Merge commit '5bd9ea4' to apply the fix for inconsistent extensions

README.md

@@ -214,7 +214,7 @@ phyling tree -I align
 You can also use only part of the alignment results to build tree.
 
 ```
-phyling tree -i align/100957at4751.faa align/174653at4751.faa align/255412at4751.faa
+phyling tree -i align/100957at4751.aa.mfa align/174653at4751.aa.mfa align/255412at4751.aa.mfa
 ```
 
 Use VeryFastTree instead of the default UPGMA method for tree building and running with 16 threads.

src/phyling/libphyling.py

@@ -196,8 +196,10 @@ def align(self, output: Path, method: str, non_trim: bool, concat: bool, threads
 
             if hasattr(self, "_cds_seqs"):
                 alignmentList = cds_msa_List
+                ext = phyling.config.cds_aln_ext
             else:
                 alignmentList = pep_msa_List
+                ext = phyling.config.prot_aln_ext
 
             if concat:
                 concat_alignments = MultipleSeqAlignment([])
@@ -212,7 +214,7 @@ def align(self, output: Path, method: str, non_trim: bool, concat: bool, threads
                 logging.info("Filling missing taxon done")
 
         for hmm, alignment in zip([hmm for hmm in self.orthologs.keys()], alignmentList):
-            output_aa = output / f"{hmm}.{phyling.config.protein_ext}"
+            output_aa = output / f"{hmm}.{ext}"
             alignment.sort()
             if concat:
                 concat_alignments += alignment
@@ -221,7 +223,7 @@ def align(self, output: Path, method: str, non_trim: bool, concat: bool, threads
                     SeqIO.write(alignment, f, format="fasta")
 
         if concat:
-            output_concat = output / f"concat_alignments.{phyling.config.prot_aln_ext}"
+            output_concat = output / f"concat_alignments.{ext}"
             with open(output_concat, "w") as f:
                 SeqIO.write(concat_alignments, f, format="fasta")
             logging.info(f"Output concatenated fasta to {output_concat}")

src/phyling/phylotree.py

@@ -119,7 +119,7 @@ def phylotree(inputs, input_dir, output, method, figure, threads, **kwargs):
     else:
         inputs = [Path(sample) for sample in inputs]
     logging.info(f"Found {len(inputs)} MSA fasta")
-    if inputs[0].name == f"concat_alignments.{phyling.config.prot_aln_ext}":
+    if inputs[0].name == f"concat_alignments.{phyling.config.aln_ext}":
         logging.info("Generate phylogenetic tree the on concatenated fasta")
     else:
         logging.info("Generate phylogenetic tree on all MSA fasta and conclude an majority consensus tree")