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log.todo
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TODO
01 Feb 2018:
- js
✔ tanungin si sir kung kailangan pang ilagay yung base pair dun sa reference genome line @done (18-02-05 20:21)
✔ find the format of the node variable in tubemap.js - para sa labeling ng reference genome line @done (18-02-05 20:21)
✔ ayusin yung variables ng pagkakadraw ng line (x1, x2, y1, y2) @done (18-02-05 20:21)
✔ add variables para sa current view @done (18-02-10 20:36)
✔ current chromosome na nipili @done (18-02-06 17:48)
✔ boundary nung current chromosome @done (18-02-10 20:36)
- html
✔ add dropdown para sa selection ng chromosome number @done (18-02-05 20:22)
✔ add buttons for start and end ng view for chromosome @done (18-02-05 20:22)
✔ provide the boundary for each chromosome (end range) @done (18-02-05 20:22)
05 Feb 2018:
✔ pwedeng gawan ng options for user friendliness @done (18-02-06 17:48)
✔ adjust ruler interval @done (18-02-06 17:48)
✔ show sequence text @done (18-02-06 17:48)
✔ baka lang may ilagay ka pa kapag dinouble click yung track (rectangle representation) : trackDoubleClick() @done (18-03-15 23:28)
✔ gawin yung correct na pagrender ng start at end kapag may nakaset na @done (18-02-06 17:49)
✔ same goes with the ruler, dapat nag-aadjust yung starting variable @done (18-02-06 17:49)
06 Feb 2018:
☐ mga itatanong kay sir
✔ minimum range na iseset @done (18-03-15 23:28)
✔ kung ok na yung reference genome na initial @done (18-03-15 23:28)
✔ paano yung pagkakastore nung reference genome sa html, considering na sobrang laki nung file na iaupload @done (18-03-15 23:28)
☐ yung kung paano kukunin yung sv sa file ano yung mga gagamiting variables to represent
✘ ilan yung sv's? kasi db magmemerge siya, pag may sv magbabranch out, so ilan yung sv's na iiscan sa file @cancelled (18-03-27 15:04)
✘ medyo shitty yung panning ng svg kapag zoomed out siya - emphasis SHITTY @cancelled (18-02-13 14:03)
✔ ayusin yung limits chr(s) @done (18-02-06 20:24)
✔ kapag maliit yung range, nagana pa rin kapag nabago yung ruler interval @done (18-02-06 20:24)
✔ kapag sobra, nageextend yung ruler at yung reference genome line @done (18-02-06 20:24)
✔ reset view button sa svg @done (18-02-10 20:35)
✔ yung sa ruler, pwedeng magnegative yung value (resulting sa walang ruler interval) @done (18-02-10 20:35)
10 Feb 2018:
✔ ilipat yung basic html elements to sidebar (semantic-ized) @done (18-02-13 14:03)
☐ ayusin yung shittyness ng svgpanzoom kapag nagload ng panibagong chr
✔ yung starting interval ng ruler pag hindi 0 yung value ayusin @done (18-02-17 01:58)
✔ simulan na yung kahit pagrender ng mga sv's @done (18-02-17 01:58)
14 Feb 2017:
✘ truncate mo na yung real value @cancelled (18-02-17 01:58)
✔ flunking 20 dafault (extension nung both sides, equal extension) @done (18-03-15 23:29)
✔ deletion minimum range: 10 @done (18-03-15 23:28)
✔ insertion minimum range: 5 @done (18-03-15 23:28)
✔ limit: 100 (kung ipapakita na insertion, if below pa dun, di na ipapakita) @done (18-03-15 23:28)
✘ yung number of base pairs pag nagbabranch out depende pa rin pero ang set ni sir ay 5bp @cancelled (18-03-15 23:29)
✔ kailangang gawin na algo ay idetermine yung portions na may sv's (hotspots daw) @done (18-03-15 23:29)
✔ determine overlapping intervals para malaman yung mga regions na may sv - sila lang yung magdedetermine kung magbbranchout ba or not @done (18-03-15 23:32)
✔ maximum na range para ivisualize siya 50000bp @done (18-03-27 15:03)
✔ mutually exclusive yung pagview ng mga sv types, kung puro insertion ay puro insertion lang, ganown @done (18-02-17 01:58)
✔ insertion: parang kagaya na lang nung sa ideogram @done (18-03-27 15:03)
✔ select range @done (18-02-17 01:57)
✔ select sv types @done (18-02-17 01:57)
✘ yung issue sa file reading ay babashin muna lahat @cancelled (18-03-15 23:31)
✔ viewer na by chromosme lang @done (18-03-15 23:31)
☐ lagay sa isang array yung mga indices sa file
✔ start - 50, end + 50 yung reference lang yung may "flakning???" @done (18-03-15 23:31)
✔ strictly within the range yung mga ipapakitang sv's @done (18-03-15 23:31)
✔ pagcompute nung number of base pairs kung saan magbabranch out, in @done (18-03-15 23:31)
✔ starting range ng chromosome ay 1, 1-indexing compared sa array in cmsc na 0-indexing !important @done (18-02-17 01:57)
✔ fix the ruler intervals` @done (18-02-17 01:57)
☐ responsive width nung sv pag nakabukas yung sidenav
17 Feb 2018:
☐ yung kukunin yung endpoints (putul-putol na shit; start at end for INV|DUP|DEL) para naka .data na lang
☐ pwede yung input na 1 - 1001 (length chr: 1000) which is sad
1 Mar 2018:
✔ ayusin yung code for branching out @done (18-03-15 23:31)
✔ correctly identify kung paano yung hotspots @done (18-03-15 23:31)
15 Mar 2018:
✔ problem with even number of hotspot (shitty yung itsura) @done (18-04-16 17:54)
18 Mar 2018:
✔ ayusin yung paqgbago ng flanking value @done (18-03-18 00:50)
☐ yung pag nagnightmode, shitty yung deletions haha kita pa rin
✘ ruler highlight - may linya pababa tapos may number sa taas pag naghover sa ruler line @cancelled (18-05-07 21:49)
☐ mas ok siguro kung yung help ay modal na lang para maraming mailagay
✔ yung scrollbar ng tooltip, constant yung width and height para scrollable @done (18-05-07 21:49)
✔ highlight yung branch together with reference para hindi halata yung polyline @done (18-03-18 00:50)
pwede ko po bang iasssume na walang uulit na row na iisa yung kanilang cluster id?
