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  • Parsing Chunk of Data into Hash of Array With Perl

    - by neversaint
    I have data that looks like this: #info #info2 1:SRX004541 Submitter: UT-MGS, UT-MGS Study: Glossina morsitans transcript sequencing project(SRP000741) Sample: Glossina morsitans(SRS002835) Instrument: Illumina Genome Analyzer Total: 1 run, 8.3M spots, 299.9M bases Run #1: SRR016086, 8330172 spots, 299886192 bases 2:SRX004540 Submitter: UT-MGS Study: Anopheles stephensi transcript sequencing project(SRP000747) Sample: Anopheles stephensi(SRS002864) Instrument: Solexa 1G Genome Analyzer Total: 1 run, 8.4M spots, 401M bases Run #1: SRR017875, 8354743 spots, 401027664 bases 3:SRX002521 Submitter: UT-MGS Study: Massive transcriptional start site mapping of human cells under hypoxic conditions.(SRP000403) Sample: Human DLD-1 tissue culture cell line(SRS001843) Instrument: Solexa 1G Genome Analyzer Total: 6 runs, 27.1M spots, 977M bases Run #1: SRR013356, 4801519 spots, 172854684 bases Run #2: SRR013357, 3603355 spots, 129720780 bases Run #3: SRR013358, 3459692 spots, 124548912 bases Run #4: SRR013360, 5219342 spots, 187896312 bases Run #5: SRR013361, 5140152 spots, 185045472 bases Run #6: SRR013370, 4916054 spots, 176977944 bases What I want to do is to create a hash of array with first line of each chunk as keys and SR## part of lines with "^Run" as its array member: $VAR = { 'SRX004541' => ['SRR016086'], # etc } But why my construct doesn't work. And it must be a better way to do it. use Data::Dumper; my %bighash; my $head = ""; my @temp = (); while ( <> ) { chomp; next if (/^\#/); if ( /^\d{1,2}:(\w+)/ ) { print "$1\n"; $head = $1; } elsif (/^Run \#\d+: (\w+),.*/){ print "\t$1\n"; push @temp, $1; } elsif (/^$/) { push @{$bighash{$head}}, [@temp]; @temp =(); } } print Dumper \%bighash ;

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  • What makes good web form styling for business applications?

    - by ProfK
    Styling forms (form elements) is something that even Eric Meyer prefers to avoid. However, most business forms, and that is where styling is at issue; 'contact us' forms are easy to style, put window estate at a premium, with more 'document level' (e.g. invoice) fields, plus 'detail level' (e.g. invoice line) fields. Factors I often find at play are: At my minimum, at least two horizontally adjacent fieldsets are required. In applications vs. public web pages, fixed positioning vs fluid layout is often better. Quantity of content is important, vs. exaggerated readability. Users know the system, and cues etc. take a back seat. In light of factors like these, is there any available guidence for styling web form based applications? Are there any CSS or JavaScript frameworks that would make my quest to style these applications better than Visual Studios still pathetic 'Auto-format' (what drugs were those people on? I will never take them.)

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  • Groovy as a substitute for Java when using BigDecimal?

    - by geejay
    I have just completed an evaluation of Java, Groovy and Scala. The factors I considered were: readability, precision The factors I would like to know: performance, ease of integration I needed a BigDecimal level of precision. Here are my results: Java void someOp() { BigDecimal del_theta_1 = toDec(6); BigDecimal del_theta_2 = toDec(2); BigDecimal del_theta_m = toDec(0); del_theta_m = abs(del_theta_1.subtract(del_theta_2)) .divide(log(del_theta_1.divide(del_theta_2))); } Groovy void someOp() { def del_theta_1 = 6.0 def del_theta_2 = 2.0 def del_theta_m = 0.0 del_theta_m = Math.abs(del_theta_1 - del_theta_2) / Math.log(del_theta_1 / del_theta_2); } Scala def other(){ var del_theta_1 = toDec(6); var del_theta_2 = toDec(2); var del_theta_m = toDec(0); del_theta_m = ( abs(del_theta_1 - del_theta_2) / log(del_theta_1 / del_theta_2) ) } Note that in Java and Scala I used static imports. Java: Pros: it is Java Cons: no operator overloading (lots o methods), barely readable/codeable Groovy: Pros: default BigDecimal means no visible typing, least surprising BigDecimal support for all operations (division included) Cons: another language to learn Scala: Pros: has operator overloading for BigDecimal Cons: some surprising behaviour with division (fixed with Decimal128), another language to learn

