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msatfinder.rc
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msatfinder.rc
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##################################################################
# msatfinder.rc - configuration file for msatfinder script only. #
# Full editing instructions are included below. #
# most of these defaults should be acceptable. #
##################################################################
[COMMON]
# set to 1 to switch on debugging info
debug = 0
# no. of bp either side of each msat to extract
flank_size = 300
# directory variables: it is best to leave these
# values as they are. If you change them, the trailing
# slash MUST be left on the name
mine_dir = "MINE/"
repeat_dir = "Repeats/"
tab_dir = "Msat_tabs/"
bigtab_dir = "Flank_tabs/"
fasta_dir = "Fasta/"
prime_dir = "Primers/"
align_dir = "Aligner/"
count_dir = "Counts/"
[DEPENDENCIES]
# Determine whether primers may be made from the repeat you need eprimer3
# (emboss), and primer3_core on your PATH for this to work
# (see http://www-genome.wi.mit.edu/genome_software/other/primer3.html)
# see eprimer3 documentation for additional flags.
# N.B. use "-task 0" if you have EMBOSS v.2.8.0, but "-primer" if you
# have a newer version.
run_eprimer = 1
eprimer_args = "-primer"
eprimer = "/usr/bin/eprimer3"
primer3core = "/usr/bin/primer3_core"
[FINDER]
# the override switch will, if set to 1,
# turn off most of the output files.
# they can be deactivated individually
# with separate switches (see below)
override = 0
# set the type of msat you want to search
# for here, 1=mono, 2=di etc. (default is
# for mono-hexa), with each type followed by
# the threshold (no. of units or greater to
# be detected). E.g "1,4" says "find all
# monos of length 4 or more". Separate each
# pair of "motif,threshold" with a pipe "|".
motif_threshold="1,12|2,8|3,5|4,5|5,5|6,5"
# will write a file.tab file
# with repeats formatted as embl
# features
# ready for overlay on the genbank doc
# inside the artemis annotation tool
# contains "feature table", hence "tab"
# 0 no artemis files
# 1 files for msat only
# 2 also produce separate files for msat + flanks
artemis = 1
# Write repeats and flanking areas to
# a MINE.db file? 1=yes, etc.
mine = 1
# write fasta files for repeats?
fastafile = 1
# "taxon" information: please see
# http://genomics.nerc-oxford.ac.uk/msatminer/#taxon
# for details
phages = "viruses"
viroids = "viruses"
plant_viruses = "viruses"
megaplasmids = "plasmids"
# remote link for viewing complete
# files, (Genbank, in this case)
remote_link="http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val="
# this switch turns on the Repeats/$prefix.summary
# file, which can grow rather large if your
# thresholds are low. It's an essential file, though.
sumswitch = 1
# print out filenames as they are searched
screendump = 1