biophd 0.0.1 → 0.0.2

raw patch · 2 files changed

+103/−2 lines, 2 files

Files

• biophd.cabal +2/−2
• src/Bio/Sequence/PhdData.hs +101/−0

@@ -1,5 +1,5 @@ Name:                biophd-Version:             0.0.1+Version:             0.0.2 Synopsis:            Library for reading phd sequence files Description:         Library for reading phd sequence files Homepage:	     https://patch-tag.com/r/dfornika/biophd/home@@ -14,7 +14,7 @@  Library   Build-depends:     base >= 2 && < 5, biocore, bytestring, parsec, text, binary-  Exposed-modules:   Bio.Sequence.Phd+  Exposed-modules:   Bio.Sequence.Phd, Bio.Sequence.PhdData   Hs-source-dirs:    src  source-Repository    head

@@ -0,0 +1,101 @@+module Bio.Sequence.PhdData where++import Bio.Core.Sequence+import qualified Data.ByteString.Lazy as LB+import qualified Data.ByteString.Lazy.Char8 as LBC++{-- A .phd file consists of a DNA block with base and quality +    values, followed by one or more (optional) tag blocks. --}+data PHD = PHD Comment DNABlock (Maybe [PhdTag]) deriving (Show)++{-- These types are subject to change if it improves functionality,+    but for now it's simplest to just call them String, Int etc.--}+data Comment = Comment+    { chromatFile        :: FilePath+    , abiThumbprint      :: String+    , phredVersion       :: String+    , callMethod         :: String+    , qualityLevels      :: Int+    , time               :: String+    , traceArrayMinIndex :: Int+    , traceArrayMaxIndex :: Int+    , trim               :: String+    , chem               :: String+    , dye                :: String+    } deriving (Eq)++instance Show Comment where+    show (Comment cf abit pv cm ql ti mintai maxtai tr ch dy) =+      ("\n" ++) $ unlines +                    [ "CHROMAT_FILE: "   ++ cf+                    , "ABI_THUMBPRINT: " ++ abit+                    , "PHRED_VERSION: "  ++ pv +                    , "CALL_METHOD: "    ++ cm+                    , "QUALITY_LEVELS: " ++ show ql +                    , "TIME: "           ++ show ti+                    , "TRACE_ARRAY_MIN_INDEX: " ++ show mintai+                    , "TRACE_ARRAY_MAX_INDEX: " ++ show maxtai+                    , "TRIM: "           ++ tr+                    , "CHEM: "           ++ ch+                    , "DYE: "            ++ dy+                    ]++data DNABlock = DNABlock+    { label        :: String+    , bases        :: SeqData+    , qualities    :: QualData+    , traceIndices :: [Int]+    }++instance Show DNABlock where+  show = LBC.unpack . toFasta++data PhdTag = PhdTag+    { tagType              :: String+    , source               :: String+    , unpaddedReadPosition :: [Offset]+    , date                 :: String+    , comment              :: String  +    } deriving (Eq)++instance Show PhdTag where+  show (PhdTag tt so urp da co) =+    ("\n" ++) $ unlines $ map (" " ++)+      [ "TYPE: "              ++ show tt+      , "SOURCE: "            ++ show so+      , "UNPADDED_READ_POS: " ++ show (map unOff urp)+      , "DATE: "              ++ show da+      , "COMMENT: "           ++ show co ]++instance BioSeq DNABlock where+  seqlabel  db = SeqLabel $ LBC.pack $ label db+  seqdata   db = bases db+  seqlength db = Offset $ LBC.length $ unSD $ bases db++instance BioSeqQual DNABlock where+  seqqual = qualities++-- Some default values for the data types, useful for debugging in ghci++defaultComment = Comment { chromatFile        = ""+                         , abiThumbprint      = "0"+                         , phredVersion       = "0.980904.e"+                         , callMethod         = "phred"+                         , qualityLevels      = 99+                         , time               = "" +                         , traceArrayMinIndex = 0+                         , traceArrayMaxIndex = 1+                         , trim               = ""+                         , chem               = "unknown"+                         , dye                = "unknown" }++defaultDNABlock = DNABlock { label        = "some_dna"+                           , bases        = SeqData  $ LBC.pack "aatgcatcta"+                           , qualities    = QualData $ LBC.pack "0000000000"+                           , traceIndices = [0,1,2,3,4,5,6,7,8,9,10] }++defaultPhdTag = PhdTag { tagType              = "polymorphism"+                       , source               = "polyphred"+                       , unpaddedReadPosition = [5, 5]+                       , date                 = "01/01/70 00:00:00"+                       , comment              = "" }