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  • Regular expression to Match addresses

    - by Burfi
    I have below set of strings to be searched : 1Dept Neurosci, The Univ. of New Mexico, ALBUQUERQUE, NM; 2Mol. and Human Genet., Baylor Col. of Med., Houston,, TX; 3Psychiatry, Univ. of Texas Southwestern Med. Ctr., Dallas, TX; 4Clin. Genet., Erasmus Univ. Med. Ctr., Rotterdam, Netherlands; 5Human Genet., Emory Univ., Atlanta, GA Above is a set of addresses , which starts with a digit (used to link it to the person).Need to search all the address as : 1Dept Neurosci, The Univ. of New Mexico, ALBUQUERQUE, NM 2Mol. and Human Genet., Baylor Col. of Med., Houston,, TX 3Psychiatry, Univ. of Texas Southwestern Med. Ctr., Dallas, TX 4Clin. Genet., ErasmusUniv. Med. Ctr., Rotterdam, Netherlands 5Human Genet., Emory Univ.Atlanta, GA I have written the below Regex : \d\w+,* It only matches a digit followed by a word . How can I modify it .Please suggest is there any better way.

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  • Where to start when doing a Domain Model?

    - by devoured elysium
    Let's say I've made a list of concepts I'll use to draw my Domain Model. Furthermore, I have a couple of Use Cases from which I did a couple of System Sequence Diagrams. When drawing the Domain Model, I never know where to start from: Designing the model as I believe the system to be. This is, if I am modelling a the human body, I start by adding the class concepts of Heart, Brain, Bowels, Stomach, Eyes, Head, etc. Start by designing what the Use Cases need to get done. This is, if I have a Use Case which is about making the human body swallow something, I'd first draw the class concepts for Mouth, Throat, Stomatch, Bowels, etc. The order in which I do things is irrelevant? I'd say probably it'd be best to try to design from the Use Case concepts, as they are generally what you want to work with, not other kind of concepts that although help describe the whole system well, much of the time might not even be needed for the current project. Is there any other approach that I am not taking in consideration here? How do you usually approach this? Thanks

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  • Screenscraping and reverse engineering health based web tool

    - by ArbInv
    Hi There is a publicly available free tool which has been built to help people understand the impact of various risk factors on their health / life expectancy. I am interested in understanding the data that sits behind the tool. To get this out it would require putting in a range of different socio-demographic factors and analyzing the resulting outputs. This would need to be done across many thousand different individual profiles. The tool was probably built on some standard BI platorm. I have no interest in how the tool was built but do want to get to the data within it. The site has a Terms of Use Agreement which includes: Not copying, distribute, adapt, create derivative works of, translate, or otherwise modify the said tool Not decompile, disassemble, reverse assemble, or otherwise reverse engineer the tool. The said institution retains all rights, title and interest in and to the Tool, and any and all modifications thereof, including all copyright, copyright registrations, trade secrets, trademarks, goodwill and confidential and proprietary information related thereto. Would i be in effect breaking the law if i were to point a screen scraping tool which downloaded the data that sits behind the tool in question?? Any advice welcomed? THANKS

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  • User submitted content filtering

