Module:ImportProtein

MyWikiBiz, Author Your Legacy — Saturday March 02, 2024
Jump to navigationJump to search

Template:Module rating

Purpose

This module is meant to allow you to take a plaintext protein file and paste it in as a template parameter to get an annotated figure and legend. See Module talk:ImportProtein/Src (gene) for an example in trial use at Src (gene)

Usually, the figure should be placed on a separate page and transcluded. Until people advise to the contrary, the space Module talk:ImportProtein/(Article name) is being used for this (note Wikipedia article space doesn't have subpages set AFAIK).

Parameters

The parameters are:

  • The file is an unnamed parameter. It should be a standard GenPept format file cut and pasted from a site like [1] or [2].
  • tableoutput -- determines if/how the long table of protein features is displayed. collapsed, the default value, begins by displaying the table in closed form. collapsible leaves it open at the beginning. no means no table output. Anything else leaves a non-collapsible table.
  • height (default 50) -- the height of the protein bar itself in pixels not counting any surrounding content
  • width (default 500) -- the width of the protein bar and all other table and legend material in pixels
  • background (default #333333) -- the color of the unadorned protein bar (such as in disordered N- and C-terminal regions)
  • vtext (default 25) -- the number of characters of annotation written vertically beneath each site
  • vwidth (default 4) -- determines how close the vertical labels can be to one another. Labels that don't fit are not shown, but the numeric position of the missing labels is mentioned further down. Typically the user should look them up in the table and use the parameters at the end to process them to be able to fit.
  • largeonlyregion (default 20) -- the number of vertical pixels set aside only for the large domains that are labelled horizontally in bold within themselves.

Many parameters exist to try to make it easier to customize the output. Overlapping features marked vertically are randomly not displayed, so these features may be necessary to adequately describe all the known sites. Others improve the labels used.

  • usenotes -- a list of "region_name" or "site_type" names that aren't very informative. The entry under "notes" will be used as the feature name for all other operations.
  • include -- defaults to all, in which case labels to be excluded must be mentioned individually with exclude. If another value is given, it should be a list of names in quotes - only those names will be shown in the figure or in the table.
  • exclude -- omit for default no effect. A list of features by name, in quotes, not to be mentioned. These are also omitted from the table.
  • substitute -- a list of feature names and replacements, each in quotes, separated by a colon. "binding":"ATP binding site" will convert a feature labelled "binding" to display the second name instead. This affects all annotations. Note that substituting a name with "" will suppress the text, but not the marking on the protein diagram.
  • replaceregion -- a list of numeric ranges xx..yy followed by a colon and a quoted phrase. Use this when a lump of different features requires a single summary. So 77..85:"PS/PT/PY" can annotate a group of several phosphorylated amino acids with this short text. Note that placement of the text is at the center of the region you select; this feature therefore can be used to add extra markings if you like. Replaceregion does not affect the table of motifs.
  • toprow - a list of motifs (for example secondary structure - helices, sheets, and turns) that are to be displayed as colored markings at the top of the protein graphics box. No vertical annotation is given. A legend beneath the vertical annotation will list them by color.

It is also, of course, possible to edit the original protein sequence annotations directly to remedy any problems, though the module flexibility is provided in the hope that for many proteins an undamaged copy of the original can be kept for versatility

Usage

This module requires a very large text input that would usually overwhelm a page if #invoked in it directly. The output is generally large masses of styled HTML that would overwhelm the page if substed. So it is usually best #invoked from a subpage. (Another option for compactness might be to use a screencap) The recommended policy in this area hasn't been queried yet.


local p = {}

function p.main (frame)
    ---- Set up the initial frame parameters
   local debuglog="|}|}"
   local args=frame.args
   local parent=frame.getParent(frame)
   local pargs={}
   if parent then pargs=parent.args end
   local height=args.height or pargs.height or "50"
   local width=args.width or pargs.width or "600"
   local background=args.background or pargs.background or "#333333"
   local vtext=args.vtext or pargs.vtext or 25 -- characters of legend text to display vertically down from motifs
   local largeonlyregion=args.largeonlyregion or pargs.largeonlyregion or 20
   local vtext=tonumber(vtext) -- no meaning except as a number
   local tableoutput=args.tableoutput or pargs.tableoutput or "mw-collapsed" -- I've decided to use the table as the legend much of the time after all, I think.  (previously defaulted to "nil" to suppress)
   if tableoutput=="no" then tableoutput=nil end
   local vwidth=args.vwidth or pargs.vwidth or 4 -- number of PIXELS to tag as not overwriteable with vertical text.
   local vclaim={} --- if vclaim[pixel] is true, that pixel is taken
   local vprotest='' --- list of positions not shown separated by spaces
   local nowiki=args.nowiki or pargs.nowiki
   
