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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
share|improve this question
    
what is showing up in your output file? what errors are you receiving? csv reader/writer, can make code cleaner, ' '.join(TermGeneDic[Term]) would print your list with a seperate space in between each item –  dm03514 Jul 24 '13 at 15:57

2 Answers 2

up vote 2 down vote accepted

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])
share|improve this answer
    
This does the trick! Thank you! –  user2145578 Jul 24 '13 at 20:21
up vote 0 down vote

A couple of pointers on your code: your code will be incomprehensible to anyone else if you don't follow pep 8 conventions fairly closely. This means, no CamelCase except for class names.

Secondly, reusing variable is generally bad, and a sign that you should just chain up those method calls. It's especially bad when you have a variable like line whose type you actually change.

Thirdly, brackets (parentheses) are mandatory for calling a method or function.

Fourthly, you join the elements of a list into a string with '\t'.join(termgenes[term])

Finally, use templating to generate long strings - it ends up being easier to work with.

Your code should look like:

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)

progname,gtffilename,funcencrfilename,outfilename = sys.argv

termgenes = defaultdict(list)

with open(gtffilename, 'r') as gtf :
    for line in gtf:
        linefields = line.strip().split('\t')
        term, gene = linefields[8],linefields[0]
        termgenes[term].append(gene) 

#write output file
with open(funcencrfilename, 'r') as funcencrfile, open(outfilename, 'w') as outfile:
    for line in funcencrfile:
        term, des = line.strip().split('\t')
        outfile.write('%s\t%s%s\n' % term,des,'\t'.join(termgenes[term]))
share|improve this answer
    
Thanks for the tips! –  user2145578 Jul 24 '13 at 20:22

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