I am doing command-line BLAST with BioPython. I need to search against TrEMBL, but I have not been able to find how to do that. I know I can select db="nr", and that works, but I want to search only against TrEMBL, which constitues a subset of nr sequences. Also, I need to be able to do that on-line, not remotely!
EDIT: If anyone ever encounters the same problem: After much experimentation, the only way that I managed to make this work was to download NCBI BLAST+ and do a remote search on a stand-alone prepared library. Get in touch with me if in doubt.
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I am starting to get acquainted with the use of ELK for work purposes, but struggle to find a solution to use simple mathematic requests in my database.
As shown on the picture, my DB contains 16 available fields, but I would like to create others, without doing it on Excel before converting my file in CVS again.
For example, I would like to create a variable #Bugs/Release. I've heard that this is quite easy to make with no need of scripting, but I can't find the way to do it... Has anybody the solution of this problem?
Huge thanksenter image description here
I am new to this site and I would like to get some inputs regarding parsing STDF files. Generally speaking, I am trying to parse a STDF file to gather only the results (numbers) and not the rest of the line. If I am able to achieve this, I would then like to compare all the numbers together through a bubble sort or insertion sort and see if any numbers are equal to each other. I am capable of doing this in C/C++ and Java but I have no experience parsing documents using Scripts.
Could anyone push me in the right direction? What should I be reading to learn my way around this?
Are you already using an STDF library?
You did not mention one, so I assume not.
You should find a library you are comfortable with (the list changes over time, but you can find some by Googling or looking at the STDF page on Wikipedia) rather than attempting to parse STDF yourself, unless you have a good reason to recreate the STDF parser wheel.
An STDF file contains many tests. It generally does not make sense to compare the results for different tests, so I assume you are looking for matching values within the set of results for each test.
I would use your chosen STDF parser to read the value of each test for each part. Keep a set of the results for each test. As you read each new result, check the set to see if already exists. If it does, you have found the case you were looking for, otherwise add the result to the set.
I'm hoping somebody out there can help me with this. I'm attempting to extract some barcode data from some .dat files. Its a B Tree file system with groups of three files .dat .ix. .dia. The company that wrote the software (a long time ago) say that the program is written in Pascal. I have no experience in reverse engineering but from what I read its most likely the only way to extract the data as the structure of the database is contained in the code of the program. I'm looking for advice on where to start.
I suppose the first thing you need to do is to see if the exe you've got was written with Delphi. You can check with this: http://cc.embarcadero.com/Item/15250
Then, to see if the exe that creates those .dat files were made with 'TurboPower B-Tree Filer', the I'd suggest you download and take a look at this: http://sourceforge.net/projects/tpbtreefiler/
At this step, looking at these sources is needed to familiarize yourself with the class names used in 'TurboPower B-Tree Filer' to help determine if any of those classes were used in your exe.
Then, using 'XN Resource Editor' [search the Internet for this] or, probhably better, 'MiTeC Portable Executable Reader' [ http://www.mitec.cz/pe.html ], see if any class names are relevant.
If they are, then you're in luck --sort of. All you will need to do is to write an app using 'TurboPower B-Tree Filer' to import the data in your dat files to export or manipulate as you wish.
At that point, you might find this link useful.
TurboPower B-Tree Filer and Delphi XE2 - Anyone done it?
If, OTOH, none of the above applies; I fear the only option is to reverse engineer the exe you have.
I'm thinking of building an application that helps you find local businesses (just an example). You might enter your zip code (or GPS if this is on a phone) and find the closest business within 10 miles, etc. My question is how can I achieve this type of logic? Is there a library or service that I will need to use? Or can this be done with math? I'm not familiar with how this sort of thing usually works, so let me know how I need to store the records so I can query them later. Note: I will be using Ruby and MongoDB.
It should be easy to find the math to solve that, providing lat/long coordinates.
Or you could use some full featured gem to do that for you like Geocoder, that supports Mongoid or MongoMapper.
Next time you need some feature that might be a commun world problem, first check if there is a gem for that at ruby-toolbox, for this case here are some other gems for geocoding
One more solution here...
http://geokit.rubyforge.org/
I think, this topic is already discussed here..
Sadly, a project that I have been working on lately has a large amount of copy-and-paste code, even within single files. Are there any tools or techniques that can detect duplication or near-duplication within a single file? I have Beyond Compare 3 and it works well for comparing separate files, but I am at a loss for comparing single files.
Thanks in advance.
Edit:
Thanks for all the great tools! I'll definitely check them out.
This project is an ASP.NET/C# project, but I work with a variety of languages including Java; I'm interested in what tools are best (for any language) to remove duplication.
Check out Atomiq. It finds code that is duplicate that is prime for extracting to one location.
http://www.getatomiq.com/
If you're using Eclipse, you can use the copy paste detector (CPD) https://olex.openlogic.com/packages/cpd.
You don't say what language you are using, which is going to affect what tools you can use.
For Python there is CloneDigger. It also supports Java but I have not tried that. It can find code duplication both with a single file and between files, and gives you the result as a diff-like report in HTML.
See SD CloneDR, a tool for detecting copy-paste-edit code within and across multiple files. It detects exact copyies, copies that have been reformatted, and near-miss copies with different identifiers, literals, and even different seqeunces of statements.
The CloneDR handles many languages, including Java (1.4,1.5,1.6) and C# especially up to C#4.0. You can see sample clone detection reports at the website, also including one for C#.
Resharper does this automagically - it suggests when it thinks code should be extracted into a method, and will do the extraction for you
Check out PMD , once you have configured it (which is tad simple) you can run its copy paste detector to find duplicate code.
One with some Office skills can do following sequence in 1 minute:
use ordinary formatter to unify the code style, preferably without line wrapping
feed the code text into Microsoft Excel as a single column
search and replace all dual spaces with single one and do other replacements
sort column
At this point the keywords for duplicates will be already well detected. But to go further
add comparator formula to 2nd column and counter to 3rd
copy and paste values again, sort and see the most repetitive lines
There is an analysis tool, called Simian, which I haven't yet tried. Supposedly it can be run on any kind of text and point out duplicated items. It can be used via a command line interface.
Another option similar to those above, but with a different tool chain: https://www.npmjs.com/package/jscpd