bio-0.5.2: A bioinformatics library

Safe Haskell | Safe-Infered

Bio.Alignment.ACE

Description

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.

Synopsis

- readACE :: FilePath -> IO [[Assembly]]
- writeACE :: FilePath -> [Assembly] -> IO ()
- data Assembly = Asm {
  - contig :: (Sequence Nuc, Gaps)
  - fragments :: Alignment Nuc
  }
- ptest :: Show a => String -> AceParser a -> [ACE] -> IO ()
- reads :: Assembly -> Alignment Nuc

# 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'.