bar=True)
                         curr_phyloDict[genome_id] = seq
                         missing_genomes -= set([genome_id])
                         curr_len = len(seq)
-                genome_id = pangenome.getGene(line[1:].strip()).organism.name
+                if use_gene_id:
+                    genome_id = pangenome.getGene(line[1:].strip()).organism.name
+                else:
+                    genome_id = line[1:].strip()
                 seq = ""
             else:
                 seq += line.strip()
@@ -201,7 +204,7 @@ def writeMSAFiles(pangenome, output, cpu = 1, partition = "core", tmpdir = "/tmp
             phylo_name = output + f"/{partition}_{soft_core}_genome_alignment.aln"
         else:
             phylo_name = output + f"/{partition}_genome_alignment.aln"
-        writeWholeGenomeMSA(pangenome, families, phylo_name, outname, show_bar=show_bar)
+        writeWholeGenomeMSA(pangenome, families, phylo_name, outname, use_gene_id=use_gene_id, show_bar=show_bar)
         logging.getLogger().info(f"Done writing the {partition} genome alignment in: '{phylo_name}'")
 
 def launchMSA(args):