vcf | Genetic variant analysis tool | Genomics library

You have lots of unnecessary for loops. The only loop you need is for the lines in the file, you don't need to loop over the characters in fields when you're splitting them or removing something from the whole field.

At the end, you should be adding the result of the calculation to a dictionary.

The problem would be simpler if the data were transposed.

GNU datamash provides such functionality:

You need to solve the problems one by one:

• The first column should start with chr and end with any number between 1-99 or one of the letters M,X,Y - chr(?:0?[1-9]|[1-9][0-9]|[MXY])
• Second column need to be all int numbers that are bigger than 0 - 0*[1-9][0-9]*
• 4th and 5th columns need to be one of the next letters “ATCG” (only one of them) - [ATCG].

Now, considering the column delimiter is the one you used in the code sample (a TAB char, \t), you can use

First you could start by merging your dataframes so that you get a new dataframe with columns from both dataframes, and only keep rows from the Diseases dataframe (column SNP) that exist in the IndividualSNPs dataframe (column SNP). It would be like :

With PyPi regex:

Make sure to see the proper MIME type for the file hosted on S3?

Text: text/vcard

Accepted Content Types for Media

You are evaluating the match in scalar context. As a result, it is returning whether the match was successful or not.

You want to evaluate the match in list context. This is done by making the left-hand side of the assignment "list-like".

Here's how you want to do it. I have added comments in the code so you can understand what I am doing.

Approach: Create a globals variable. Then use the globals variable to define the dynamic dataframe. Then access the value as that is now your dynamic dataframe.

If you are not very clear about how this work, see this Stack Overflow solution where I am defining a dynamic dataframe

I'm not sure I completely understand what you're trying to do, but I'll give it a shot since you seem to have asked this question many times already (which usually isn't a good idea). I believe that there's a lack of clarity in your question - it would help a lot if you could clarify what your end goal is (i.e. how do you want this to behave?)

I think you mentioned two separate problems here. The first is that you expect a new line of '******' to be placed before each separate piece of data returned from your script. This is something that can't be relied on - check out the answer to this question for more detail: Order of process.stdout.on( 'data', ... ) and process.stderr.on( 'data', ... ). The data will be passed to your stdout handler in chunks, not line-by-line, and any amount of data can be provided at a time depending how much is currently in the pipe.

The part I'm most confused about is your phrasing of "to get intermediate ouput of the python script in my nodejs script". There's not necessarily any "immediate" data - you can't rely on data coming in at any particular time with your process's stdout handler, its going to hand you data at a pace determined by the Python script itself and the process its running in. With that said, it sounds like your main problem here is the timeout happening on your POST. You aren't ever ending your request - that's why you're getting a timeout. I'm going to assume that you want to wait for the first chunk of data - regardless of how many lines it contains - before sending a response back. In that case, you'll need to add res.send, like this: