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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 |
Instances
Show Assembly
ptest :: Show a => String -> AceParser a -> [ACE] -> IO () | Source
Test parser p on a list of ACE elements
reads :: Assembly -> Alignment Nuc | Source
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