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Download for Rare SNP Analysis

Discussion in 'Genetic Testing and SNPs' started by Valentijn, Aug 29, 2013.

  1. Valentijn

    Valentijn Activity Level: 3

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    Amersfoort, Netherlands
    It's done! It can now be downloaded from https://sourceforge.net/projects/analyzemygenes/

    What it does:
    Instead of determining your rare SNPs by sending your 23andMe results out to the internet, you can download this much smaller program to your computer. Currently it will only search for alleles with a prevalence rate of 1% or below.

    It takes 30-60 seconds to run, completely with status bar and a display of your results as it finds them. Then you can save the results as a text file (tab separated) and/or .pdf file with nicely aligned columns and such. The results display allows you to move and sort the columns prior to generating the pdf file.

    Homozygous results are flagged, and 23andMe "i" numbers are translated to "rs" numbers in the "ETC" column, when possible. Additional rs numbers are also provided, when available.

    Why you'd use it:
    It provides useful information regarding very rare SNPs. As someone with a debilitating disease featuring a lot of malfunctioning, it is possible that this information can help in uncovering the sources of problems.

    One way to do that is by looking up the SNPs and seeing if they're pathogenic. Homozygous results are the most likely to cause problems, though multiple heterozygous pathogenic mutations on different strands of the same gene is often very problematic as well.

    Another way to use the rare allele information is by comparing it to the rare alleles present in other people with the same illness. This has been done somewhat at http://forums.phoenixrising.me/index.php?threads/rare-allele-data.23978/ , but really we need data from a lot more people, and a better way to sort and display it.

    How to use the program:
    (First you need to have downloaded and unzipped your 23andMe results from https://www.23andme.com/you/download/ )

    REQUIRED
    Java - if you don't have Java, it's available for free at http://java.com/en/ .

    DOWNLOAD
    1) Go to https://sourceforge.net/projects/analyzemygenes/
    2) Click the dark green "download" button near the top center of the page
    3) Chose "Open with", and hit OK - download should be very fast :thumbsup:
    4) Click on "Extract all files" near the top left
    5) Select a folder to extract them to, where you can find the files easily again. I suggest using the same folder you have your 23andMe results stored in.

    RUN
    6) Go to the folder where you extracted the files
    7) Double-click on the "Genes"
    8) A grey box with three buttons appears. The top one should be green. If it isn't, click on it to navigate to whatever dodgy location you've put the "one_percent" file in.
    9) Click on the orange middle box to select your 23andMe file.
    10) Click the yellow "Analyze" button, and wait for it to finish. This takes 52 seconds on my newish but basic laptop.

    SAVING (Optional)
    11) From the "Analysis results" chart which has appeared, you can drag the columns to change their order, or click on the tops of the columns to sort them (first click low to high, second click high to low).
    12) Click on the "Save as text" button near the top of the chart. This creates a tab-separated text file.
    13) Click on the "Save as PDF" button near the top of the chart. This creates a nice looking PDF file which is ideal for printing or easy reading.

    IMPORTING TO EXCEL (Optional)
    14) After saving the results as text, open Excel.
    15) From the menu in Excel, select "Open".
    16) Click on the "All Excel Files" button in the lower right corner and select "Text files" instead.
    17) Navigate to the folder where you saved your results as a text file, and select it.
    18) In the Excel "Text Import Wizard" which pops up, choose "Delimited" then click "Next"
    19) Select "Tab" only, then click "Finish"

    Any feedback, questions, suggestions, etc, very much appreciated, especially if it helps make the instructions clearer!

    And here's a tag for Bluebell
    Waverunner, Radio, adreno and 6 others like this.
  2. Thinktank

    Thinktank Senior Member

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    Bangkok, Thailand
    Thanks for sharing! I'm still waiting for my 23andme results because i had to redo the test, hopefully this program will give me some more insight in my mutations!
    Valentijn likes this.
  3. future_man

    future_man

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    Looks really cool Valentijn!

    I've downloaded it and run it on my Mac and was able to get as far as the analysis results.

    However, the 'Save as text' and 'Save as PDF' buttons are greyed out for me preventing me from exporting the results. See screenshot.

    Attached Files:

    Valentijn likes this.
  4. Thinktank

    Thinktank Senior Member

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    Bangkok, Thailand
    @ Valentijn, Did you create the program or contribute to the development of it?
  5. Valentijn

    Valentijn Activity Level: 3

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    Odd, I'll ask the programmer about that. It was designed and tested on Windows, so maybe we need to change something for saving on Macs.
  6. Valentijn

    Valentijn Activity Level: 3

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    My fiance did all of the programming, based on my specifications.

