Update on Bioinformatics WIKI, scripting challenges, and a general question

I am waiting for my site to go on-line at Oak Ridge National Labs (USA, Tennessee). Should be another week or so, maybe less.
When that happens, you will see a veritable explosion of scripting challenges in my wiki (Emerging Technologies->Bioinformatics.)
One general question in preparation for these challenges.
There are a number of standard bioinformatic programs that can be run interactively via the web at various sites, e.g. "BLAST" and "STRIDE".
Although these can also be run locally, this requires that you download large databases and keep them updated.
So here's my question to the scripting experts:
Are scripting languages powerful enough to submit queries to web pages and then use regex's to parse the html that is returned?
Bill Mann has used PERL to do some of the required regex parsing, but there is a lot left to do, and, his stuff only works when a perl program is invoking a bioinformatic program locally, not interactively.
If so, we all can do some beautiful stuff together , if anyone is interested ...

...my wiki on...
There is by it's very nature no such thing as MY WIKI, except you run your own wiki project in an exclusive mode. Which were...well ... unusual.
Are scripting languages powerful enough to submit queries to web pages and then use regex's to parse the html that is returned?
Yes.
anton

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Hi Steve,
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SAP CM25 which profile to use and why and some general questions

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Hello
In a manufacturing environment, is CM25 more used to finite schedule the work centers or labor or both ?
It can be used for both depend upon bottle neck resource whether machine or labour.
Is it a good idea to even finite schedule the planned orders or just production orders ? We want to create production orders 1 week ahead of the production schedule and planned orders gets created 3-4 weeks earlier than production order gets created.
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It depends upon the data load and selection,
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I have been trying my solutions using CM25 and not CM21 or CM27 using the profile SAPSFCG005, is there any other profile that I need to consider and other transactions to consider like CM21 or CM27 for certain purposes?
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JimBuitt wrote:
I've seen suggested on several posts here on this forum and from other Sun engineers that the mshttpd Webmail process should (must?) be run on the same server as Convergence.The webmail process does not have to run on the same server as Convergence.
I didn't find this anywhere in the documentation for Convergence, so if it is there and I missed it, please point out where I overlooked it.http://wikis.sun.com/display/CommSuite7/Communications+Suite+7+Installation+Scenario+-+Convergence
<snip>
Recommended:
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We recommend that you install the Webmail Server on this host.
About Webmail Server
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Note: From a functional perspective, Convergence provides complete mail service when the Webmail Server is located on a different host than Convergence. Therefore, in some deployments, the Webmail Server may be located on a different host.
Other Messaging Server components such as the message store and MTA, Calendar Server, and Instant Messaging Server may be located on other hosts.
</snip>
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=> If a user session is processed by different front-ends then there may be synchronization issues e.g. an email marked "Read" in one webmail instance may be "Unread" in another.
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Coding Problem 6 Now Defined in Scripting Languages/Bioinformatics WIKI

In the "Scripting Languages and Bioinformatics" WIKI, I have completed a new page here:
https://wiki.sdn.sap.com/wiki/display/EmTech/Bio-InformaticBasicsPartII-AlignmentToolsforRelatingProteinGenestoProteinPrimaryStructures
and also defined Coding Problem 6 at the end of this page.
This problem involves scripting an interactive session with a web site and parsing what the web site returns at various points duing the session.
Am looking foward to a script that solves this problem, if anyone feels like spending the time to do it.

