cobot-io-0.1.4.2: test/FastaWriterSpec.hs

{-# LANGUAGE TypeApplications #-}

module FastaWriterSpec where

import Bio.FASTA.Type   (FastaItem (..))
import Bio.FASTA.Writer (fastaToText)
import Bio.Sequence     (bareSequence)
import Test.Hspec

fastaWriterSpec :: Spec
fastaWriterSpec = describe "Fasta format parser." $ do
    emptyFasta
    oneShortSequence
    oneLongSequence
    twoSequences

emptyFasta :: Spec
emptyFasta = describe "emptyFasta" $ do
    it "correctly write empty fasta" $ do
        let res = fastaToText ([] :: [FastaItem Char])
        res `shouldBe` ""

oneShortSequence :: Spec
oneShortSequence = describe "oneShortSequence" $ do
    it "correctly write one correct short (less than 80 chars) sequence" $ do
        let res = fastaToText [FastaItem @Char "3HMX:A|PDBID|CHAIN|SEQUENCE" (bareSequence "IWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLL")]
        res `shouldBe` ">3HMX:A|PDBID|CHAIN|SEQUENCE\nIWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLL\n"

oneLongSequence :: Spec
oneLongSequence = describe "oneLongSequence" $ do
    it "correctly write one correct long (more than 80 chars) sequence" $ do
        let res = fastaToText [FastaItem @Char "3HMX:A|PDBID|CHAIN|SEQUENCE" (bareSequence "IWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLLLLHKKEDGIWSTDILKDQKEPKNKTFLRCEAKNYSGRFTCWWLTTISTDLTFSVKSSRGSSDPQGVTCGAATLSAERVRGDNKEYEYSVECQEDSACPAAEESLPIEVMVDAVHKLKYENYTSSFFIRDIIKPDPPKNLQLKPLKNSRQVEVSWEYPDTWSTPHSYFSLTFCVQVQGKSKREKKDRVFTDKTSATVICRKNASISVRAQDRYYSSSWSEWASVPCS")]
        res `shouldBe` ">3HMX:A|PDBID|CHAIN|SEQUENCE\nIWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLL\nLLHKKEDGIWSTDILKDQKEPKNKTFLRCEAKNYSGRFTCWWLTTISTDLTFSVKSSRGSSDPQGVTCGAATLSAERVRG\nDNKEYEYSVECQEDSACPAAEESLPIEVMVDAVHKLKYENYTSSFFIRDIIKPDPPKNLQLKPLKNSRQVEVSWEYPDTW\nSTPHSYFSLTFCVQVQGKSKREKKDRVFTDKTSATVICRKNASISVRAQDRYYSSSWSEWASVPCS\n"

twoSequences :: Spec
twoSequences = describe "twoSequences" $ do
    it "correctly write two correct sequences" $ do
        let res = fastaToText [FastaItem @Char "3HMX:A|PDBID|CHAIN|SEQUENCE" (bareSequence "IWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLL"), FastaItem @Char "7HMX:A|PDBID|CHAIN|SEQUENCE" (bareSequence "IWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLLLLHKKEDGIWSTDILKDQKEPKNKTFLRCEAKNYSGRFTCWWLTTISTDLTFSVKSSRGSSDPQGVTCGAATLSAERVRGDNKEYEYSVECQEDSACPAAEESLPIEVMVDAVHKLKYENYTSSFFIRDIIKPDPPKNLQLKPLKNSRQVEVSWEYPDTWSTPHSYFSLTFCVQVQGKSKREKKDRVFTDKTSATVICRKNASISVRAQDRYYSSSWSEWASVPCS")]
        res `shouldBe` ">3HMX:A|PDBID|CHAIN|SEQUENCE\nIWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLL\n>7HMX:A|PDBID|CHAIN|SEQUENCE\nIWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLL\nLLHKKEDGIWSTDILKDQKEPKNKTFLRCEAKNYSGRFTCWWLTTISTDLTFSVKSSRGSSDPQGVTCGAATLSAERVRG\nDNKEYEYSVECQEDSACPAAEESLPIEVMVDAVHKLKYENYTSSFFIRDIIKPDPPKNLQLKPLKNSRQVEVSWEYPDTW\nSTPHSYFSLTFCVQVQGKSKREKKDRVFTDKTSATVICRKNASISVRAQDRYYSSSWSEWASVPCS\n"