CODEWITHSUNDEEP
pythonlookup-tables
user2180513
user2180513

Reputation: 75

Python - have list and want to pull values from a table and put in new table

Hello I am very new to python and apologize for asking something that may be silly. Any reference in the right direction is very much appreciated.

I have a list of strings (3500 gene names)

I have a table that contains 35000 genes along with several characteristics of those genes. Ie. Gene_ID Gene_Name chr_loc FPKM1 FPKM2 LFC ...etc

I want to find the genes in my list and pull out two values associated with those genes and place these three things for all 3500 genes in a new table.

I really appreciate any help!

Upvotes: 0

Views: 118

Answers (1)

Alan
Alan

Reputation: 9620

Assuming the headers are in the file, here is the basic idea:

import csv
namelist = ['name1', 'name2']
fout = open('out.csv','w')
fout.write('header1,header2,header3')
fin = open('temp.csv','r')
reader = csv.DictReader(fin)
for row in reader:
  if row['header1'] in namelist:
      fout.write(newrow(row))

You will of course need to write a newrow function and adjust details for your input file format.

Upvotes: 1

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