<?
// sequence to search ---------------------------------------------
$bquery      = "MTQIIKIDPLNPEIDKIKIAADVIRNGGTVAFPTETVYGLGANAFDG";
$bquery     .= "NACLKIFQAKNRPVDNPLIVHIADFNQLFEVAKDIPDKVLEIAQIVW";
$bquery     .= "PGPLTFVLKKTERVPKEVTAGLDTVAVRMPAHPIALQLIRESGVPIA";
$bquery     .= "APSANLATRPSPTKAEDVIVDLNGRVDVIIDGGHTFFGVESTIINVT";
$bquery     .= "VEPPVLLRPGPFTIEELKKLFGEIVIPEFAQGKKEAEIALAPGMKYK";
$bquery     .= "HYAPNTRLLLVENRNIFKDVVSLLSKKYKVALLIPKELSKEFEGLQQ";
$bquery     .= "IILGSDENLYEVARNLFDSFRELDKLNVDLGIMIGFPERGIGFAIMN";
$bquery     .= "RARKASGFSIIKAISDVYKYVNI";
// url for form1 --------------------------------------------------
$url = "http://blast.ncbi.nlm.nih.gov:80/Blast.cgi";
// parameters for form1 -------------------------------------------
$bdb         = "protein";
$bgeneticcode= "1";
$bquery_from = "";
$bquery_to   = "";
$bjobtitle   = "ACW-" . time();
$bdatabase   = "nr";
$bblastprog = "tblastn";
$bpagetype   = "BlastSearch";
$pf = "";
$pf .= "QUERY=" . $bquery;
$pf .= "&db=" . $bdb;
$pf .= "&QUERY_FROM=" . $bquery_from;
$pf .= "&QUERY_TO=" . $bquery_to;
$pf .= "&JOB_TITLE=" . $bjobtitle;
$pf .= "&DATABASE=" . $bdatabase;
$pf .= "&BLAST_PROGRAMS=" . $bblastprog;
$pf .= "&PAGE_TYPE=" . $bpagetype;
$pf .= "&GENETIC_CODE=1";
$pf .= "&DBTYPE=";
$pf .= "&EQ_MENU=";
$pf .= "&EQ_TEXT=";
$pf .= "&NEWWIN=";
$pf .= "&MATCH_SCORES=";
$pf .= "&MAX_NUM_SEQ=100";
$pf .= "&EXPECT=10";
$pf .= "&WORD_SIZE=3";
$pf .= "&MATRIX_NAME=BLOSUM62";
$pf .= "&GAPCOSTS=11 1";
$pf .= "&COMPOSITION_BASED_STATISTICS=2";
$pf .= "&REPEATS=";
$pf .= "&FILTER=";
$pf .= "&LCASE_MASK=";
$pf .= "&TEMPLATE_LENGTH=";
$pf .= "&TEMPLATE_TYPE=";
$pf .= "&I_THRESH=0.005";
$pf .= "&CLIENT=web";
$pf .= "&SERVICE=plain";
$pf .= "&CMD=request";
$pf .= "&PAGE=Translations";
$pf .= "&PROGRAM=tblastn";
$pf .= "&MEGABLAST=";
$pf .= "&RUN_PSIBLAST=";
$pf .= "&SELECTED_PROG_TYPE=tblastn";
$pf .= "&SAVED_SEARCH=true";
$pf .= "&BLAST_SPEC=";
$pf .= "&QUERY_BELIEVE_DEFLINE=";
$pf .= "&DB_DIR_PREFIX=";
$pf .= "&SHOW_OVERVIEW=true";
$pf .= "&SHOW_LINKOUT=true";
$pf .= "&GET_SEQUENCE=true";
$pf .= "&FORMAT_OBJECT=Alignment";
$pf .= "&FORMAT_TYPE=HTML";
$pf .= "&ALIGNMENT_VIEW=Pairwise";
$pf .= "&MASK_CHAR=2";
$pf .= "&MASK_COLOR=1";
$pf .= "&DESCRIPTIONS=100";
$pf .= "&ALIGNMENTS=100";
$pf .= "&NEW_VIEW=true";
$pf .= "&OLD_BLAST=true";
$pf .= "&NCBI_GI=false";
$pf .= "&SHOW_CDS_FEATURE=false";
$pf .= "&NUM_OVERVIEW=100";
$pf .= "&FORMAT_EQ_TEXT=";
$pf .= "&FORMAT_ORGANISM=";
$pf .= "&EXPECT_LOW=";
$pf .= "&EXPECT_HIGH=true";
$pf .= "&QUERY_INDEX=0";
// define the HTTP connection -----------------------------
$ch = curl_init();
curl_setopt($ch,CURLOPT_URL,$url);
curl_setopt($ch, CURLOPT_POST, 1);
