"GC" A script to rapidly manipulate DNA sequences

[sebgg 1]

Hi all,

This is a short and again messy script (as far as the source code is concerned), but its been very very usefull to me over the past 3-4 months so I thought id post it up.

simply if you have some DNA sequences with other characters or spaces or /n in it, It will strip it down to the ATGC.

you simply highlight and select whatever you want to manipluate, copy it, then press the past from clipboard button to put it into the GUI. (to copy anything out of the GUI simply press the copy button)

once in the edit you can do usefull things such as reverse complement, switch all to upper or lower case, and analyse the GC content and possible methylation sites.

Included in download is the source and the icon, so it can be compiled whenever.

Any suggestions as to what else would be usefull to add would be greatly appreciated.

Cheers

Sebastian Eves-van den Akker.

GC autoit.zip

[jchd 1,823]

You can simplify and speed up things a lot.

For instance:

if $msg = $getclip Then
  $promoter = clipget()
  $promoterr = StringStripWS($promoter,8)
  $sStripped_1 = StringRegExpReplace($promoterr,"[1,2,3,4,5,6,7,8,9,0,-,=,+,_,q,w,e,r,y,u,i,o,p,},{,s,d,f,h,j,k,l,;,:,',@,#,~,,|,z,x,v,b,n,m,<,>,.,?,/,Q,W,E,R,Y,U,I,O,P,S,D,F,H,J,K,L,Z,X,V,B,N,M,`,!]","")
$sStripped_2 = StringReplace($sStripped_1, "[", "")
$sStripped_3 = StringReplace($sStripped_2, "]", "")
$sStripped_4 = StringReplace($sStripped_3, "$", "")
$sStripped_5 = StringReplace($sStripped_4, "â, "")
$sStripped_6 = StringReplace($sStripped_5, "%", "")
$sStripped_7 = StringReplace($sStripped_6, "*", "")
$sStripped_8 = StringReplace($sStripped_7, "&", "")
$sStripped_9 = StringReplace($sStripped_8, "", "")
$sStripped_10 = StringReplace($sStripped_9, "-", "")
$sStripped_11 = StringReplace($sStripped_10, ")", "")
$sStripped_12= StringReplace($sStripped_11, "(", "")
$sStripped_13= StringReplace($sStripped_12, "]", "")
$sStripped_14= StringReplace($sStripped_13, "Ң, "")
;$sStripped_15= StringReplace($sStripped_14, "C", "T") ;for methylation if you want
$string7 = StringUpper($sStripped_14)
GUICtrlSetData($string1,$string7)
endif

make that:

If $msg = $getclip Then
  $promoter = StringUpper(ClipGet())
  $promoter = StringRegExpReplace($promoter, "(?m)[^AGCT]", "")
  ;$promoter_methyl = StringReplace($promoter, "C", "T") ;for methylation if you want
  GUICtrlSetData($string1, $promoter)
EndIf