Mercurial > repos > morinlab > oncocircos
comparison parse.conf @ 3:0f30d19bc378 draft
Uploaded
| author | morinlab |
|---|---|
| date | Wed, 30 Nov 2016 13:34:10 -0500 |
| parents | b77ab858eac1 |
| children |
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| 2:55571b9980b0 | 3:0f30d19bc378 |
|---|---|
| 1 | |
| 1 <filter> | 2 <filter> |
| 2 SNV_FILTER | 3 SNV_FILTER |
| 3 SNV_FILTER_NUM | 4 SNV_FILTER_NUM |
| 4 CHR | 5 CHR |
| 5 </filter> | 6 </filter> |
| 6 | 7 |
| 7 <files> | 8 <files> |
| 8 ROOT | 9 ROOT |
| 9 CNV | 10 cnv = data/cnv.txt |
| 10 SNV | 11 cnvlg = data/cnv.large.scale.txt |
| 11 MART | 12 sv = data/snv.txt |
| 12 CIRCOS | 13 mart = data/biomart.txt |
| 14 CIRCOS | |
| 15 mask = data/genes_to_hide.txt | |
| 16 genes = data/genes_to_label.txt | |
| 13 </files> | 17 </files> |
| 14 | 18 |
| 19 | |
| 20 <map> | |
| 21 log2 = avg:sprintf("%.2f",2*2**x) | |
| 22 </map> | |
| 23 | |
| 24 # 0-indexed column numbers and names | |
| 15 <fields> | 25 <fields> |
| 26 <cnvlg> | |
| 27 key = chr | |
| 28 0 = chr | |
| 29 1 = start | |
| 30 2 = end | |
| 31 3 = type:lc | |
| 32 </cnvlg> | |
| 16 <cnv> | 33 <cnv> |
| 17 key = sample,chr | 34 key = sample,chr |
| 18 0 = sample | 35 0 = sample |
| 19 1 = chr | 36 1 = chr |
| 20 2 = start | 37 2 = start |
| 21 3 = end | 38 3 = end |
| 22 5 = avg | 39 # :map(x,y) will create a new field x based on intervals defined in a block |
| 23 6 = category:lc | 40 # |
| 41 # e.g. | |
| 42 # value of 2*2**(log2) (see <map> block above) will be used to assign key "category" | |
| 43 # based on <cnv><log2> intervals | |
| 44 5 = log2:map(category,cnv/log2) | |
| 24 </cnv> | 45 </cnv> |
| 25 | |
| 26 <sv> | 46 <sv> |
| 27 key = id,sample | 47 key = id,sample |
| 28 4 = chr | 48 4 = chr |
| 29 5 = start | 49 5 = start |
| 30 6 = end | 50 6 = end |
| 31 8 = type:lc | 51 8 = type:lc |
| 32 15 = sample | 52 15 = sample |
| 33 47 = id | 53 47 = id |
| 34 53 = aa | 54 53 = aa |
| 35 </sv> | 55 </sv> |
| 36 | |
| 37 <genes> | 56 <genes> |
| 38 key = chr | 57 key = chr |
| 39 0 = id | 58 0 = id |
| 40 2 = end | 59 3 = end |
| 41 3 = start | 60 2 = start |
| 42 4 = chr | 61 1 = chr |
| 43 5 = name | 62 4 = name |
| 44 </genes> | 63 </genes> |
| 45 </fields> | 64 </fields> |
| 46 | 65 |
| 47 <cnv> | 66 <cnv> |
| 48 filter = yes | 67 filter = yes |
| 52 neut = 0 | 71 neut = 0 |
| 53 hetd = 10 | 72 hetd = 10 |
| 54 homd = 5 | 73 homd = 5 |
| 55 hlamp = 0 | 74 hlamp = 0 |
| 56 </types> | 75 </types> |
| 76 # assign log2 ranges to CNV event categories | |
| 77 # | |
| 78 # ( indicates open interval | |
| 79 # [ indicates closed interval | |
| 80 # | |
| 81 # e.g. (1,2] is 1 < x <= 2 | |
| 82 # [2,3) is 2 <= x < 3 | |
| 83 # | |
| 84 # The intervals must be disjoint and completely cover | |
| 85 # all possible values you're going to test. | |
| 86 <log2> | |
| 87 # max = category | |
| 88 (,1) = homd | |
| 89 [1,2) = hetd | |
| 90 2 = neut | |
| 91 (2,3] = gain | |
| 92 (3,) = amp | |
| 93 </log2> | |
| 57 </cnv> | 94 </cnv> |
| 58 | 95 |
| 59 <sv> | 96 <sv> |
| 97 # only pay attention to SV types listed <types> | |
| 60 filter = yes | 98 filter = yes |
| 99 # only consider the most damaging type of mutation in a patient | |
| 100 # (one with top score in <types> | |
| 101 # the absolute value of the damage weight is unimportant, only order matters | |
| 61 top_damage_only = yes | 102 top_damage_only = yes |
| 62 <types> | 103 <types> |
| 63 nonsense_mutation = 35 | 104 nonsense_mutation = 35 |
| 64 frame_shift_del = 30 | 105 frame_shift_del = 30 |
| 65 frame_shift_ins = 25 | 106 frame_shift_ins = 25 |