I am trying to print values(a list) from a dictionary to the third column of another file that contains the dictionary key in the first column. I would like the list of values to print in the third column of the output file with a space separating each value. I know my problem lies somewhere in the fact that python can't write things that aren't strings and that the list is separated by a "," but I am new to programming and am not sure how to accomplish this - any help is much appreciated, thanks!

The GtfFile.txt is a 10 column file (sep = '\t') which I generate the dictionary from... using the Gene name as the key and the Term (functional category) as the values. Several genes have more than one Term attributed to them and are repeated as new lines for each term. There are varying numbers of genes associated with each Term as well and thus I generate a list as the key for each Term. THIS PART OF MY SCRIPT APPEARS TO BE WORKING AS I WOULD LIKE IT TO!

The FuncEnr_terms.txt is a 2 column file (sep ='\t') which consists of a Term in the first column and a description of the term in the 2 column. My desired output file would be to duplicate this file with a third column that contains the Genes associated with the Term separated by a space. WRITING THIS TO THE OUTPUT FILE IS WHERE MY PROBLEM LIES.

Below is my code:

#!/usr/bin/env python import sys from collections import defaultdict if len(sys.argv) != 4 : print("Usage: GeneSetFileGen.py <GtfFile.txt> <FuncEnr_terms.txt> <OutputFile.txt>") sys.exit(0) OutFileName = sys.argv[3] OutFile = open(OutFileName, 'w') TermGeneDic = defaultdict(list) with open(sys.argv[1], 'r') as f : for line in f : line = line.strip() line = line.split('\t') Term = line[8] Gene = line[0] TermGeneDic[Term].append(Gene) #write output file with open(sys.argv[2], 'r') as f : for line in f : line = line.strip() Term, Des = line.split('\t') OutFile.write(Term + '\t' + Des + '\t' + str(TermGeneDic[Term]) + '\n') OutFile.close

If I understand what you require correctly then what you need is to replace this expression:

str(TermGeneDic[Term])

with something like:

" ".join(TermGeneDic[Term])

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