Bio.Alignment.ACE

Read ACE format assembly files

These are typically output by sequence assembly tools, like CAP3 or Phrap.

Documented in the section labelled "ACE FILE FORMAT" at http://bozeman.mbt.washington.edu/consed/distributions/README.14.0.txt

Briefly: each field is a line starting with a two letter code, in some cases followed by data lines termintated by a blank line. Here's an brief example how an ACE file looks like:

          AS contigs reads
          CO contig_name bases reads segments compl (CAP3: segments=0)
          sequence
          BQ base_qualities
          AF read1 compl padded_start_consensus (negatives meaning?)
          AF read2 ..
          BS segments
          RD read1 bases info_items info_tags (latter two set to 0 by CAP3)
          sequence
          QA read1 qual_start qual_end align_start align_end
          DS (phred header? left empty by CAP3)
          RD read2 ...

As far as I know, this is only used for nucleotide sequences.

Documentation

readACE :: FilePath -> IO [[Assembly]]

Reading an ACE file.

writeACE :: FilePath -> [Assembly] -> IO ()

data Assembly

Constructors

Asm

Fields

contig :: (Sequence Nuc, Gaps)

fragments :: Alignment Nuc

Instances

Show Assembly

ptest :: Show a => String -> AceParser a -> [ACE] -> IO ()

Test parser p on a list of ACE elements

reads :: Assembly -> Alignment Nuc

Deprecated: Stupid name, replaced by fragments.