    - by Jim
    Hey all, Does anyone have any ideas on what could be used as a way to filter untrustworthy user submitted content? Take Yelp for instance, they would need to prevent competitors writing business reviews on their competitors. They would need to prevent business owners favourably reviewing their own business, or forcing friends/family to do so. They would need to prevent poor quality reviews from affecting a businesses rating and so on. I can't think what they might use to do this: Prevent multiple users from the same IP reviewing certain things Prevent business owners reviewing their own business (maybe even other businesses in the same categories as their own?) Somehow determine what a review is about and what the actual intentions behind it are Other than the first and second points, I can't think of any clever/easy way to filter potentially harmful reviews from being made available, other than a human doing it. Obviously for a site the size of Yelp this wouldn't be feasible, so what parameters could they take into consideration? Even with human intervention, how would anyone know it was the owners best buddy writing a fake review without knowing the people? I'm using this as an example in a larger study on the subject of filtering user content automatically. Does anyone have any ideas how these systems may work and what they take into consideration? Thanks!

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  • Optimizing a "set in a string list" to a "set as a matrix" operation

    - by Eric Fournier
    I have a set of strings which contain space-separated elements. I want to build a matrix which will tell me which elements were part of which strings. For example: "" "A B C" "D" "B D" Should give something like: A B C D 1 2 1 1 1 3 1 4 1 1 Now I've got a solution, but it runs slow as molasse, and I've run out of ideas on how to make it faster: reverseIn <- function(vector, value) { return(value %in% vector) } buildCategoryMatrix <- function(valueVector) { allClasses <- c() for(classVec in unique(valueVector)) { allClasses <- unique(c(allClasses, strsplit(classVec, " ", fixed=TRUE)[[1]])) } resMatrix <- matrix(ncol=0, nrow=length(valueVector)) splitValues <- strsplit(valueVector, " ", fixed=TRUE) for(cat in allClasses) { if(cat=="") { catIsPart <- (valueVector == "") } else { catIsPart <- sapply(splitValues, reverseIn, cat) } resMatrix <- cbind(resMatrix, catIsPart) } colnames(resMatrix) <- allClasses return(resMatrix) } Profiling the function gives me this: $by.self self.time self.pct total.time total.pct "match" 31.20 34.74 31.24 34.79 "FUN" 30.26 33.70 74.30 82.74 "lapply" 13.56 15.10 87.86 97.84 "%in%" 12.92 14.39 44.10 49.11 So my actual questions would be: - Where are the 33% spent in "FUN" coming from? - Would there be any way to speed up the %in% call? I tried turning the strings into factors prior to going into the loop so that I'd be matching numbers instead of strings, but that actually makes R crash. I've also tried going for partial matrix assignment (IE, resMatrix[i,x] <- 1) where i is the number of the string and x is the vector of factors. No dice there either, as it seems to keep on running infinitely.

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  • How can I read and parse chunks of data into a Perl hash of arrays?

    - by neversaint
    I have data that looks like this: #info #info2 1:SRX004541 Submitter: UT-MGS, UT-MGS Study: Glossina morsitans transcript sequencing project(SRP000741) Sample: Glossina morsitans(SRS002835) Instrument: Illumina Genome Analyzer Total: 1 run, 8.3M spots, 299.9M bases Run #1: SRR016086, 8330172 spots, 299886192 bases 2:SRX004540 Submitter: UT-MGS Study: Anopheles stephensi transcript sequencing project(SRP000747) Sample: Anopheles stephensi(SRS002864) Instrument: Solexa 1G Genome Analyzer Total: 1 run, 8.4M spots, 401M bases Run #1: SRR017875, 8354743 spots, 401027664 bases 3:SRX002521 Submitter: UT-MGS Study: Massive transcriptional start site mapping of human cells under hypoxic conditions.(SRP000403) Sample: Human DLD-1 tissue culture cell line(SRS001843) Instrument: Solexa 1G Genome Analyzer Total: 6 runs, 27.1M spots, 977M bases Run #1: SRR013356, 4801519 spots, 172854684 bases Run #2: SRR013357, 3603355 spots, 129720780 bases Run #3: SRR013358, 3459692 spots, 124548912 bases Run #4: SRR013360, 5219342 spots, 187896312 bases Run #5: SRR013361, 5140152 spots, 185045472 bases Run #6: SRR013370, 4916054 spots, 176977944 bases What I want to do is to create a hash of array with first line of each chunk as keys and SR## part of lines with "^Run" as its array member: $VAR = { 'SRX004541' => ['SRR016086'], # etc } But why my construct doesn't work. And it must be a better way to do it. use Data::Dumper; my %bighash; my $head = ""; my @temp = (); while ( <> ) { chomp; next if (/^\#/); if ( /^\d{1,2}:(\w+)/ ) { print "$1\n"; $head = $1; } elsif (/^Run \#\d+: (\w+),.*/){ print "\t$1\n"; push @temp, $1; } elsif (/^$/) { push @{$bighash{$head}}, [@temp]; @temp =(); } } print Dumper \%bighash ;