curl_setopt($ch,CURLOPT_POSTFIELDS, $pf);
curl_setopt($ch,CURLOPT_COOKIEJAR,
dirname(__FILE__).'/cookie.txt');
curl_setopt($ch,CURLOPT_FOLLOWLOCATION,1);
curl_setopt($ch, CURLOPT_HEADER , 1);
curl_setopt($ch, CURLOPT_RETURNTRANSFER,1);
// call it ------------------------------------------------
$my_result = curl_exec($ch);
// get the request ID; the query takes some time and this ID
// allows to identify the original request
$query = "/<tr><td>Request ID<\/td><td> <b>([0-9A-Z]*)<\/b><\/td><\/tr>/";
preg_match($query, $my_result, $request_id);
// query for the result page every 2 seconds...when the result
// is ready, we recognize it by its signature
$not_ready = true;
$result_url = "http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&VIEW_RESULTS=FromRes&RID=" . $request_id[1];
while($not_ready){
$temp_page = null;
curl_setopt($ch,CURLOPT_URL,$result_url);
curl_setopt($ch, CURLOPT_POST, 0);
$my_result = curl_exec($ch);
$query = "/This page will be automatically updated in <b>(\d*)<\/b> seconds/";
preg_match($query, $my_result, $temp_page);
if(isset($temp_page[1])) { sleep(2); }
else { $not_ready = false; }
// parse the results page; split it into result fragments first --------
$pat = "/";
$pat .= "><input type=\"checkbox\" name=\"getSeqGi\"([^\n]*)\n";
$pat .= "Length=\d*\n\n";
$pat .= "[\w\s]*:\n";
$pat .= "(\s*<a[^>]*>[^<]*<\/a>\n)*\n";
$pat .= "([^\n]*\n){3}\n";
$pat .= "(([^\n]*\n){3}\n[^n])*";
$pat .= "/";
preg_match_all($pat, $my_result, $fragments);
// 'fine parse the result fragments and get some important parameters -----
foreach($fragments[0] as $fragment){
$query = "/<a href=\"http:\/\/(www\.ncbi\.nlm\.nih\.gov\/entrez\/query\.fcgi\?";
$query .= "[^>]*)>([^<]*)<\/a><a[^>]*>[^<]*<\/a>\s*<a[^>]*><img[^>]*><\/a>([^\n]*)/";
preg_match($query, $fragment, $u);
$query = "/\s*Score\s*=\s*(\d*) bits\s*$\d*$,\s*Expect\s*=\s*([^,]*),";
$query .= "[^\n]*\n\s*Identities\s*=\s*\d*\/\d*\s*$(\d*%)$[^\n]*\n\s*Frame\s*=\s*([^\n]*)\n/";
preg_match($query, $fragment, $u1);
preg_match_all("/Sbjct\s*(\d*)\s*[A-Z\-]*\s*(\d*)\n/", $fragment, $positions);
$fr["url"]        = $u[1];
$fr["shname"]     = $u[2];
$fr["name"]       = $u[3];
$fr["score"]      = $u1[1];
$fr["expect"]     = $u1[2];
$fr["identities"] = $u1[3];
$fr["frame"]      = $u1[4];
// find out if we have to reverse the strand direction or not; adjust
// lower and upper limit
if ($fr["frame"] >= 0) {
    $fr["high"] = $positions[2][count($positions)-1]; $fr["low"] = $positions[1][0]; $fr["reverse"] = ""; }
else {
    $fr["high"] = $positions[1][0]; $fr["low"] = $positions[2][count($positions)-1]; $fr["reverse"] = true;}
$frx[] = $fr;
// we call the final details form for the top ranked result
// here we could loop over several results
