NAME

SYNOPSIS

  CreateSubProjectPrimers.pl [options]
  Options:
  -if <file>    input file of sub-project paths
  -log <file>   log file (optional; default is createSubPRojectPrimers.pl.log)
  -warn <file>  warnings log file (optional; default is defined in gapRes.config)
  -h            detailed message (optional)

DESCRIPTION

This is a wrapper program for the Gap Resolution software. It takes a list of Gap project directories and then attempts to design primers for a gap and places the designed primers in the gap directory and also in a file in the current working directory.

For eachs of the sub project directories the program performs the following:

1) Check for the existence of a fasta file and associated primer info file.

2) If the appropriate files exist then primer3 is called on the files

3) If primers were successfully designed, an output file is created within the gap project sub directory. An entry is also added to the primer file in the current working directory.

The output files created are based on the parameters below are:

      {gapname}createSubProjectPrimers.subProjectPrimersExtension
      {current workingdir}/createSubProjectPrimers.allProjectPrimersFile

The output file format is as follows:

  name=<primer_name>
  position=<contig> <primerStart> <primerEnd>
  type=<primer type>
  sequence=<sequence>
  template=<clone1> <clone2> ...
  date=YYMMDD:HHMMSS temp=<annealing temp>

Parameters are read from the configuration file and are as follows:

createSubProjectPrimers.primer3ParameterFile= primer3.parameters file createSubProjectPrimers.primerInfoFile= name of primer info file ex. "primerinfo.txt" createSubProjectPrimers.gapFastaFileExtension= fasta file extension ex. ".gap.fasta" createSubProjectPrimers.subProjectPrimersExtension= file extension ex. ".subProjectPrimers.txt" createSubProjectPrimers.allProjectPrimersFile= global primer files in working dir ex. "primers.txt"

This wrapper executes the following scripts/programs:

primer3Design.pl

VERSION

$Revision: 1.11 $

$Date: 2010-01-06 22:00:39 $

AUTHOR(S)

Brian Foster

HISTORY