degapseqrunner

 

Function

Degapseq all sequence pairs in a directory

Description

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Algorithm

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Usage

Under development, no final example yet

Command line arguments

   Standard (Mandatory) qualifiers:
  [-gappedseqsdir]     dirlist    Input directory of files containing sequence
                                  pairs for degapping
  [-commandpath]       directory  Directory where degapping executable lives
  [-commandname]       string     Name of degapping executable
  [-degappedseqsoutdir] outdir     Directory where degapped sequence pairs will
                                  be written
  [-outfilesuffix]     string     Appended to end of all output file names

   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
[-gappedseqsdir]
(Parameter 1)
Input directory of files containing sequence pairs for degapping Directory with files .
[-commandpath]
(Parameter 2)
Directory where degapping executable lives Directory  
[-commandname]
(Parameter 3)
Name of degapping executable Any string is accepted degapseq
[-degappedseqsoutdir]
(Parameter 4)
Directory where degapped sequence pairs will be written Output directory  
[-outfilesuffix]
(Parameter 5)
Appended to end of all output file names Any string is accepted .deg
Additional (Optional) qualifiers Allowed values Default
(none)
Advanced (Unprompted) qualifiers Allowed values Default
(none)

Input file format

degapseqrunner reads any normal sequence USAs.

Under development, no example input file(s) yet

Output file format

degapseqrunner 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
biosedReplace or delete sequence sections
codcopyReads and writes a codon usage table
cutseqRemoves a specified section from a sequence
degapseqRemoves gap characters from sequences
descseqAlter the name or description of a sequence
entretReads and writes (returns) flatfile entries
extractfeatExtract features from a sequence
extractseqExtract regions from a sequence
listorWrite a list file of the logical OR of two sets of sequences
maskfeatMask off features of a sequence
maskseqMask off regions of a sequence
newseqType in a short new sequence
noreturnRemoves carriage return from ASCII files
notseqExclude a set of sequences and write out the remaining ones
nthseqWrites one sequence from a multiple set of sequences
pasteseqInsert one sequence into another
revseqReverse and complement a sequence
seqretReads and writes (returns) sequences
seqretsplitReads and writes (returns) sequences in individual files
skipseqReads and writes (returns) sequences, skipping first few
splitterSplit a sequence into (overlapping) smaller sequences
trimestTrim poly-A tails off EST sequences
trimseqTrim ambiguous bits off the ends of sequences
unionReads sequence fragments and builds one sequence
vectorstripStrips out DNA between a pair of vector sequences
yankReads a sequence range, appends the full USA to a list file

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