bio-0.4.5: A bioinformatics librarySource codeContentsIndex
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]]Source
Reading an ACE file.
writeACE :: FilePath -> [Assembly] -> IO ()Source
data Assembly Source
Constructors
Asm
contig :: (Sequence Nuc, Gaps)
fragments :: Alignment Nuc
show/hide Instances
ptest :: Show a => String -> AceParser a -> [ACE] -> IO ()Source
Test parser p on a list of ACE elements
reads :: Assembly -> Alignment NucSource
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