    He's very patient :D
  7. Critterina

    Critterina Senior Member

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    Arizona, USA
    I'm on Windows running XP and got hung up at the same place. I never got a status bar. It's not chewing up any cpu, either. I'm trying to update java to see if that helps.
  8. roxie60

    roxie60 Senior Member

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    Central Illinois, USA
    I downloaded the zip then hit the extract all files. I have three files, a JAR, and two DB files. There is no 'program' file called 'Genes', did I miss something? Running WINS7 IE8

    Downloaded 2nd time and same result. 2 db and one JAR file extracted, noting to double click on...
  9. Mogwai

    Mogwai

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    'Save as text' and 'Save as PDF' buttons are greyed out for me as well - on Windows here. However, I Ctrl-C its arse, and it appears to have worked. Pasted results below - hopefully!


    rs34248917 1 T 1.00 CT
    rs2933080 1 C 1.00 CT rs146227525
    rs6684642 1 A 1.00 AG
    rs12751479 1 T 0.14 GT
    rs9333412 1 A 0.23 AG
    rs9332701 1 G 1.00 AG
    rs12141357 1 C 1.00 CT
    rs12145368 1 G 1.00 GT
    rs17012587 1 G 1.00 GT
    rs6424227 1 C 0.00 CT
    rs2084045 2 A 1.00 AC
    rs13410003 2 G 1.00 AG
    rs9678388 2 G 1.00 AG
    rs1427409 2 T 1.00 CT
    rs72466496 2 A 0.05 AG
    rs17746486 2 T 1.00 CT
    rs6577014 2 C 1.00 CT
    rs4150523 2 A 0.37 AG
    rs35732034 2 T 1.00 CT
    rs17467902 2 A 1.00 AG
    rs13032621 2 A 1.00 AG
    rs4135292 3 A 1.00 AG
    rs2317332 3 A 1.00 AG
    rs17212030 3 C 1.00 CT
    rs9883197 3 G 1.00 AG
    rs4432598 3 G 1.00 AG
    rs1836914 3 C 1.00 CC Homozygous
    rs2231223 3 A 1.00 AG
    rs17532890 4 C 1.00 CT
    rs2322180 4 A 1.00 AC
    rs17286457 4 C 1.00 CT
    rs13133439 4 T 1.00 CT
    rs16902661 5 A 1.00 AG
    rs6449780 5 A 1.00 AC
    rs2229994 5 T 1.00 CT
    rs2229995 5 A 1.00 AG
    rs17165890 5 T 0.46 GT
    rs10482714 5 T 1.00 CT
    rs10482653 5 A 1.00 AG
    rs245071 5 T 1.00 CT
    rs6863809 5 A 1.00 AG
    rs17548315 6 A 1.00 AA Homozygous
    rs12195092 6 A 1.00 AG
    rs13210989 6 C 1.00 CT
    rs9501680 6 G 1.00 AG
    rs6902544 6 G 1.00 AG rs149249712
    rs17190762 6 A 1.00 AG rs116107010
    rs8192576 6 G 1.00 AG rs144367613
    rs41271310 6 T 0.41 CT
    rs20512 6 T 1.00 CT
    rs2230513 6 T 1.00 CT
    rs13194696 6 C 0.41 CT
    rs1978133 7 T 1.00 CT
    rs2470990 7 A 1.00 AG
    rs17249588 7 C 1.00 CT
    rs10487818 7 T 1.00 AT
    rs17431071 7 G 1.00 AG
    rs11563711 7 A 0.05 AG
    rs35909721 8 A 1.00 AG
    rs17526980 8 T 1.00 CT
    rs13254260 8 A 1.00 AG
    rs16938754 8 G 1.00 GT
    rs632216 8 T 1.00 GT
    rs13248783 8 T 1.00 CT
    rs2295843 9 A 0.37 AG
    rs1999661 9 T 1.00 CT
    rs4135233 9 C 1.00 CT
    rs41302905 9 T 1.00 CT
    rs55876802 9 A 1.00 AC
    rs12769372 10 C 1.00 CT
    rs2461180 10 T 1.00 TT Homozygous, rs55796641
    rs8177062 10 T 1.00 AT
    rs17577398 10 A 1.00 AG
    rs9415964 10 A 1.00 AA Homozygous
    rs9332235 10 A 1.00 AG
    rs11572180 10 A 1.00 AG
    rs1666 10 G 1.00 GT
    rs17881586 11 A 1.00 AG
    rs607969 11 T 1.00 CT
    rs6589689 11 G 1.00 AG
    rs17725914 12 G 0.05 AG
    rs10492162 12 A 1.00 AG
    rs10505888 12 A 1.00 AG
    rs35303786 12 C 1.00 CT
    rs10492249 12 T 1.00 CT
    rs17722134 12 G 1.00 AG
    rs17030365 12 A 1.00 AC
    rs12871209 13 A 1.00 AC
    rs2812230 13 C 1.00 CT
    rs10507792 13 A 1.00 AC
    rs12184642 13 T 1.00 CT
    rs466802 13 G 1.00 AG
    rs1326407 13 A 1.00 AG
    rs7146672 14 T 1.00 GT
    rs17393098 14 T 1.00 CT
    rs6151562 15 A 1.00 AG
    rs5745908 15 C 0.32 CT
    rs8176928 16 G 0.37 GG Homozygous
    rs58073789 16 T 1.00 CT
    rs1500349 16 A 1.00 AG
    rs219600 16 G 0.41 AG
    rs3848286 16 A 1.00 AG
    rs11657647 17 A 1.00 AG
    rs17806333 17 C 1.00 CT
    rs1107651 17 T 1.00 CT
    rs11867995 17 T 1.00 GT
    rs11871303 17 G 1.00 GT
    rs17680289 17 C 1.00 AC
    rs11656940 17 A 1.00 AA Homozygous
    rs11651306 17 C 1.00 CC Homozygous
    rs11651676 17 G 1.00 GG Homozygous
    rs17614694 17 C 1.00 CT
    rs6504459 17 G 1.00 AG
    rs11871837 17 A 1.00 AG
    rs2227376 19 T 1.00 CT
    rs2434844 19 T 1.00 CT
    rs1003467 19 C 1.00 AC
    rs6076053 20 A 1.00 AG
    rs1739587 20 C 0.00 CT
    rs2792379 21 T 1.00 TT Homozygous, rs141815311
    rs743067 21 T 0.09 TT Homozygous, rs181838571
    rs2825300 21 C 1.00 AC
    rs17885407 21 A 0.14 AG
    rs17293705 21 A 1.00 AG
    rs5746879 22 C 1.00 CC Homozygous, rs79553865
    rs34798692 22 T 1.00 CT
    rs138936 22 A 1.00 AG
    snowathlete and Valentijn like this.
  10. frenchmoxie

