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Search found 8 results on 1 pages for 'seafoid'.

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• Python - Nested List to Tab Delimited File?

  - by Seafoid

  Hi, I have a nested list comprising ~30,000 sub-lists, each with three entries, e.g., nested_list = [['x', 'y', 'z'], ['a', 'b', 'c']]. I wish to create a function in order to output this data construct into a tab delimited format, e.g., x y z a b c Any help greatly appreciated! Thanks in advance, Seafoid.

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• Python - compare nested lists and append matches to new list?

  - by Seafoid

  Hi, I wish to compare to nested lists of unequal length. I am interested only in a match between the first element of each sub list. Should a match exist, I wish to add the match to another list for subsequent transformation into a tab delimited file. Here is an example of what I am working with: x = [['1', 'a', 'b'], ['2', 'c', 'd']] y = [['1',…

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• Python - Calling a non python program from python?

  - by Seafoid

  Hi, I am currently struggling to call a non python program from a python script. I have a ~1000 files that when passed through this C++ program will generate ~1000 outputs. Each output file must have a distinct name. The command I wish to run is of the form: program_name -input -output -o1 -o2 -o3 To date I have tried: import os cwd =…

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• Python - calculate multinomial probability density functions on large dataset?

  - by Seafoid

  Hi, I originally intended to use MATLAB to tackle this problem but the inbuilt functions has limitations that do not suit my goal. The same limitation occurs in NumPy. I have two tab-delimited files. The first is a file showing amino acid residue, frequency and count for an in-house database of protein structures, i.e. A 0.25 1 S …

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• Python - from file to data structure?

  - by Seafoid

  Hi, I have large file comprising ~100,000 lines. Each line corresponds to a cluster and each entry within each line is a reference i.d. for another file (protein structure in this case), e.g. 1hgn 1dju 3nmj 8kfn 9opu 7gfb 4bui I need to read in the file as a list of lists where each line is a sublist, thus preserving the integrity of…

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• Python - output from functions?

  - by Seafoid

  Hi I have a very rudimentary question. Assume I call a function, e.g., def foo(): x = 'hello world' How do I get the function to return x in such a way that I can use it as the input for another function or use the variable within the body of a program? When I use return and call the variable within another functions I get a…

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• Python - a clean approach to this problem?

  - by Seafoid

  Hi, I am having trouble picking the best data structure for solving a problem. The problem is as below: I have a nested list of identity codes where the sublists are of varying length. li = [['abc', 'ghi', 'lmn'], ['kop'], ['hgi', 'ghy']] I have a file with two entries on each line; an identity code and a number. abc 2.93…

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• Python - alternative to list.remove(x)?

  - by Seafoid

  Hi, I wish to compare two lists. Generally this is not a problem as I usually use a nested for loop and append the intersection to a new list. In this case, I need to delete the intersection of A and B from A. A = [['ab', 'cd', 'ef', '0', '567'], ['ghy5'], ['pop', 'eye']] B = [['ab'], ['hi'], ['op'], ['ej']] My objective is…

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