curl_setopt($ch,CURLOPT_URL,$frx[0]["url"]);
curl_setopt($ch, CURLOPT_POST, 0);
$my_result = curl_exec($ch);
// parse the final details form to get the necessary parameters to execute
// the final details form
preg_match("/<input name=\"WebEnv\" type=\"hidden\" value=\"([^\"]*)\"/",
           $my_result, $u5);
preg_match("/<input name=\"query_key\" type=\"hidden\" value=\"([^\"]*)\"/",
           $my_result, $u6);
preg_match("/<input name=\"db\" type=\"hidden\" value=\"([^\"]*)\"/",
           $my_result, $u7);
preg_match("/<input name=\"qty\" type=\"hidden\" value=\"([^\"]*)\"/",
           $my_result, $u8);
preg_match("/<input name=\"c_start\" type=\"hidden\" value=\"([^\"]*)\"/",
           $my_result, $u9);
preg_match(
"/<select name=\"dopt\".*<option value=\"([^\"]*)\" selected=\"1\">/",
$my_result, $u10);
preg_match(
"/<select name=\"dispmax\".*<option value=\"([^\"]*)\" selected=\"1\">/",
$my_result, $u11);
preg_match(
"/<select name=\"sendto\".*<option value=\"([^\"]*)\" selected=\"1\">/",
$my_result, $u12);
preg_match(
"/<input type=\"hidden\" id=\"([^\"]*)\" name=\"fmt_mask\".*value=\"([^\"]*)\"/",
$my_result, $u13);
preg_match(
"/<input type=\"checkbox\" id=\"truncate\" name=\"truncate\" value=\"([^\"]*)\"\/>/",
$my_result, $u14);
// fill in the necessary parameters parsed out now and earlier
$of = "WebEnv=" . $u5[1];
$of .= "&query_key=" . $u6[1];
$of .= "&db=" . $u7[1];
$of .= "&qty=" . $u8[1];
$of .= "&c_start=" . $u9[1];
$of .= "&dopt=" . $u10[1];
$of .= "&dispmax=" . $u11[1];
$of .= "&sendto=" . $u12[1];
$of .= "&fmt_mask=" . $u13[1];
$of .= "&truncate=" . $u14[1];
$of .= "&less_feat=";
$of .= "&from=" . $fr["low"];
$of .= "&to=" . $fr["high"];
$of .= "&strand=" . $fr["reverse"];
$of .= "&extrafeatpresent=1";
$of .= "&ef_SNP=1";
$of .= "&ef_CDD=8";
$of .= "&ef_MGC=16";
$of .= "&ef_HPRD=32";
$of .= "&ef_STS=64";
$of .= "&ef_tRNA=128";
$of .= "&ef_microRNA=256";
$of .= "&ef_Exon=512";
$of .= "&submit=Refresh";
$ourl = "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?" . $of;
// execute the final details form
curl_setopt($ch,CURLOPT_URL,$ourl);
curl_setopt($ch, CURLOPT_POST, 0);
curl_setopt($ch,CURLOPT_POSTFIELDS, $of);
curl_setopt($ch,CURLOPT_FOLLOWLOCATION,1);
curl_setopt($ch, CURLOPT_HEADER , 1);
curl_setopt($ch, CURLOPT_RETURNTRANSFER,1);
$my_result = curl_exec($ch);
// parse the result page and get the final ORIGIN snippet
preg_match("/ORIGIN\s*\n\s*<a name=\"[^\"]*\"><\/a>\s*([^\/]*)\//", $my_result, $u99);
// output the final result ----------------------------------
echo "\n" . preg_replace("/\s{2,}/", "\n", preg_replace("/\d+\s/", "", $u99[1]));
?>
Edited by: Anton Wenzelhuemer on Aug 6, 2008 8:08 PM (Re-Formatted)

