
                                alignrunner 



Function

   Align sequence pairs in a directory

Description

   **************** EDIT HERE ****************

Algorithm

   **************** EDIT HERE ****************

Usage

   Under development, no final example yet

Command line arguments

   Standard (Mandatory) qualifiers:
  [-seqpairsdir]       dirlist    Input directory of files containing sequence
                                  pairs for alignment
  [-firstcommandpath]  directory  Directory where conventional alignment
                                  executable lives
  [-secondcommandpath] directory  Directory where structure-weighted alignment
                                  executable lives
  [-firstcommandname]  string     Name of conventional alignment executable
  [-secondcommandname] string     Name of structure-weighted alignment
                                  executable
  [-scoringmatrixdir]  directory  Directory where conventional scoring matrix
                                  lives
  [-scoringmatrixname] string     Name of scoring matrix
   -gapopen            float      The gap opening penalty is subtracted from
                                  the total score every time a gap is inserted
                                  in the alignment. The default value is
                                  chosen for the EBLOSUM62 scoring matrix when
                                  you are aligning protein sequences, and the
                                  EDNAFULL matrix when you are aligning
                                  nucleotide sequences. If you sequence
                                  contains many small errors you should set a
                                  low gap opening penalty (near zero) to avoid
                                  over-penalizing those errors.
   -gapextend          float      The gap extension penalty is the score
                                  substracted when more spaces are added to an
                                  existing alignment gap. Often a single
                                  insertion or deletion affects multiple
                                  residues/nucleotides; separate opening and
                                  extension penalties reduce the excessive
                                  penalty such events would otherwise carry;
                                  generally the gap extension penalty should
                                  be significantly lower than the gap opening
                                  penalty.
   -zeroend            boolean    If this option is true then no penalty is
                                  added for gaps at either ends of a trace.
  [-firstalignedseqsoutdir] outdir     Name of directory containing sequences
                                  aligned by first method
  [-secondalignedseqsoutdir] outdir     Name of directory containing sequences
                                  aligned by second method
  [-firstoutfilesuffix] string     Appended to end of all output file names of
                                  sequences aligned by first alignment method
  [-secondoutfilesuffix] string     Appended to end of all output file names of
                                  sequences aligned by second alignment method
  [-outfileformat]     string     Format of output alignments for both methods

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers: (none)
   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report deaths


   Standard (Mandatory) qualifiers Allowed values Default
   [-seqpairsdir]
   (Parameter 1) Input directory of files containing sequence pairs for
   alignment Directory with files .
   [-firstcommandpath]
   (Parameter 2) Directory where conventional alignment executable lives
   Directory
   [-secondcommandpath]
   (Parameter 3) Directory where structure-weighted alignment executable
   lives Directory
   [-firstcommandname]
   (Parameter 4) Name of conventional alignment executable Any string is
   accepted An empty string is accepted
   [-secondcommandname]
   (Parameter 5) Name of structure-weighted alignment executable Any
   string is accepted An empty string is accepted
   [-scoringmatrixdir]
   (Parameter 6) Directory where conventional scoring matrix lives
   Directory
   [-scoringmatrixname]
   (Parameter 7) Name of scoring matrix Any string is accepted An empty
   string is accepted
   -gapopen The gap opening penalty is subtracted from the total score
   every time a gap is inserted in the alignment. The default value is
   chosen for the EBLOSUM62 scoring matrix when you are aligning protein
   sequences, and the EDNAFULL matrix when you are aligning nucleotide
   sequences. If you sequence contains many small errors you should set a
   low gap opening penalty (near zero) to avoid over-penalizing those
   errors. Floating point number from 1.0 to 100.0 10.0 for any sequence
   -gapextend The gap extension penalty is the score substracted when
   more spaces are added to an existing alignment gap. Often a single
   insertion or deletion affects multiple residues/nucleotides; separate
   opening and extension penalties reduce the excessive penalty such
   events would otherwise carry; generally the gap extension penalty
   should be significantly lower than the gap opening penalty. Floating
   point number from 0.0 to 10.0 0.5 for any sequence
   -zeroend If this option is true then no penalty is added for gaps at
   either ends of a trace. Boolean value Yes/No No
   [-firstalignedseqsoutdir]
   (Parameter 8) Name of directory containing sequences aligned by first
   method Output directory
   [-secondalignedseqsoutdir]
   (Parameter 9) Name of directory containing sequences aligned by second
   method Output directory
   [-firstoutfilesuffix]
   (Parameter 10) Appended to end of all output file names of sequences
   aligned by first alignment method Any string is accepted An empty
   string is accepted
   [-secondoutfilesuffix]
   (Parameter 11) Appended to end of all output file names of sequences
   aligned by second alignment method Any string is accepted An empty
   string is accepted
   [-outfileformat]
   (Parameter 12) Format of output alignments for both methods Any string
   is accepted fasta
   Additional (Optional) qualifiers Allowed values Default
   (none)
   Advanced (Unprompted) qualifiers Allowed values Default
   (none)

Input file format

   alignrunner reads any normal sequence USAs.

   Under development, no example input file(s) yet

Output file format

   alignrunner outputs a graph to the specified graphics device. outputs
   a report format file. The default format is ...

   Under development, no example output file(s) yet

Data files

   **************** EDIT HERE ****************

Notes

   None.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

     Program name                         Description
   comparator       Compare contact scores of two sequence alignments
   contactalign     Damian Counsell's experimental 2.5-D alignment algorithm
   esim4            Align an mRNA to a genomic DNA sequence
   est2genome       Align EST and genomic DNA sequences
   nawalign         Damian Counsell's NW implementation
   nawalignrunner   Nawalign all sequence pairs in a directory
   needle           Needleman-Wunsch global alignment
   needlerunner     Needle all sequence pairs in a directory
   scorer           Score alignments using structural alignments
   scorerrunner     SCORER for ordered pairs of substituted seqs
   stretcher        Finds the best global alignment between two sequences
   substitute       Substitute matches into a template
   substituterunner Run SUBSTITUTE on a directory of traces

Author(s)

   Damian Counsell (d.counsell © rfcgr.mrc.ac.uk)
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

History

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.

Comments

   None
