blastxml 0.3.1 → 0.3.2

raw patch · 3 files changed

+9/−23 lines, 3 files

Files

blastxml.cabal +1/−1
src/Bio/BlastData.hs +6/−2
src/Bio/BlastXML.hs +2/−20

blastxml.cabal view

@@ -1,5 +1,5 @@ Name:                blastxml-Version:             0.3.1+Version:             0.3.2 Synopsis:            Library for reading Blast XML output Description:         This library contains a data structure and functions for  		     reading output from the BLAST sequence alignment program.

src/Bio/BlastData.hs view

@@ -42,8 +42,12 @@  -- | Each match between a query and a target sequence (or subject) --   is a 'BlastHit'.-data BlastHit = BlastHit { subject :: !SeqLabel, slength :: !Int -                         , matches :: [BlastMatch] } deriving Show+data BlastHit = BlastHit +    { hitId :: !ByteString+    , subject :: !SeqLabel+    , slength :: !Int+    , matches :: [BlastMatch] } deriving Show+ -- | A 'BlastHit' may contain multiple separate matches (typcially when --   an indel causes a frameshift that blastx is unable to bridge). data BlastMatch = BlastMatch { bits :: !Double, e_val :: !Double

src/Bio/BlastXML.hs view

@@ -90,7 +90,8 @@  hit2hit :: [STag] -> BlastHit hit2hit hs = BlastHit -             { subject = SeqLabel $ get "Hit_def"+             { hitId = get "Hit_id"+             , subject = SeqLabel $ get "Hit_def"              , slength = readI $ get "Hit_len"              , matches = map hsp2match $ partitions (isTagOpenName "Hsp") hs              }@@ -134,22 +135,3 @@           -- ignore frame also for tblastx hits (it can be reconstructed from location)           strand' :: Int -> Strand           strand' s = if s > 0 then Plus else Minus--fields :: [String]-fields = [ "Hsp_bit-score"-         , "Hsp_evalue"-         , "Hsp_query-from"-         , "Hsp_query-to"-         , "Hsp_hit-from"-         , "Hsp_identity"-         , "Hsp_align-len"-         , "Hsp_qseq"-         , "Hsp_hseq"-         , "Hsp_hit-frame"           -         , "Hsp_query-frame"         -         , "Iteration_query-def"-         , "Iteration_query-len"-         , "Hit_def"-         , "Hit_len"         -         , "Hsp"-         ]