HT4623 I did the latest update to my i pad 2 and now Safari does not work properly . I get messages that the java script needs to be turned on which I did. How do I get this all back after this update?

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Try a reset: hold down the home button along with the power button until you see the Apple, then let go.

I updated iTunes 10.3.1 today, and now it won't let me open itunes it keeps saying error 7 (windows error 14001) and also says (apple mobile failed to start verify significant privileges to start system services)

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For general advice see Troubleshooting issues with iTunes for Windows updates.
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The further information area has direct links to the current and recent builds in case you have problems downloading, need to revert to an older version or want to try the iTunes for Windows (64-bit - for older video cards) release as a workaround for performance issues or compatibility with QuickTime or third party software.
Your library should be unaffected by these steps but there are also links to backup and recovery advice should it be needed.
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tt2

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Reset your User Agent. See the following articles:
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'''If this reply solves your problem, please click "Solved It" next to this reply when <u>signed-in</u> to the forum.'''
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Does not relate to your question, but...
You have multiple old Java Console extensions that Java did not clean-up during updates. You need Java Console only if you do Java programming/development or debug Java applets on web pages. You can see them in Add-ons > Extensions, '''''but you can not remove them from there'''''. Removing them will not affect the functioning of Java on websites. You can '''''manually''''' remove them, '''''if you do not do Java development work''''' to avoid future, possible problems/conflicts:
*http://kb.mozillazine.org/Java#Multiple_Java_Console_extensions
Your old Java Console extensions:
*Java Console 6.0.13 {CAFEEFAC-0016-0000-0013-ABCDEFFEDCBA}
*Java Console 6.0.14 {CAFEEFAC-0016-0000-0014-ABCDEFFEDCBA}
*Java Console 6.0.15 {CAFEEFAC-0016-0000-0015-ABCDEFFEDCBA}
*Java Console 6.0.17 {CAFEEFAC-0016-0000-0017-ABCDEFFEDCBA}
*Java Console 6.0.19 {CAFEEFAC-0016-0000-0019-ABCDEFFEDCBA}
*Java Console 6.0.20 {CAFEEFAC-0016-0000-0020-ABCDEFFEDCBA}
*Java Console 6.0.21 {CAFEEFAC-0016-0000-0021-ABCDEFFEDCBA}
*Java Console 6.0.22 {CAFEEFAC-0016-0000-0022-ABCDEFFEDCBA}
*Java Console 6.0.23 {CAFEEFAC-0016-0000-0023-ABCDEFFEDCBA}
*Java Console 6.0.24 {CAFEEFAC-0016-0000-0024-ABCDEFFEDCBA}

Windows Update story - how it's made and how evolved!

I am searching for as much information as possible about Windows Update. When it was realeased for the first time, how it evolved to this moment, what was the first update, is there something more than security tuesday patch, everything that could give me full
overview of it. I thout it will be easy but it is quiet hard to find such info.
I will really appreaciate for sources, books, links info.
Thanks in advance!

Hello,
The TechNet Wiki Discussion Forum is a place for the TechNet Wiki Community to engage, question, organize, debate, help, influence and foster the TechNet Wiki content, platform and Community.
Please note that this forum exists to discuss TechNet Wiki as a technology/application.
As it's off-topic here, I am moving the question to the
Where is the forum for... forum.
Karl
When you see answers and helpful posts, please click Vote As Helpful, Propose As Answer, and/or Mark As Answer.
My Blog: Unlock PowerShell
My Book:
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Debugging SAP Scripts MR_PRINT and MR_REKL

Hi All,
Can anybody tell me if there is an easy way to debug the SAP Script Layoutsets MR_PRINT and MR_REKL, which are triggered through MRKO and MIRO transactions. Also I need to know how to repeat the print out of the above layouts, which are outputs of Invoice reductions and Invoice corrections.
I already tried SE71 -> Utilities -> Activate Debugger and also placing a break-point in one of the performs, I call, but I think the print program is a dynamic call and it is not stopping at the break-points.
Let me know what I am missing.
Thank you for your time,
yrkanth

Sorry, if it sounds dumb. But how will you put a hard breakpoint in a SAP Script? I don't hink there is a BREAK-POINT command which can be used in SAP Script? I activated the sap script debugger and am running the MRKO transaction which triggers the layoutset, but it is not stopping as it does stop for any other layouset.
The other way I tried was, to put in BREAK-POINT command in one of the performs the SAP script calls and I was able to stop at that only when I debug in Update debugging mode. This only allows me to debug the perform code but it still does not allow me to debug the script as we debug the script for PO (Purchase Order) by activating the SAP Script debugger and print previewing the PO.
Hope this helps?
I really appreciate your time.
Thank you,
yrkanth