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  • Listing all objects that share a common variable in Javascript

    - by ntgCleaner
    I'm not exactly sure how to ask this because I am just learning OOP in Javascript, but here it goes: I am trying to be able to make a call (eventually be able to sort) for all objects with the same variable. Here's an example below: function animal(name, numLegs, option2, option3){ this.name = name; this.numLegs = numLegs; this.option2 = option2; this.option3 = option3; } var human = new animal(Human, 2, example1, example2); var horse = new animal(Horse, 4, example1, example2); var dog = new animal(Dog, 4, example1, example2); Using this example, I would like to be able to do a console.log() and show all animal NAMES that have 4 legs. (Should only show Horse and Dog, of course...) I eventually want to be able to make a drop-down list or a filtered search list with this information. I would do this with php and mySQL but I'm doing this for the sake of learning OOP in javascript. I only ask here because I don't exactly know what to ask. Thank you!

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  • Open Garmin GPI files in Linux

    - by zero
    i have several files that are in the Garmin GPI format, from here, and want to access them in Linux. How can I do that? hello dear renan - well i found the solution - so thanks for your try to add some sense to the question. GEREAT work - and here we have the answer: i will Install gpsbabel to convert the stuff. The gpi.files are just xml files, You can - after converting with gpsbabel read them as a human being.

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  • Email: X-Authentication-Warning

    - by stef
    We're sending out 1000's of mails per day from our site (mainly "click here to verify your subscription") and too many are getting flagged by spam (mainly hotmail). One of the things I noticed in the headers is X-Authentication-Warning: srv01.site.com: www-data set sender to [email protected] using -f Is this something I should be worried about, that may cause spam flags to raise? (I'm already checking various issues that have been mentioned regarding spam flagging over at stackoverflow, I know there are many factors in play)

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  • What are some SMART Criteria I can use when comparing "green" datacenters?

    - by makerofthings7
    I'm looking to reduce my carbon footprint and want to find a "green" datacenter. There are so many ways to define a "green datacenter' I'm looking for examples of SMART Criteria such as 20% of power from renewable resources Low Power Usage Effectiveness When it comes to running a green datacenter, what are additional key factors I need to look for? What key words or technologies might those energy efficient datacenters be using?

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  • Investigate high load on RHEL

    - by Adam Matan
    One of my RHEL 5 was showing high load (~4-5) on uptime. The load increased, and when it reached 6 (±), the server froze and needed restart. top-wise, the server had no significant CPU or memory issues and sar showed no increase in iowait. Therefore, the thrashing must have been related to other factors. Any ideas how to investigate this? In particular, how do I know that which processes are waiting in the queue?

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  • Diagnosing and debugging LAN congestion / connection issues

    - by John Weldon
    What are the top N tools / methodologies used to diagnose and repair network issues? Given a LAN, for example, where users are able to consistently ping an outside server, but any data intensive connections are flaky; how would you begin solving the network issues? I imagine issues like congestion, bandwidth constraints, throughput constraints, etc. are all factors, but I don't know how to diagnose those issues. I'm especially interested in LAN environments (rather than WAN)

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  • Is it generally better to compress content on the proxy server or the app server?

