Help for a python BEGINNER

Question

[kjacobs8]

Please help, I am a python newbie, and I'm trying to figure how to convert a list of about a million ensembl gene ID's into gene symbols. I have imported pandas and numpy and have gotten to the point where I have the csv imported.

data = pd.read_csv("genes_affected_2.csv")

data.head()

I am trying to use a code like this:

ginfo = mg.querymany(ens, scopes='ensembl.gene')

for g in ginfo:
 for k, v in g.iteritems():
  print "- {0: <10}: {1}".format(k, v)
 print

but I can't figure out how to take the column values from the "genes_affected_2.csv" file and convert them.

[Alex Reynolds]

What does data.head() return?

[kjacobs8]

It just returns the first five lines of my table!

Answer 1

[Alex Reynolds]

You could use the following example. You want to figure out building a list of genes from what data.head() tells you about column headers.

#!/usr/bin/env python

import sys
from mygene import MyGeneInfo

mg = MyGeneInfo()

genes = [
    "ENSG00000099308",
    "ENSG00000150676",
    "ENSG00000180776",
    "ENSG00000108848",
    "ENSG00000101473"
]

results = mg.querymany(genes, scopes=["ensembl.gene"], fields=["symbol"], species="human", verbose=False)

for res in results:
    q = res['query']
    s = 'NA'
    if 'symbol' in res:
        s = res['symbol']
    sys.stdout.write('{}\t{}\n'.format(q, s))

This example gives the response:

$ ./test.py
ENSG00000099308 MAST3
ENSG00000150676 CCDC83
ENSG00000180776 ZDHHC20
ENSG00000108848 LUC7L3
ENSG00000101473 ACOT8

[kjacobs8]

Wow! Yes, that is exactly what I need! How do I make it run that same thing for the entire document instead of the first five lines?

[kjacobs8]

I just figured it out! Used the iloc code and a foreloop for the entire table. Thank you so much!!!! Honestly couldn't have done it without your help.