## staden-package — General purpose discussion related to the package.

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Showing 2 results of 2

 Re: [Staden-package] Problems with "add_tags" (pregap scripting) From: Stefan Kesberg - 2006-12-06 12:36:26 ```Hello, Finally I was able to solve my problem. The "find=5Fprimers" result includes some confusing start positions for prim= er in "-" directions. By example the primer tag is set at position 42 on t= he reading, in the result list the start position for this primer is state= d with 1592. The trick is to count from right side of reading, reading len= gth - 1592 results in 42. Ok, solved one misunderstanding. But "add=5Ftags" refused to work with this new list. So I came over with a workaround. Instead of calling "add=5Ftags" after my l= oop which creates a big list of tags to add I call "add=5Ftags" now in every= loop with the values for the current tag to add. Not the best solution, but now it works. It seems as if I'm not able to build a proper Tcl list which "add=5Ftags" ac= cepts. Thank you for your hints and help. With best regards, Stefan Kesberg =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F= =5F=5F=5F=5F "Ein Herz f=FCr Kinder" - Ihre Spende hilft! Aktion: http://www.deutschlandsegelt.d= e Unser Dankesch=F6n: Ihr Name auf dem Segel der 1. deutschen America's Cup-Ya= cht! ```
 [Staden-package] Problems with "add_tags" (pregap scripting) From: - 2006-12-01 08:29:06 ```Hello, I'm doing a little pregap scripting trying to write primer information dir= ectly on the consensus sequenz of my gap4 database. In a first step I'm collecting the primer data by using "find=5Fprimers". Th= is returns a list of primers and also seems to set tags on the correspondi= ng reads. Now I'm walking through the list of primers, determine reading <-> contig = pairs and create a new list entry with primer data. Finally I want to add the content of the list of the gap4 database by usin= g the "add=5Ftags" function. Here a short section of code showing only the relevant part (without "find= =5Fprimers"): set primer=5Flist {} foreach primer \$primers { # get reading=5Fname of the current primer # MSC-08=5FG08 MSC-08=5FG08=5FT3 test=5Fproject.47 CGTCTGCTGTCAGATAAAGTC 764 + set reading=5Fname [lindex \$primer 1] # get number of the leftmost reading of the config on which \$reading=5Fname = resides set leftmost=5Freading=5Fnum [db=5Finfo chain=5Fleft \$io \$reading=5Fname] # walk throug all contigs, \$contig contains name of the contig foreach contig \$contig=5Flist { # get number of leftmost reading from \$contig set tmp [db=5Finfo chain=5Fleft \$io \$contig] # check if both numbers are equal, it true the primer resides on this cont= ig if {\$leftmost=5Freading=5Fnum =3D=3D \$tmp} then { # add primer data to tag list set start=5Fpos [lindex \$primer 4] set tmp=5Fpos [string length [lindex \$primer 3]] set end=5Fpos [expr {\$start=5Fpos +\$tmp=5Fpos}] set direction [lindex \$primer 5] set comment [lindex \$primer 3] lappend primer=5Flist "-\$tmp PRIM \$direction \$start=5Fpos..\$end=5Fpos \$comment" break } } } add=5Ftags -io \$io -tags \$primer=5Flist Executing this script ends with something like this: Level 2: gatc=5Fprimer::run {/home/sk/workspace/faaf/documents/users/stefan/= faaf/test=5Fproject/MSC2-A19Y-B21=5FT3- 1.exp /home/sk/workspace/faaf/documents/users/stefan/faaf/test=5Fproject/MSC= 2-A2Y-G13=5FT7-2.exp /home/sk/workspa ce/faaf/documents/users/stefan/faaf/test=5Fproject/MSC2-A3Y-B20=5FT3-1.exp /ho= me/sk/workspace/faaf/documents/user s/stefan/faaf/test=5Fproject/MSC2-A14Y-I18=5FT3-1.exp /home/sk/workspace/faaf/= documents/users/stefan/faaf/test=5Fpr oject/MSC2-A8Y-H04=5FT3-2.exp /home/sk/workspace/faaf/documents/users/stefan= /faaf/test=5Fproject/MSC2-B2D-A12=5FT7. exp /home/sk/workspace/faaf/documents/users/stefan/faaf/test=5Fproject/MSC2-= A20Y-H18=5FT3-1.exp .... This seems to be a dump of the files, coming into my script. Also the program terminates unexpected: Thu 23 Nov 10:51:48 2006 [5031@...] ...opened Thu 23 Nov 10:52:00 2006 [5031@...] Program terminated unexpectedly with = signal 2. By commenting the "add=5Ftags" function out the script runs to the end. Would it be possible to recive a hint or is there a fault I'm not able to = see=3F Thank you for your efforts. With kind regards, Stefan Kesberg =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F= Erweitern Sie FreeMail zu einem noch leistungsst=E4rkeren E-Mail-Postfach! =09 Mehr Infos unter http://freemail.web.de/home/landingpad/=3Fmc=3D021131 ```

Showing 2 results of 2