    - by Dan
    We're using an F5 for load balancing and SSL proxying. Behind it we're serving up java applications with Tomcat instances. These are fairly small applications - hundreds of concurrent users. I'd like to compress some of the content, and I'm looking for advice on choosing to configure compression on the F5, or on the tomcat instances. Any big factors in the decision, or is it 6-of-one half-dozen of the other?

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  • Sleep or Hibernate for a laptop

    - by Tim
    I was wondering whether it is better to put a laptop into sleep or hibernation in Windows 7, and suspend or hibernate in Ubuntu: when carrying the laptop in a backpack and walking or slow-running to another place in around 15 minutes, Or just when the lid is closed. My concerns are if the heat generated and accumulated and bumping from transmit will do harm to the laptop, and I can miss other important factors. Is sleep in Windows 7 same as suspend in Ubuntu? Thanks and regards!

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  • qmail throws error "CNAME_­lookup_­failed_­temporarily"

    - by Supratik
    I am using Qmail and when I am sending mails I am sometimes getting the bellow error in my log for a particular domain. Jun 22 05:20:47 221832-web1 qmail: 1308738047.397431 delivery 1040373: deferral: CNAME_lookup_failed_temporarily._(#4.4.3)/ Can anyone please tell me what are the factors responsible for such error ? What are the DNS requests sent by Qmail when sending an email ? FYI: The patch for the DNS cache size issue is already included in Qmail.

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  • CalDav web application

    - by aaron
    Is there an open-source web app for viewing .ics calendars? I have a server running the open source CalDAV server "DAViCal" to share calendars between co-workers. I (the admin) add/delete the calendars by configuring my Mac OS X iCal application, but I want to also host a web app that displays a human-readable calendar, so without any configuration my coworkers can visit a web page and see the calendar. Thanks

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  • Fan Error on Lenovo R61

    - by OrangeRind
    Problem Since the last two days, my Lenovo R61 is giving me a "Fan Error" message during boot, after showing which, it powers down. It does so for 3-4 boot attempts, and after a bit of tapping and such human treatment, in the 6th or so attempt, it luckily starts. Question Why is this happening ? How do I fix it ? Thanks in Advance. :)

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  • Connecting via Ethernet on second AirPort Extreme

    - by b-b
    Would It be possible to connec my xbox 360 to a second AirPort Extreme, wherein this AirPort Extreme is wirelessly linked to the first? I assume it is and is straight forward, but I thought I'd ask first. Also, would an Ethernet to a second AirPort Extreme be any faster than, say, a dual band wifi connection from a MacBook? Obviously environmental factors play in, but I'm mostly curious about the relative receiving strength of the airport vs laptop.

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  • How did you find your current job?

    - by sanksjaya
    I'm a student looking for a job as a Jr. Sys Admin / Information Security position. The moment I click search from simplyhired.com or dice.com my job gets complicated. It's so hard to spot the ones that you definitely want to apply for. So, just share your story of how you spot your current job online? What factors did you consider before applying? And any tips for young job seekers. Thanks :)

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  • ssh authentication with public-private key pair

    - by Rui Gonçalves
    Hi! I'm wonder if is possible to authenticate the same user with different public-private keys pairs on the same remote host. For all production servers, the public-private key pair has been generated for the same user and then exported to the backup server for allowing ssh authentication without human intervention. However, I'm having problems on some production servers, once the password prompt is always displayed. Thanks in advance for the help, Best regards!

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  • open source web application for viewing .ics calendars

    - by aaron
    I need an open source web application that allows users to view .ics calendars I am hosting a calendar with DAViCal, and users can view/edit calendars with their own clients (like Apple iCal or Mozilla Sunbird), but I want a web app that will display the public calendars so people w/o a user account can view the calendar just by visiting a URL. Requirements: Open source web app: something I can host right along with DAViCal Human-readable calendar: i.e. it has a day/week/month view to visualize calendar events

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