diff --git a/doc/project/zmap_lace_tasks.txt b/doc/project/zmap_lace_tasks.txt new file mode 100755 index 0000000000000000000000000000000000000000..b1830b31abf59f26dd9603668f6d8ae13872f0e2 --- /dev/null +++ b/doc/project/zmap_lace_tasks.txt @@ -0,0 +1,217 @@ +From edgrif@sanger.ac.uk Thu Mar 9 11:16:51 2006 +Date: Thu, 9 Mar 2006 11:16:50 +0000 (GMT) +From: Ed Griffiths <edgrif@sanger.ac.uk> +To: Roy Storey <rds@sanger.ac.uk> +Subject: lace stuff... + +Roy, + +Here is a list of stuff from my list and Laurens. I'm going to start doing some +of this stuff so I'll say what I'm doing and when you take one of them, just let +me know... + +Ed + + + +ZMap - items for lace integration +--------------------------------- + + +The plan is to put zmap into test_otterlace straight away even though we know +not everything that is required is implemented yet. Liz/Charlie will be the +guinea pigs for the test initially. We will meet again in a month to review +how it's gone and what we need to do next. + + + +Priorities: +----------- + +*** Do right now +** Do this month +* Think about + + + +Configuration +------------- + +* +- need to be able to do "per team" configurations of different parts of zmap +(e.g. of what goes in the cut buffer and in what format). + + + +Transcript operations +--------------------- + +** + +- contextual menu on gene object: + + show CDS translation in zmap + + show CDS translation (including *stopcodon) in separate (copy-pastable) + window + + export CDS translation (fasta seq saved to file) + + show CDS sequence (nucleotide seq of CDS incl stop codon) in separate + (copy-pastable) window + + export CDS sequence (fasta of nucleotide seq of CDS incl stop codon + saved to a file) + + + export entire mRNA sequence (fasta seq saved to file) + + show entire mRNA sequence in separate (copy-pastable) window + + + export genomic sequence of transcript (fasta seq saved to file) + (we could colour the genomic span when displayed in a separate + window to make it obvious which are exons and which introns. + +EG acedb has translation code which handles different translation tables, I +will pinch the code.... + + +I have a comment about showing the size of a protein translation, I think this +might be in the status line if you click on the translation ? + + +** +- objects should carry http links so that web pages (e.g. ensemble/pfam) that +carry more information about them can be displayed. + +EG Sequence class has a web_location tag which points to a url object, this is +quite complex and poorly documented so I will need to look in the code....so +it maybe very simple for us to add this. + + +* +- pattern or word search (peptide and nucleotide) of genomic seq as currently +under "restriction enzyme digest" and highlight results in fmap (currently +when DNA is shown, highlighted with colored background (different colors for +forward and reverse match) and also the matches are indicated by printing out +the search term in a column close to the central yellow divider) + +EG This is probably best implemented by lace doing a patten search and then +sending us the results as a new column + matches that we need to draw as +"features" in the column. + + + +Display stuff +------------- + +*** +- copy-paste from pfetch text window +EG I think this is done already via gtk text widget.. + + + +** +- display ORF's +EG I will hack ace server to allow ORFs to be dumped. + + + +** +- need 3 frame translation in the window. +- show ORFs in all three frames (i.e. show stopcodons) +- show 3-frame translation of genomic seq (sequence selectable and copyable +like dna seq above) + + +** +- clicking on a transcript or exon should highlight that exons dna if the dna +is displayed (agreed that dna could be highlighted by colouring the +background). +- if dna seq is shown, highlight the extent of any box/feature user clicks on. + + +*** +- column configuration should be a main button in the zmap window, should be +able to reset to defaults with single click....perhaps reset should reset the +whole interface. +- "configure all columns" button in button bar at top (currently a submenu in +column contextual menu) +- "restore global default" button in button bar at top (i.e. restore default +columns etc.) + + +*** +- double clicking on an object should display the "properties" window. +- double click (proper double click !!!) on a feature and get a "property +inspector" window (like tree display in fmap). Possibly super-user (but not +user!) configurable + + +*** +- put the scale by the yellow strand separator + + + +*** +- cut displayed DNA direct into the cut buffer for access from other +applications. +- when dna seq is shown in zmap, select a stretch of sequence -> contextual +menu item "copy" or it could happen automatically + + +** +- allow printing of the current zmap to a file +- postscript printing the zmap + +EG acedb does this by steam and we could pinch the code. + + +*** +- clicking on a column will turn the background of that column to light grey +to emphasise that it has been selected. +- trial of subtly highlighting entire column background when left-clicking on +the column background + + +*** +- each sub window of a zmap should contain more information in the title which +should include at least the species. + + +* +- the current left hand scroll bar should be replaced with a locator which +shows clone position/direction/overlaps/names in a similar "stepped" display +as fmap does currently. We could also put a scale in this window. +- canvas with clone tiling path (with names) on the left and proprtional +scroll thumb for navigational purposes. + + +** +- users should be able to lock windows together in positions they choose. + + + +Blixem +------ + +* +- there should be more communication between blixem and zmap so that things +clicked on in zmap get highlighted in zmap and vice versa. Probably we need to +fork blixem so that we can leave behind the old acedb version. + + + +Genefinder +---------- + +* +we can get the genefinder information from gifaceserver but it requires a +change to the server to the ORFs output and we need to decide whether to get +it all at the start or to get some later... +- genefinder features (start codons (with Kozak score), coding potential, +splice sites, etc.) + + + +-- + ------------------------------------------------------------------------ +| Ed Griffiths, Acedb development, Informatics Group, | +| The Morgan Building, Sanger Institute, Wellcome Trust Genome Campus | +| Hinxton, Cambridge CB10 1HH | +| | +| email: edgrif@sanger.ac.uk Tel: +44-1223-496844 Fax: +44-1223-494919 | + ------------------------------------------------------------------------