Update command in Shell script

Hi friends
sqlplus -s / <<END
set feedback on;
update tran2 set sno=1;
exit;
END
when i am using update command in shell script like above
it is updating the database well...but i just want to know how many rows it is updating and i dont want to commit
for that
sqlplus -s / <<END
set feedback on;
update tran2 set sno=1;
set feedback off;
rollback;
exit;
END
It's working fine
is there any other method to do the same

Well what's exactly your requirement? The current requirement doesn't make a lot of sense.
How many row is going to be updated depends on where clause, if you have no where clause that essentially updating whole table, the number of row updated is count of your rows.

Firefox 16.0.1 Crashes, Not Responding with Unresponsive Script Warnings and Adobe Flash Plugin Crashes

Hello,
I'm experiencing some issues with Firefox 16.0.1 which I had also experienced with Firefox 15.0.1.
On numerous occasions Firefox has crashed while attempting to access a website link contained in an AOL e-mail message.
Unrelated to that issue, Firefox has hung up frequently with associated unresponsive script warnings and occasionally with the Adobe Flash Plugin crashing. Some of the unresponsive script warnings are:
http://connect.facebook.net/en_US/all.js:127
http://e.huffpost.com/elections/assets/pregeneral_rr.js?d2e0923f3d19471c9e93c391a701ef30e3f427e8:1
http://o.aolcdn.com/cdn.webmail.aol.com/37001/js/dojo-custom/dojo/dojo.xd.js:102
http://o.aolcdn.com/cdn.webmail.aol.com/37001/js/dojo-custom/dojo/dojo2.xd.js:14
http://o.aolcdn.com/cdn.webmail.aol.com/37043/js/dojo-custom/dojo/MessageList.xd.js:52
http://o.aolcdn.com/cdn.webmail.aol.com/37092/js/dojo-custom/dojo/dojo.xd.js:102
http://o.aolcdn.com/cdn.webmail.aol.com/37092/js/dojo-custom/dojo/dojo.xd.js:122
http://o.aolcdn.com/cdn.webmail.aol.com/37092/js/dojo-custom/dojo/dojo2.xd.js:516
http://o.aolcdn.com/cdn.webmail.aol.com/37092/js/dojo-custom/dojo/dojo.xd.js:70
http://o.aolcdn.com/cdn.webmail.aol.com/37092/js/dojo-custom/dojo/dojo3.xd.js:45
http://o.aolcdn.com/cdn.webmail.aol.com/37092/js/dojo-custom/dojo/dojo3.xd.js:76
http://q.aolcdn.com/cdn.webmail.aol.com/37001/js/dojo-custom/dojo/dojo2.xd.js:940
http://partner.googleadservices.com/gampad/google_ads_gpt.js:12
I've reset Firefox and disabled all the plugins and yet these problems persist.
What are those script warnings actually telling me and are there any recommendations on how to resolve these issues?
Thank you,
Mike

You can check for problems caused by recent Flash updates and try these:
*disable a possible RealPlayer Browser Record Plugin extension for Firefox and update the RealPlayer if installed
*disable protected mode in Flash 11.3 and later
*disable hardware acceleration in the Flash plugin
*http://kb.mozillazine.org/Flash#Troubleshooting
*https://support.mozilla.org/kb/flash-113-doesnt-load-video-firefox

When I try to go to icloud I get 'script problem' and cannot enter. Could someone please advise me what to try. Thanks.

When I try to go to ilcoud I get 'script problem' and can't enter. Please advise what I should try. Thanks.

I use e-trade and a couple of times, years back, I found them behind the Java updates.
So, now I install new Java platforms on my backup disk and test the streaming data on that first because I know it will be over-written that evening with my nightly backup.
Of course, since I began doing that there hasn't been a problem. Do the same with printer driver updates.
Anyway, call ScottTrade and howl! Tell them how many Macs are out there and why aren't they in Apple Developers Program?

Update on Bioinformatics WIKI, scripting challenges, and a general question

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