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sebgg

"GC" A script to rapidly manipulate DNA sequences

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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


GC - Program to rapidly manipulate DNA SequencesRotaMol - Program to measure Protein Size

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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

This wonderful site allows debugging and testing regular expressions (many flavors available). An absolute must have in your bookmarks.
Another excellent RegExp tutorial. Don't forget downloading your copy of up-to-date pcretest.exe and pcregrep.exe here
RegExp tutorial: enough to get started
PCRE v8.33 regexp documentation latest available release and currently implemented in AutoIt beta.

SQLitespeed is another feature-rich premier SQLite manager (includes import/export). Well worth a try.
SQLite Expert (freeware Personal Edition or payware Pro version) is a very useful SQLite database manager.
An excellent eBook covering almost every aspect of SQLite3: a must-read for anyone doing serious work.
SQL tutorial (covers "generic" SQL, but most of it applies to SQLite as well)
A work-in-progress SQLite3 tutorial. Don't miss other LxyzTHW pages!
SQLite official website with full documentation (may be newer than the SQLite library that comes standard with AutoIt)

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  • Similar Content

    • sebgg
      By sebgg
      RotaMol is a user-friendly program that allows rapid analyses of protein size during viewing/editing in PyMOL.

      Wrote this a while ago and have been coming up with slight improvements every now and then when I get free time, so the source isn’t really "finished", but it works well.

      This script, named RotaMol, has to be used in conjunction with a protein modelling program called PyMol (not written by me). So if you dont have PyMol you wont be able to test this.

      Once your protein is loaded into PyMol this script will essentially calculate the area of every face, for a user defined level of accuracy (pixelskip) and angle of rotation. It is then calibrated using the Zoom function in PyMol, and it spits out the average rotational area of the protein in Angstroms squared.
      Included here is the source,
      Also is a link to the Google code page where it is hosted for Full .EXE download, as well as all documentation - tutorials - back versions, and a more in depth description of how it works and various links,


      Download here:
      http://code.google.com/p/rotamol/downloads/list
      latest version should be on top


      Cheers,

      Sebastian Eves-van den Akker
      =====================================================================================================
      Any questions about compatibility issues with older PyMOL versions or different language keyboards - don't hesitate to ask! (Preferably by email)
      RotaMol v1.11 - APBS.au3
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