    ---- These parameters send text that needs to be processed into tables
    ---- include is nil to include everything.  If it exists then only what is in it is used.
    ---- format is "I want only this" (any junk) "and this" etc.  Note weakness - a stray quote would foul up the whole template.
   local include=args.include or pargs.include or "all"
   if include == "all" then include = nil end
   local tinclude={}
   if include then
      for i in mw.ustring.gmatch(include,[[%"(.-)%"]]) do
         tinclude[i]=1
      end
   end
    ---- replaceregion defines a section with too many features to note individually.
    ---- Instead you group them with a new text.
    ---- The format is xx..yy:"Use this text"
   local replaceregion=args.replaceregion or pargs.replaceregion or ""
   local treplaceregion={}
      treplaceregion.s={};treplaceregion.e={};treplaceregion.t={}
      for i,j,k in mw.ustring.gmatch(replaceregion,[[(%d+)%.%.(%d+):%"(.-)%"]]) do
          table.insert(treplaceregion.s,tonumber(i));table.insert(treplaceregion.e,tonumber(j));table.insert(treplaceregion.t,tostring(k))
      end
    ---- exclude "Forget about this" (junk between ignored).
    ---- this prevents things from showing up even in the table and all motifs of this kind
   local exclude=args.exclude or pargs.exclude or "" -- for these empty arrays will be ignored later.
   local texclude={}
   for i in mw.ustring.gmatch(exclude,[[%"(.-)%"]]) do
      texclude[i]=1
   end
    ---- usenotes "This is a crummy motif name" (junk between ignored).  Uses /note entries instead
   local usenotes=args.usenotes or pargs.usenotes or ""
   local tusenotes={}
   for i in mw.ustring.gmatch(usenotes,[[%"(.-)%"]]) do
      tusenotes[i]=1
   end
    ---- substitute "Don't like this wording":"That's what I want" (anything between these ignored)
   local substitute=args.substitute or pargs.substitute or ""
   local tsubstitute={}
   for i,j in mw.ustring.gmatch(substitute,[[%"(.-)%":%"(.-)%"]]) do
      tsubstitute[i]=j
   end
    ---- toprow "Put this motif in the top row, no vertical annotation"
    ---- If present, defines an upper part of the graphic to mark certain features by color only - most likely, helices and sheets and turns
   local toprowtext=args.toprow or pargs.toprow or ""
   local ttoprow={}
   local toprowheight=0 -- no height unless one exists
   local toprow -- boolean to mark if anything is actually on the top row
   for i in mw.ustring.gmatch(toprowtext,[[%"(.-)%"]]) do
      ttoprow[i]=1;toprow=true
   end
   if toprow then toprowheight=args.toprowheight or pargs.toprowheight or 10 end
    ---- Check there is a protein sequence file and figure out where the CDS in it starts and ends
   local file=args.file or pargs.file
   if not(file) then return "error: use 'file=some cut-and-pasted NCBI protein sequence' to input a protein to be diagrammed" end
   local cdsstart, cdsend = mw.ustring.match(file,"Protein%s-(%d+)%.%.(%d+)")
   cdsstart=tonumber(cdsstart);cdsend=tonumber(cdsend)
   if ((cdsstart<1) or (cdsend<1)) then return [[error: the module expected a line "Protein: ''start amino acid''..''end amino acid''" to define the CDS.]] end
   local cdswidth=cdsend-cdsstart
    ---- Find and replace Site and Region to create unique separators
    ---- so that every one of these sections can be individually processed in the main loop
   file = mw.ustring.gsub(file,"Site%s+","|##|S") -- there are no pipe characters in the input or it would have choked
   file = mw.ustring.gsub(file,"Region%s+","|##|R")
   file = mw.ustring.gsub(file,"$","|##|") --- close last feature at the EOF
    ---- Load a set of colors to use for the different motifs.
    ---- Any unicode separator changes them.  No format expectations.
   local colorpage=mw.title.new("Template:ImportProtein/DefaultColors")
   local content
   local color={}
   if colorpage then
       content=colorpage.getContent(colorpage)
       if content then
          for x in mw.ustring.gmatch(content,"(%S+)") do
              table.insert(color,x)
          end
       end
   end
   if #color<1 then color={"#000055","#000099","#0000CC","#0000FF","#550055","#550099","#5500CC","#5500FF","#990055","#990099","#9900CC","#9900FF","#CC0055","#CC0099","#CC00CC","#CC00FF","#FF0000","#FF0055","#FF0099","#FF00CC","#FF00FF","#005555","#005599","#0055CC","#0055FF","#55555","#555599","#5555CC","#5555FF","#995555","#995599","#9955CC","#9955FF","#CC5555","#CC5599","#CC55CC","#CC55FF","#FF5500","#FF5555","#FF5599","#FF55CC","#FF55FF"} end
   local claim={};local nextcolor=1 -- keeps track of the colors assigned to specific nkeys throughout the loop
       ---- Begin the output and graphics files
   local output
   local tlegend="" -- legend for top row entries only, shown above table
   if tableoutput=="collapsed" then output=[[{| class="wikitable mw-collapsible mw-collapsed" style="width:]].. width .. [[px;"]] .. "\n" .. [[!colspan=4|List of protein features]] .. "\n" .. [[|-]] else if tableoutput=="collapsible" then output=[[{| class="wikitable collapsible" style="width:]].. width .. [[px;"]] .. "\n" .. [[!colspan=4|List of protein features]] .. "\n" .. [[|-]] else output=[[{| class="wikitable"]] end end
   local graphics=[[<div style="position:relative;background-color:]].. background .. [[;width:]] .. width .. [[px;height:]] .. height .. [[px;">]]
    ---- MAIN LOOP ----
    ---- this goes through features one by one and marks them down in "output" (legend/table) and "graphics" (protein box and vertical annotation)
    ---- Note that this does NOT create an array of features to sort, but is purely once through.
    ---- This means, for example, that there is no easy way to reposition adjacent motifs left and right to fit automatically.
    ---- You could, of course, array the output and retroactively process it ... maybe even turn this into a sortable array of function tail calls???  (My head hurts)
   for feature, range in mw.ustring.gmatch(file,"#|(.-)|#") do
       local t=mw.ustring.match(feature,"^(%a)") -- S or R placed in previous find/replace
       local s=mw.ustring.match(feature,"(%d+)") -- first number is the beginning of site or region
       local e=mw.ustring.match(feature,"^.%s-%d+%.%.(%d+)") or s -- second number in xx..yy range ; this needs updating!
 