    frenchmoxie

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    Michigan
    roxie60: I downloaded the Java program to my Mac and now I can run the gene analysis program. Maybe give it a try? Link to Java download:http://www.java.com/en/download/manual.jsp#win
    Valentijn and roxie60 like this.
  11. Mogwai

    Mogwai

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    Auckland, NZ
    Thanks, Valentijn. Very interesting...

    I'm fairly certain, having looked through my results, that I have the ability to teleport. Just need to work out how...
  12. Critterina

    Critterina Senior Member

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    Arizona, USA
    Thanks, Mogwai! I needed the laugh! :rofl:
    Mogwai likes this.
  13. Mogwai

    Mogwai

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    Auckland, NZ
    rs12751479 GT

    rs17526980 CT

    That's the two that stand out.
  14. Critterina

    Critterina Senior Member

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    Arizona, USA
    roxie60, The JAR file is the executable.
    Valentijn likes this.
  15. Critterina

    Critterina Senior Member

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    Arizona, USA
    OK, I updated Java and uninstalled the old versions. I even hit analyze and the CTRL-C a bunch of times. Still no joy.
  16. Valentijn

    Valentijn Activity Level: 3

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    The JAR file ("executable Jar File") should be called "Genes". That's the one to double click on after the three files are extracted.

    Was lack of Java the problem, and if so, is it working now? I've added info to my original post to clarify that Java is needed - I'd forgotten all about that! :p
  17. Valentijn

    Valentijn Activity Level: 3

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    But you do get to the point where it's generated a full list? Then just can't save?

    Oh, it also creates a temporary database from the results to save from ... maybe that's what is running into problems. Lack of a status bar is odd though.

    We'll definitely look into things this weekend! Thanks to everyone for being so patient :)
  18. Valentijn

    Valentijn Activity Level: 3

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    Okay, it looks like everything just stops if the progress bar gets closed. So in the short term, be very careful to not close it :p

    We should be able to get it properly fixed this weekend.
  19. Valentijn

    Valentijn Activity Level: 3

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    Okay, the progress bar issues has been fixed - closing it now ends the analysis with a message in nice red print on the results chart. It can then be started again immediately.

    To get the new version, download at https://sourceforge.net/projects/analyzemygenes/

    Critterina, roxie60, future_man - are things working now? If not, where's things going wrong, and is there any red text showing up?
  20. roxie60

    roxie60 Senior Member

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    Central Illinois, USA
    sorry Val, have not had energy to test. I downloaded 32 and 64 Java but have not installed yet.
    Valentijn likes this.

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