LRR / Polloc-v1.5.3 / examples / vntrs.bme 

            

              
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###################################################################################
# The current file defines different parameters for the analysis of VNTR loci
# using Polloc (Perl package `Bio::Polloc`).  This format is interpreted by the
# Perl module `Bio::Polloc::Polloc::Config`.
###################################################################################
# This a variable not used by Polloc, but used in the construction of other vars
root = "biome-project/thebio.me/"
# This variable tells Polloc where to look (alternatively) for software exacutables
path = "${.root}bins/"
[ rule ]
# This tells Polloc to use 'VNTR' as the base of the locus IDs.
glob prefix_id='VNTR'
# Define the VNTR variable, containing the parameters to detect VNTR.
VNTR = "-minsize 30 -maxsize 1000 -minperiod 5 -maxperiod 9 -exp 6 -res 2 -minscore 50 -maxscore 0 -minsim 80 -maxsim 100 -match 2 -mismatch 3 -indels 5 -pm 80 -pi 20"
# Register the VNTR variable as a Rule of type 'tandemrepeat' called 'VNTR repeat'.
# Use 'Repeat' instead of 'TandemRepeat' in order to use 'mreps' instead of 'TRF'.
add TandemRepeat:VNTR as 'VNTR repeat'
# Turn execution on for the VNTR variable (rule)
set VNTR executable = 'Yes'
[ GroupCriteria ]
# Create the variable simLimit, later used as minimum similarity for grouping
var num simLimit = 0.9
# Extract flanking sequences (500 nt up- and downstream)
var seq left1 = FEAT1 at [-1, -500..0]
var seq left2 = FEAT2 at [-1, -500..0]
var seq right1 = FEAT1 at [1, 500..0]
var seq right2 = FEAT2 at [1, 500..0]
# Compare flanking sequences
var num leftSim = left1 aln-sim with left2
var num rightSim = right1 aln-sim with right2
var num leftSimR = left1 aln-sim with right2
var num rightSimR = right1 aln-sim with left2
# Evaluate if similarity is above the minimum
var bool leftSame = leftSim > simLimit
var bool rightSame = rightSim > simLimit
var bool leftSameR = leftSimR > simLimit
var bool rightSameR = rightSimR > simLimit
# Boolean operations for different orientation cases
var bool same = leftSame | rightSame
var bool sameR = leftSameR | rightSameR
var bool isPair = same | sameR
# Tells Polloc to use 'VNTR' as source loci, and compares them against 'VNTR'
glob source = 'VNTR'
glob target = 'VNTR'
# Register isPair variable as the criterion of equivalency (isPair must be boolean)
eval isPair
[ GroupExtension ]
# Create context variable containing parameters of the extension (identification of additional loci)
context = "-function context -upstream 500 -downstream 500 -detectstrand 1 -feature 0 -maxlen 500 -similarity 0.9 -algorithm blast -consensusperc 60 -e 1e-5 -score 200 -p blastn"
# Register context variable as criterion for the groups extension
eval context
[ Typing ]
# Maximum amplicon size
maxSize = 2000
# Minimum amplicon size
minSize = 1
# Minimum conservation for primer design
primerConservation = 0.9
# Length of primers
primerSize = 20
# Define bandingPatter::amplification as the typing class
eval banding::ampl