substituterunner

 

Function

Runs substitute on directory of traces and writes substituted sequences to another

Description

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Algorithm

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Usage

Under development, no final example yet

Command line arguments

   Standard (Mandatory) qualifiers:
  [-pathtocommands]    directory  Directory where alignment executables live
  [-alignedpairsdirlist] dirlist    Directory containing paired traces
  [-substitutedseqsoutdir] outdir     Directory to write substituted sequences to

   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


Error: File /homes/pmr/local/share/EMBOSS/acd/substituterunner.acd line 21: (alignedpairsdirlist) Unknown attribute 'name'

Input file format

substituterunner reads any normal sequence USAs.

Under development, no example input file(s) yet

Output file format

substituterunner 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

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Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

Program nameDescription
alignrunnerRuns alignment program on all sequence pairs in a directory
contactalignEMBOSS implementation of Damian Counsell's 2.5-D alignment algorithm
esim4Align an mRNA to a genomic DNA sequence
est2genomeAlign EST and genomic DNA sequences
nawalignDamian Counsell's implementation for protein sequences of the Needleman and Wunsch alignment algorithm
nawalignrunnerRuns nawalign alignment program on all sequence pairs in a directory
needleNeedleman-Wunsch global alignment
needlerunnerRuns needle alignment program on all sequence pairs in a directory
scorerScores accuracy of protein-protein sequence alignment against gold standard structure-structure alignment
scorerrunnerRuns scorer to compare ordered pairs of substituted seqs in two directories and write the scores to a third
stretcherFinds the best global alignment between two sequences
substituteSubstitutes matches from first (query) sequence of two aligned sequences in a trace into second (template sequence)

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