added function to call mafft with FastaIO dataformat as input

hng · Mar 17, 2015 · 4821dde · 4821dde
1 parent c92252b
commit 4821dde
Showing 1 changed file with 10 additions and 1 deletion.
diff --git a/src/MAFFT/mafft.jl b/src/MAFFT/mafft.jl
@@ -3,7 +3,7 @@
     - group to group alignments
 """
 module MAFFT
-export mafft, mafft_from_string, mafft_linsi, linsi, mafft_ginsi, ginsi, mafft_einsi, einsi, mafft_fftnsi, fftnsi, mafft_fftns, fftns, mafft_nwnsi, nwnsi, mafft_nwns, nwns, print_aligned_fasta, alignment_length
+export mafft, mafft_from_string, mafft_from_fasta, mafft_linsi, linsi, mafft_ginsi, ginsi, mafft_einsi, einsi, mafft_fftnsi, fftnsi, mafft_fftns, fftns, mafft_nwnsi, nwnsi, mafft_nwns, nwns, print_aligned_fasta, alignment_length
 
     using FastaIO
 
@@ -32,6 +32,15 @@ export mafft, mafft_from_string, mafft_linsi, linsi, mafft_ginsi, ginsi, mafft_e
         return mafft(tempfile_path, args)
     end
 
+    " calls MAFFT with the given FASTA in FastaIO format
+      fasta_in: FASTA in FastaIO format
+      args: optional commandline arguments for MAFFT (array of strings) "
+    function mafft_from_fasta(fasta_in, args=["--auto"])
+        io = IOBuffer()
+        writefasta(io, fasta_in)
+        return mafft_from_string(takebuf_string(io), args)
+    end
+
     # Accuracy-oriented methods
 
     """ L-INS-i (probably most accurate; recommended for <200 sequences;