       if s then
           ---- decide on the name to be used for the motif and annotation
          local n,c
          if t=="R" then n=mw.ustring.match(feature,[[/region_name=%"(.-)%"]]) end
          if t=="S" then n=mw.ustring.match(feature,[[/site_type=%"(.-)%"]]) end
          n=tostring(n)
          if tusenotes[n] then n=mw.ustring.match(feature,[[/note=%"(.-)%"]]) or n end
          n=tostring(n)
          n=mw.ustring.match(n,"^%s+(.+)%s+$") or n -- kill white space
          n=mw.ustring.gsub(n,"\n"," ") or n -- remove line feeds
          n=tostring(n) -- am I paranoid?
          if tsubstitute[n] then n=tostring(tsubstitute[n]) end
          n = mw.ustring.match(n,"(.+)%.") or n -- Don't need the ubiquitous final periods
           ---- from the name (n) pull out an nkey that excludes parenthesized stuff
           ---- each unique nkey can claim its own color to use from here on out
          local nkey=mw.ustring.match(n,"(.+)[%.;,%(%[]") or n
          local newcolor=false; -- is this a new color (if so, then if it is toprow, then add to legend for those)
          if claim[nkey] then c=claim[nkey] else c=color[nextcolor];claim[nkey]=c;nextcolor=nextcolor+1;newcolor=true end
          local cstyle=[[style="color:]] .. c .. [[;"|]]
           ---- decide whether to show the motif, and crop it to the CDS
          local showthismotif=true
          s=tonumber(s);e=tonumber(e)
          if s<cdsstart then s=cdsstart end
          if e>cdsend then e=cdsend end
          if s==cdsstart and e==cdsend then showthismotif=nil end
          if include then if not (tinclude[n]) then showthismotif=nil end end -- if include is set, and n isn't in it, don't add to table or graphic
          if exclude then if texclude[n] then showthismotif=nil end end -- if exclude is set and n is in it don't add
          if showthismotif then
              ---- update the table output for the legend
             if tostring(t)=="R" then output = output .. "\n|" .. cstyle .. "region\n|" else output = output .. "\n|" .. cstyle .. "site\n|" end
             output = output .. cstyle .. tostring(s) .. "\n|" .. cstyle .. tostring(e) .. "\n|" .. cstyle .. n .. "\n|-"
              ---- update the graphic display: first determine if the block is large to be displayed full height and annotated inside itself
             nkey=mw.ustring.sub(nkey,1,vtext) -- for graphics purposes, truncate the string (default 25 characters)
             local large
             local boxleft=math.floor(width*tonumber(s)/cdswidth)
             local boxwidth=math.floor(width*tonumber(e)/cdswidth)-boxleft
             if boxwidth>8*tonumber(mw.ustring.len(nkey)) then large=true else large=nil end
              ---- then work out the horizontal or vertical display
             local vertical -- height substring of the drawn block
             local annot="" -- text contents of a large block
             if ttoprow[n] then
                vertical=tostring(toprowheight)
                if newcolor then tlegend=tlegend..[[<span style="background-color:]] .. c .. [[;">&nbsp;&nbsp;</span> ]] .. nkey .. "\n" end
                nkey=""
             else
                if large then
                    vertical=tostring(height-toprowheight)
                    if toprow then vertical=vertical .. "px;top:" .. tostring(toprowheight) end
                    annot="'''" .. nkey .."'''"
                    nkey="" -- no vertical text display
                else vertical=tostring(math.floor(height) - toprowheight - largeonlyregion) .. "px;top:" .. tostring(toprowheight + largeonlyregion)
                    nkey=mw.ustring.gsub(nkey,"(.)","%1<br />") -- verticalize the text 
                end
             end
             local z=10000-1*boxwidth --- smaller elements in front of larger ones
             if not(large) then z=z+10000 end --- large elements reliably to the back
