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root/msatfinder/msatfinder.rc
Revision: 1.1.1.1 (vendor branch)
Committed: Mon Mar 7 15:34:44 2005 UTC (11 years, 6 months ago) by knirirr
Branch: MAIN
CVS Tags: HEAD, HEAD
Changes since 1.1: +0 -0 lines
Log Message:
First import

Line File contents
1 ##################################################################
2 # msatfinder.rc - configuration file for msatfinder script only. #
3 # Full editing instructions are included below. #
4 # most of these defaults should be acceptable. #
5 ##################################################################
6
7
8 [COMMON]
9
10 # set to 1 to switch on debugging info
11 debug = 0
12
13 # no. of bp either side of each msat to extract
14 flank_size = 300
15
16 # directory variables: it is best to leave these
17 # values as they are. If you change them, the trailing
18 # slash MUST be left on the name
19 mine_dir = "MINE/"
20 repeat_dir = "Repeats/"
21 tab_dir = "Msat_tabs/"
22 bigtab_dir = "Flank_tabs/"
23 fasta_dir = "Fasta/"
24 prime_dir = "Primers/"
25 align_dir = "Aligner/"
26 count_dir = "Counts/"
27
28
29 [DEPENDENCIES]
30
31 # Determine whether primers may be made from the repeat you need eprimer3
32 # (emboss), and primer3_core on your PATH for this to work
33 # (see http://www-genome.wi.mit.edu/genome_software/other/primer3.html)
34 # see eprimer3 documentation for additional flags.
35 # N.B. use "-task 0" if you have EMBOSS v.2.8.0, but "-primer" if you
36 # have a newer version.
37 run_eprimer = 1
38 eprimer_args = "-primer"
39 eprimer = "/usr/bin/eprimer3"
40 primer3core = "/usr/bin/primer3_core"
41
42
43 [FINDER]
44
45 # the override switch will, if set to 1,
46 # turn off most of the output files.
47 # they can be deactivated individually
48 # with separate switches (see below)
49 override = 0
50
51 # set the type of msat you want to search
52 # for here, 1=mono, 2=di etc. (default is
53 # for mono-hexa), with each type followed by
54 # the threshold (no. of units or greater to
55 # be detected). E.g "1,4" says "find all
56 # monos of length 4 or more". Separate each
57 # pair of "motif,threshold" with a pipe "|".
58 motif_threshold="1,12|2,8|3,5|4,5|5,5|6,5"
59
60 # will write a file.tab file
61 # with repeats formatted as embl
62 # features
63 # ready for overlay on the genbank doc
64 # inside the artemis annotation tool
65 # contains "feature table", hence "tab"
66 # 0 no artemis files
67 # 1 files for msat only
68 # 2 also produce separate files for msat + flanks
69 artemis = 1
70
71 # Write repeats and flanking areas to
72 # a MINE.db file? 1=yes, etc.
73 mine = 1
74
75 # write fasta files for repeats?
76 fastafile = 1
77
78 # "taxon" information: please see
79 # http://genomics.nerc-oxford.ac.uk/msatminer/#taxon
80 # for details
81 phages = "viruses"
82 viroids = "viruses"
83 plant_viruses = "viruses"
84 megaplasmids = "plasmids"
85
86 # remote link for viewing complete
87 # files, (Genbank, in this case)
88 remote_link="http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val="
89
90 # this switch turns on the Repeats/$prefix.summary
91 # file, which can grow rather large if your
92 # thresholds are low. It's an essential file, though.
93 sumswitch = 1
94
95 # print out filenames as they are searched
96 screendump = 1