more mafft test. covered.

hng · Mar 26, 2015 · ef80939 · ef80939
1 parent a7f6994
commit ef80939
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Showing 2 changed files with 18 additions and 1 deletion.
diff --git a/src/MAFFT/mafft.jl b/src/MAFFT/mafft.jl
@@ -104,9 +104,12 @@ export mafft, mafft_from_string, mafft_from_fasta, mafft_linsi, linsi, mafft_gin
     # helper methods for aligned FASTA
 
     function print_aligned_fasta(fasta)
+        aligned = String[]
         for f in fasta
+            push!(aligned, f[2])
             println(f[2])
         end
+        return aligned
     end
 
     # returns the length of the alignment (FastaIO-format as input)

diff --git a/test/mafft.jl b/test/mafft.jl
@@ -1,5 +1,7 @@
 using BiomolecularStructures.Mafft
 using Base.Test
+using FastaIO
+using BioSeq
 
 mafft_expected = [("gi|166158130|ref|NP_001107279.1| interleukin 4 [Xenopus (Silurana) tropicalis]","MSNLGRILCAVLGLFHLLSANPVPSSKLQIAIEEIISELVNNKITHK-----KCFVPTPYDDEEEASVEEISCRAFKSLKHVCASER--------------------KNLRLLNASLITMFSE-----NVECSINNDEQKDLISVIEDLLTFFRAQM-RKLVMNPKH")  
  ("gi|55742622|ref|NP_999288.1| interleukin-4 precursor [Sus scrofa]","M-GLTSQLIPTLVCLLACTSNFVHGHKCDITLQEIIKTL--NILTARKNSCMELPVTDVFAAPENTTEKETFCRASTVLRHIYRHHT----CMK-------------SLLSGLDRNLSSMAN-------MTCSVHEAKKSTLKDFLERLKTIMKEKY-SKC------")               
@@ -56,5 +58,17 @@ mafft_nwns_expected = {("gi|166158130|ref|NP_001107279.1| interleukin 4 [Xenopus
 
 @test mafft_nwns(Pkg.dir("BiomolecularStructures","examples/fasta","il4.fasta")) == mafft_nwns_expected
 
+@test alignment_length(mafft_expected_from_string) == 150
 
-@test alignment_length(mafft_expected_from_string) == 150
+expected_amino_acids = Array{AminoAcid,1}[]
+push!(expected_amino_acids, aminoacid("MSNLGRILCAVLGLFHLLSANPVPSSKLQIAIEEIISELVNNKITHKKCFVPTPYDDEEEASVEEISCRAFKSLKHVCASERKNLRLLNASLITMFSENVECSINNDEQKDLISVIEDLLTFFRAQMRKLVMNPKH"))
+
+@test to_aminoacids([readfasta(Pkg.dir("BiomolecularStructures","examples/fasta","il4.fasta"))[1]]) == expected_amino_acids
+
+@test mafft_from_fasta(readfasta(Pkg.dir("BiomolecularStructures","examples/fasta","il4.fasta"))) == mafft_expected
+
+expected_aligned_output = String["MSNLGRILCAVLGLFHLLSANPVPSSKLQIAIEEIISELVNNKITHKKCFVPTPYDDEEEASVEEISCRAFKSLKHVCASERKNLRLLNASLITMFSENVECSINNDEQKDLISVIEDLLTFFRAQMRKLVMNPKH","MGLTSQLIPTLVCLLACTSNFVHGHKCDITLQEIIKTLNILTARKNSCMELPVTDVFAAPENTTEKETFCRASTVLRHIYRHHTCMKSLLSGLDRNLSSMANMTCSVHEAKKSTLKDFLERLKTIMKEKYSKC","MSSSLPTLLALLVLLAGPGAVPTLCLQLSVPLMESIRIVNDIQGEVSCVKMNVTDIFADNKTNNKTELLCKASTIVWESQHCHKNLQGLFLNMRQLLNASSTSLKAPCPTAAGNTTSMEKFLADLRTFFHQLAKNK","MGLTSQLIPTLVCLLALTSTFVHGHNFNITIKEIIKMLNILTARNDSCMELTVKDVFTAPKNTSDKEIFCRAATVLRQIYTHNCSNRYLRGLYRNLSSMANKTCSMNEIKKSTLKDFLERLKVIMQKKYYRH","MGLSPHLAVTLFCFLICTGNGIHGCNDSPLREIINTLNQVTEKGTPCTEMFVPDVLTATRNTTENELICRASRVLRKFYFPRDVPPCLKNKSGVLGELRKLCRGVSGLNSLRSCTVNESTLTTLKDFLESLKSILRGKYLQSCTSMS","MGLTSQLLPPLFFLLACAGNFVHGHKCDITLQEIIKTLNSLTEQKNTTEKETFCRAATVLRQFYSHHEKDTRCLGATAQQFHRHKQLIRFLKRLDRNLWGLAGLNSCPVKEANQSTLENFLERLKTIMREKYSKCSS","MDLTSQLIPALVCLLAFTSTFVHGQNFNNTLKEIIKTLNILTARNDSCMELTVMDVLAAPKNTSDKEIFCRATTVLRQIYTHHNCSTKFLKGLDRNLSSMANRTCSVNEVKKCTLKDFLERLKAIMQKKYSKH","HKCDITLQEIIKTLNSLTEQKTLCTELTVTDIFAASKNTTEKETFCRAATVLRQFYSHHEKDTRCLGATAQQFHRHKQLIRFLKRLDRNLWGLAGLNSCPVKEANQSTLENFLERLKTIMREKYSKCSS"]
+
+aligned = readfasta(Pkg.dir("BiomolecularStructures","examples/fasta","il4.fasta"))
+
+@test print_aligned_fasta(aligned) == expected_aligned_output