               -- draw graphics within the protein rectangle
             graphics = graphics .. [[<div style="position:absolute;overflow:hidden;z-index:]] .. z .. [[;left:]] .. boxleft .. [[px;border-top:0px;border-bottom:0px;border-left:1px;border-right:1px;border-style:solid;border-color:]].. c .. [[;background-color:]].. c .. [[;width:]] .. boxwidth .. [[px;height:]] .. vertical .. [[px;text-align:center;">]] .. annot .. [[</div>]]
               -- draw annotations vertically below it
               -- don't do at all if no text (nkey=="", such as on the top row)
             if not (nkey=="") then
                  -- first decide if in a replaceregion - if so, don't draw
                local toreplace;local ri=1
                while treplaceregion.s[ri] do
                   local rs=treplaceregion.s[ri]
                   local re=treplaceregion.e[ri]
                   if s>=rs and e<=re then toreplace=true;break end
                   ri=ri+1
                end          
                if not toreplace and not large then 
                    --- center vt in the feature; then claim pixels one by one around it.
                    --- Don't draw in a claimed pixel, but file a protest at bottom.
                   local vt=math.floor(boxleft+boxwidth/2 - 2) -- vertical text's horizontal position
                   if not vclaim[vt] then
                      for i = vt-vwidth,vt+vwidth,1 do
                          vclaim[i]=true
                      end
                      graphics = graphics .. [[<span style="position:absolute;text-align:center;line-height:90%;font-size:85%;overflow:visible;z-index:100;left:]] .. vt .. [[px;top:]] .. math.floor(height+5) .. [[px;">]] .. nkey .. [[</span>]]
                      else vprotest=vprotest .. s .. "-" .. e .. " "
                   end -- (if not ttoprow[n])
                end -- (if not vclaim)
             end -- (if not toreplace)
          end -- (if showthismotif)
       end -- (if s)
   end -- for feature, range
    --- we're out of the loop - now draw annotations for the chosen replace regions based on user text
   local ri=1
      while treplaceregion.s[ri] do
         local rs=treplaceregion.s[ri]
         local re=treplaceregion.e[ri]
         local rt=mw.ustring.gsub(mw.ustring.sub(treplaceregion.t[ri],1,vtext),"(.)","%1<br />") -- verticalize the text
         local boxleft=math.floor(width*tonumber(rs)/cdswidth)
         local boxwidth=math.floor(width*tonumber(re)/cdswidth)-boxleft
         local vt = math.floor(boxleft+boxwidth/2 -2) -- this formula should be synchronized with above, but defining constants seems silly.
          -- this ignores vclaim - it's a user input, therefore repositionable field
         graphics = graphics .. [[<span style="position:absolute;text-align:center;line-height:90%;font-size:85%;overflow:visible;z-index:100;left:]] .. vt .. [[px;top:]] .. math.floor(height+5) .. [[px;">]] .. rt .. [[</span>]]
         ri=ri+1
      end
   if not(tableoutput) then output = "" end
   if tlegend == "" then else tlegend = [[<span style="width:]]..width..[[;">]] .. [[''Top row:'' ]] .. tlegend .. [[</span>]] end
   if vprotest == "" then else vprotest = "''Overlapping vertical annotations not shown above: " .. vprotest .. "''" end
   if debuglog == "|}|}" then debuglog="" else debuglog = debuglog .. "\n" end
   if vtext>2 then vtext=vtext-2 end -- make up for extra return required to start a table at the end there.
   local output = [=[{| style="width:]=]..width..[[px;"]] .. "\n|".. graphics .. [[</div><span style="line-height:90%;font-size:85%;">]] .. mw.ustring.rep("\n",vtext) .. "</span>" .. tlegend .. vprotest .. "\n" .. output .. "\n|}\n" .. debuglog .. "|}\n"
   if nowiki then output = frame.preprocess(frame,"<pre><nowiki>"..output.."</nowiki></pre>") end
   return output

end

return p