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comparison test-data/extrinsic.truncated.cfg @ 2:0d425a4b6896 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
author iuc
date Thu, 23 May 2019 18:17:22 -0400
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1:1fbb1135da16 2:0d425a4b6896
1 ==# extrinsic information configuration file for AUGUSTUS
2 #
3 # protein hints
4 # include with --extrinsicCfgFile=filename
5 # date: 16.10.2007
6 # Mario Stanke (mstanke@gwdg.de)
7
8
9 # source of extrinsic information:
10 # M manual anchor (required)
11 # P protein database hit
12 # E EST/cDNA database hit
13 # C combined est/protein database hit
14 # D Dialign
15 # R retroposed genes
16 # T transMapped refSeqs
17 # W wiggle track coverage info from RNA-Seq
18
19 [SOURCES]
20 M RM E W
21
22 #
23 # individual_liability: Only unsatisfiable hints are disregarded. By default this flag is not set
24 # and the whole hint group is disregarded when one hint in it is unsatisfiable.
25 # 1group1gene: Try to predict a single gene that covers all hints of a given group. This is relevant for
26 # hint groups with gaps, e.g. when two ESTs, say 5' and 3', from the same clone align nearby.
27 #
28 [SOURCE-PARAMETERS]
29
30
31 # feature bonus malus gradelevelcolumns
32 # r+/r-
33 #
34 # the gradelevel colums have the following format for each source
35 # sourcecharacter numscoreclasses boundary ... boundary gradequot ... gradequot
36 #
37
38 [GENERAL]
39 start 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1
40 stop 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1
41 tss 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1
42 tts 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1
43 ass 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1
44 dss 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1
45 exonpart 1 .992 M 1 1e+100 RM 1 1 E 1 1 W 1 1.005
46 exon 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1
47 intronpart 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1
48 intron 1 .8 M 1 1e+100 RM 1 1 E 1 1000 W 1 1
49 CDSpart 1 1 0.985 M 1 1e+100 RM 1 1 E 1 1 W 1 1
50 CDS 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1
51 UTRpart 1 1 .973 M 1 1e+100 RM 1 1 E 1 1 W 1 1
52 UTR 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1
53 irpart 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1
54 nonexonpart 1 1 M 1 1e+100 RM 1 1.01 E 1 1 W 1 1
55 genicpart 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1
56
57 #
58 # Explanation:
59 #
60 # The gff/gtf file containint the hints must contain somewhere in the last
61 # column an entry source=?, where ? is one of the source characters listed in
62 # the line after [SOURCES] above. You can use different sources when you have
63 # hints of different reliability of the same type, e.g. exon hints from ESTs
64 # and exon hints from evolutionary conservation information.
65 #
66 # In the [GENERAL] section the entries second column specify a bonus for obeying
67 # a hint and the entry in the third column specify a malus (penalty) for
68 # predicting a feature that is not supported by any hint. The bonus and the
69 # malus is a factor that is multiplied to the posterior probability of gene
70 # structueres.
71 # Example:
72 # CDS 1000 0.7 ....
73 # means that, when AUGUSTUS is searching for the most likely gene structure,
74 # every gene structure that has a CDS exactly as given in a hint gets
75 # a bonus factor of 1000. Also, for every CDS that is not supported the
76 # probability of the gene structure gets a malus of 0.7. Increase the bonus to
77 # make AUGUSTUS obey more hints, decrease the malus to make AUGUSTUS predict few
78 # features that are not supported by hints. The malus helps increasing
79 # specificity, e.g. when the exons predicted by AUGUSTUS are suspicious because
80 # there is no evidence from ESTs, mRNAs, protein databases, sequence
81 # conservation, transMapped expressed sequences.
82 # Setting the malus to 1.0 disables those penalties. Setting the bonus to 1.0
83 # disables the boni.
84 #
85 # start: translation start (start codon), specifies an interval that contains
86 # the start codon. The interval can be larger than 3bp, in which case
87 # every ATG in the interval gets a bonus. The highest bonus is given
88 # to ATGs in the middle of the interval, the bonus fades off towards the ends.
89 # stop: translation end (stop codon), see 'start'
90 # tss: transcription start site, see 'start'
91 # tts: transcription termination site, see 'start'
92 # ass: acceptor (3') splice site, the last intron position
93 # dss: donor (5') splice site, the first intron position
94 # exonpart: part of an exon in the biological sense. The bonus applies only
95 # to exons that contain the interval from the hint. Just
96 # overlapping means no bonus at all. The malus applies to every
97 # base of an exon. Therefore the malus for an exon is exponential
98 # in the length of an exon: malus=exonpartmalus^length.
99 # Therefore the malus should be close to 1, e.g. 0.99.
100 # exon: exon in the biological sense. Only exons that exactly match the
101 # hint get a bonus. Exception: The exons that contain the start
102 # codon and stop codon. This malus applies to a complete exon
103 # independent of its length.