sample;
chr01 10 11 AAAATGCATCGATG,GTCAGT,ATCTAG Rangifer tarandus 1
chr01 10 11 tgAGgatAGT,AGTA,AGTCA Amaranth 1
27 March 2018:
✔ dup and inv - same color pero may @done (18-04-05 14:36)
✔ iba iba yung kulay per type @done (18-04-05 14:36)
✔ arrowhead sa inversion @done (18-04-05 14:36)
✔ nipisan yung branch height pati yung thickness ng track @done (18-04-03 17:10)
✔ set track width to 5 px @done (18-04-03 17:10)
✔ gawin checkboxes yung radio button para makapamili siya ng multiple types to visualize @done (18-04-16 22:17)
✔ pag walang lumabas, may message na lang na wala, hindi na siya makikihati sa view @done (18-04-16 22:17)
✔ download image @done (18-04-24 18:04)
✔ yung case na same cluster @done (18-05-07 21:48)
chr01 10 100 DEL;35 Ninox superciliaris 1
chr01 20 100 DEL;35 Ninox superciliaris 1
✔ use the first occurence of the similar cluster @done (18-05-07 21:48)
✔ group via cluster @done (18-05-07 21:48)
✔ assumption: sorted by chromosome, then start, then cluster && single occurence @done (18-05-07 21:49)
✔ same cluster id, imemerge @done (18-05-07 21:49)
✔ branching factor na ay yung branch, isang branch, isang cluster (ichecheck ) @done (18-05-07 21:49)
✔ hindi pwedeng magkaroon ng in between @done (18-05-07 21:49)
✔ gagamitin ko ay walang redundant cluster @done (18-05-07 21:49)
✔ one occurence, preprocess @done (18-05-07 21:49)
✔ another file: mapping ng samples @done (18-05-07 21:49)
✔ ibibigay ni sir yung file dun sa preprocessing na pagmemerge ng clusters @done (18-05-07 21:49)
✔ isang row, isang cluster na lang @done (18-05-07 21:49)
✔ save sa SQL yung file na binigay ni sir @done (18-05-07 21:48)
✔ yung type at yung length a magkaibang column sa mysql @done (18-05-07 21:48)
✔ brush @done (18-05-01 13:26)
✔ pag gumawa siya ng brush, automatic may lalabas na modal @done (18-05-01 13:26)
✔ panibagong tapos may modal na magdiddisplay ng table @done (18-05-01 13:26)
✔ button na save as / download as .csv or .tsv @done (18-04-24 18:05)
✔ pag csv, pwedeng @done (18-04-24 18:05)
chr01,15,50,DEL;35,Ninox superciliaris,1
✔ tsv lahat ng column @done (18-04-24 18:05)
chr01 10 100 DEL;35 Ninox superciliaris 1
☐ bed chr, start, end, save file extension as .bed
chr01 60 80 DEL;20;Rana sp.;17
✘ yung admin panel na pagupload ng files @cancelled (18-05-07 21:48)
✘ append at overwrite yung files @cancelled (18-05-07 21:48)
☐ gene annotation file
☐ user defined data
☐ define new sv
☐ submit insertion to blast
☐ blastn suite tignan mo na lang yung email ni sir
☐ may button sa ilalim ng inserted sequence para gamitin sa blast something
01 May 2018:
✘ sir pwede po bang and iindicate na chr-length ay yung max interval sa sv file para hindi na mag-abala yung user na tignan yung mga empty parts? @cancelled (18-05-07 13:32)
02 May 2018:
☐ baguhin yung itsura ng deletions because it is shit
☐ extend the sequence text upto the flank value
☐ add the gene annotation file
for brush:
☐ end nasa loob || start nasa loob
☐ end > bounds && start < bounds
☐ tanggalin yung spacesa gitna ng chr at number
☐