# config.txt
# configuration file for pal_finder_v0.02.04.pl
#
# This file determines the configuration and input parameters for
# pal_finder (version 0.02.03). All lines in this file that start
# with "#" are comments and are not considered input to the
# program. All other lines containing text are considered input
# parameters and need to follow the format of:
# 
# <variable_name> <variable_vale>
# 
# Changing variable names will cause the script to run incorrectly
# or not run at all. You should chane the variable values to suit
# your experimental needs and input data type. Descriptions of
# variables and acceptable variable values are described below.  

#----------------------- Primer Design -------------------------#
#
# Enter 1 to design primers or 0 if you just want to calculate the
# microsatellite statistics (faster).

findPrimers 1

#------------------ Platform Input Parameters ------------------#
#
# The possible input values for the platform variable
# are "454" or "Illumina" (without quotes, case-sensitive).

platform Illumina

#------------------- Input Format Parameters -------------------#
#
# The possible input values for the platform variable are
# "fasta", "fastq" or "scarf" (without quotes, case-sensitive).
# Currently fasta input is required for 454 single end reads and
# fastq or scarf is required for Illumina paired end data.

inputFormat fastq

#---------------------- Paired-End Reads -----------------------#
#
# Enter 1 if your reads are paired-end or 0 if not. Currently the 
# script only takes Illumina paired-end reads and 454 single-end
# reads. Paired-end reads should have 2 separate read files.

pairedEnd  1

#----------------------- 454 Read Files ------------------------#
#
# If you are running 454 data enter the file name of the raw 454
# reads. This should be in the fasta format, not fastq. If this
# file is not in the same directory as the one you are running
# the primer_designer script from, then you must include the
# full file path.
#
# If you are running Illumina data you may disregard this section
# (but do not delete).

input454reads  test/data/454_All_python.fna

#------------------- Illumina PE Read Files --------------------#
#
# If you are running Illumina data enter the two paired-end
# files, one for each variable name below. The file format should
# be a raw Illumina scarf format, not fastq. If these file are
# not in the same directory as the primer_designer script then
# you must include the full file path.
#
# If you are running 454 data you may disregard this section (but
# do not delete).

inputReadFile  test/data/IlluminaPE_SG_10k_1.fq
pairedReadFile  test/data/IlluminaPE_SG_10k_2.fq

#------------------------ Output Files -------------------------#
#
# Enter the names of output files. Include the full path names to
# put the files in directories other than the directory you run
# the script from. The MicrosatSumOut file gives a summary of the
# types of microsatellites found in the data. The PALsummaryOut
# file lists all the read IDs with microsatellites and gives
# information about primer pairs if found and associated repeats.

MicrosatSumOut  test/output/test_microsat_summary.txt
PALsummaryOut  test/output/test_PAL_summary.txt


#----------------------- Microsat Info -------------------------#
#
# Define the minimum number of n-mer repeat units you want to
# detect for each n-mer length. Put 0 if you do not want to
# consider a particular n-mer unit size. For instance, a value of
# 6 for the 2merMinReps would mean pal_finder will record all
# 2mer repeated at least 6 times in a row (at least 12 bases;
# example: ATATATATATAT)

2merMinReps 	6
3merMinReps 	0
4merMinReps 	0
5merMinReps 	0
6merMinReps 	0


#----------------------- primer3 Files -------------------------#
#
# The primer3input and primer3output variables hold the names of
# primer3-specific files. These are internal, temporary files
# that hold the raw input and output for the primer3 program.
# These are not files you need to provide. They may, however be
# useful for debugging purposes or if you want more specific
# information about the primer metrics from primer3. You can
# specify the name and location of these files by the values for
# these variables. You can also retain these files by setting
# keepPrimer3files to 1. Setting to 0 causes these files to be
# deleted after the script finishes.

primer3input  test/output/pr3in.txt
primer3output  test/output/pr3out.txt
keepPrimer3files  0

# The primer3executable variable sets the location of the
# primer3 executable. If the location of the primer3 executable
# has been added to your system's $PATH variable, all you need
# to put is the binary executable name (usually "primer3_core").
# The primer3 version required for this script is 2.0.0. If you
# have multiple versions of primer3, make sure you put the
# location of the correct version here. The correct version of
# primer3 can be downloaded from here:
# http://primer3.sourceforge.net/releases.php

primer3executable  /usr/local/bin/primer3_core


#---------------------- primer prefix ------------------------#
#
# This value will be added onto the beginning of all primer
# names. The rest of the primer name is an id #. For instance,
# if the value is "test_" primer names will look like
# "test_123" or "test_" followed by a unique number identifier. 

prNamePrefix  test_


#-------------------- primer3 Parameters ---------------------#
#
# These settings are passed on to the primer3 program and can
# be adjusted to manipulate the primer pair requirements. For
# further details on these parameters consult the primer3 
# (version 2.0.0) documentation.

PRIMER_TASK  pick_pcr_primers

PRIMER_OPT_SIZE  20

PRIMER_MIN_SIZE  18

PRIMER_MAX_SIZE  30

PRIMER_MAX_NS_ACCEPTED  0

# The following two values are adjusted by the script for paired ends reads
# however for 454 reads they can be adjusted by the user

pr3ProductSizeRangeMinVal  60
pr3ProductSizeRangeMaxVal  500

PRIMER_OPT_SIZE  20

PRIMER_MIN_GC  30.0

PRIMER_MAX_GC  80.0

PRIMER_GC_CLAMP  2

PRIMER_MAX_END_GC  5

PRIMER_MIN_TM  58.0

PRIMER_MAX_TM  65.0

PRIMER_OPT_TM  62.0

PRIMER_PAIR_MAX_DIFF_TM  2.0

PRIMER_TM_FORMULA  0

PRIMER_MAX_SELF_ANY  8.00

PRIMER_PAIR_MAX_COMPL_ANY  8.00

PRIMER_MAX_SELF_END  3.00

PRIMER_PAIR_MAX_COMPL_END  3.00

PRIMER_MAX_POLY_X  4

PRIMER_LOWERCASE_MASKING  0 

PRIMER_NUM_RETURN  1

PRIMER_MISPRIMING_LIBRARY  simple.ref

PRIMER_MAX_LIBRARY_MISPRIMING  10.00

PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS   0