104 # intronpart: introns both between coding and non-coding exons. The bonus
105 # applies to every intronic base in the interval of the hint.
106 # intron: An intron gets the bonus if and only if it is exactly as in the hint.
107 # CDSpart: part of the coding part of an exon. (CDS = coding sequence)
108 # CDS: coding part of an exon with exact boundaries. For internal exons
109 # of a multi exon gene this is identical to the biological
110 # boundaries of the exon. For the first and the last coding exon
111 # the boundaries are the boundaries of the coding sequence (start, stop).
112 # UTR: exact boundaries of a UTR exon or the untranslated part of a
113 # partially coding exon.
114 # UTRpart: The hint interval must be included in the UTR part of an exon.
115 # irpart: The bonus applies to every base of the intergenic region. If UTR
116 # prediction is turned on (--UTR=on) then UTR is considered
117 # genic. If you choose against the usual meaning the bonus of
118 # irparts to be much smaller than 1 in the configuration file you
119 # can force AUGUSTUS to not predict an intergenic region in the
120 # specified interval. This is useful if you want to tell AUGUSTUS
121 # that two distant exons belong to the same gene, when AUGUSTUS
122 # tends to split that gene into smaller genes.
123 # nonexonpart: intergenic region or intron. The bonus applies to very non-exon
124 # base that overlaps with the interval from the hint. It is
125 # geometric in the length of that overlap, so choose it close to
126 # 1.0. This is useful as a weak kind of masking, e.g. when it is
127 # unlikely that a retroposed gene contains a coding region but you
128 # do not want to completely forbid exons.
129 # genicpart: everything that is not intergenic region, i.e. intron or exon or UTR if
130 # applicable. The bonus applies to every genic base that overlaps with the
131 # interval from the hint. This can be used in particular to make Augustus
132 # predict one gene between positions a and b if a and b are experimentally
133 # confirmed to be part of the same gene, e.g. through ESTs from the same clone.
134 # alias: nonirpart
135 #
136 # Any hints of types dss, intron, exon, CDS, UTR that (implicitly) suggest a donor splice
137 # site allow AUGUSTUS to predict a donor splice site that has a GC instead of the much more common GT.
138 # AUGUSTUS does not predict a GC donor splice site unless there is a hint for one.
139 #
140 # Starting in column number 4 you can tell AUGUSTUS how to modify the bonus
141 # depending on the source of the hint and the score of the hint.
142 # The score of the hints is specified in the 6th column of the hint gff/gtf.
143 # If the score is used at all, the score is not used directly through some
144 # conversion formula but by distinguishing different classes of scores, e.g. low
145 # score, medium score, high score. The format is the following:
146 # First, you specify the source character, then the number of classes (say n), then you
147 # specify the score boundaries that separate the classes (n-1 thresholds) and then you specify
148 # for each score class the multiplicative modifier to the bonus (n factors).
149 #
150 # Examples:
151 #
152 # M 1 1e+100
153 # means for the manual hint there is only one score class, the bonus for this
154 # type of hint is multiplied by 10^100. This practically forces AUGUSTUS to obey
155 # all manual hints.
156 #
157 # T 2 1.5 1 5e29
158 # For the transMap hints distinguish 2 classes. Those with a score below 1.5 and
159 # with a score above 1.5. The bonus if the lower score hints is unchanged and
160 # the bonus of the higher score hints is multiplied by 5x10^29.
161 #
162 # D 8 1.5 2.5 3.5 4.5 5.5 6.5 7.5 0.58 0.4 0.2 2.9 0.87 0.44 0.31 7.3
163 # Use 8 score classes for the DIALIGN hints. DIALIGN hints give a score, a strand and
164 # reading frame information for CDSpart hints. The strand and reading frame are often correct but not
165 # often enough to rely on them. To account for that I generated hints for all
166 # 6 combinations of a strand and reading frame and then used 2x2x2=8 different
167 # score classes:
168 # {low score, high score} x {DIALIGN strand, opposite strand} x {DIALIGN reading frame, other reading frame}
169 # This example shows that scores don't have to be monotonous. A higher score
170 # does not have to mean a higher bonus. They are merely a way of classifying the
171 # hints into categories as you wish. In particular, you could get the effect of
172 # having different sources by having just hints of one source and then distinguishing
173 # more scores classes.
174 #
175 #
176 # Future plans:
177 # - Add fuzzy intron hints. Introns get a bonus only when they approximately
178 # have the same boundaries as in the hint.
179 # - Make the splice site hints fuzzy also. Allow a hint interval that contains a
180 # likely splice site, as opposed to only an individual position.
181 # - Write a program that automatically optimizes the boni and mali given an
182 # annotated test set of genes and hints for that set of sequences.
183