How can I write the output from a for loop in python to a csv file?
Below is a description of a python script that determines whether or not certain words are found in a list of different files.
experiment=open('potentiation.txt')
lines=experiment.read().splitlines()
receptors=['crystal_1.txt', 'modeller_1.txt', 'moe_1.txt',
'nci5_modeller0000_1.txt', 'nci5_modeller0001_1.txt',
'nci5_modeller0002_1.txt', 'nci5_modeller0003_1.txt',
'nci5_modeller0004_1.txt', 'nci5_modeller0005_1.txt',
'nci5_modeller0006_1.txt', 'nci5_modeller0007_1.txt',
'nci5_modeller0008_1.txt', 'nci5_modeller0009_1.txt',
'nci5_modeller0010_1.txt', 'nci5_modeller0011_1.txt',
'nci5_moe0000_1.txt', 'nci5_moe0001_1.txt', 'nci5_moe0002_1.txt',
'nci5_moe0003_1.txt', 'nci5_moe0004_1.txt', 'nci5_moe0005_1.txt',
'nci5_moe0006_1.txt', 'nci5_moe0007_1.txt', 'nci5_moe0008_1.txt',
'nci5_moe0009_1.txt', 'nci5_moe0010_1.txt', 'nci5_moe0011_1.txt',
'nci5_moe0012_1.txt', 'nci5_moe0013_1.txt', 'nci5_moe0014_1.txt']
for ligand in lines:
for protein in receptors:
file1=open(protein,"r")
read1=file1.read()
find_hit=read1.find(ligand)
if find_hit == -1:
print ligand,protein,"Not Found"
else:
print ligand,protein, "Found"
Below is an example of the output of this code:
345647 nci5_moe0012_1.txt Not Found 345647 nci5_moe0013_1.txt Not Found 345647 nci5_moe0014_1.txt Found
My question is, how can I take the output and format it into a csv file that looks like the example below?
Ligand nci5_moe0012_1. nci5_moe_0013_1 nci5_moe_0014 345647 Not Found Not Found Found
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I think something like this would do it (assuming your output file is tab-delimited):
import csv
import os
receptors = ['crystal_1', 'modeller_1', 'moe_1',
'nci5_modeller0000_1', 'nci5_modeller0001_1',
'nci5_modeller0002_1', 'nci5_modeller0003_1',
'nci5_modeller0004_1', 'nci5_modeller0005_1',
'nci5_modeller0006_1', 'nci5_modeller0007_1',
'nci5_modeller0008_1', 'nci5_modeller0009_1',
'nci5_modeller0010_1', 'nci5_modeller0011_1',
'nci5_moe0000_1', 'nci5_moe0001_1', 'nci5_moe0002_1',
'nci5_moe0003_1', 'nci5_moe0004_1', 'nci5_moe0005_1',
'nci5_moe0006_1', 'nci5_moe0007_1', 'nci5_moe0008_1',
'nci5_moe0009_1', 'nci5_moe0010_1', 'nci5_moe0011_1',
'nci5_moe0012_1', 'nci5_moe0013_1', 'nci5_moe0014_1']
with open('potentiation.txt', 'rt') as experiment, \
open('output.csv', 'wb') as outfile:
csv_writer = csv.writer(outfile, delimiter='\t')
csv_writer.writerow(['Ligand'] + receptors) # header row
for ligand in (line.rstrip() for line in experiment):
row = [ligand]
for protein in receptors:
with open(protein+'.txt', "rt") as file1:
found = ['Found', 'Not Found'][file1.read().find(ligand) == -1]
row.append(found)
csv_writer.writerow(row)
print('output.csv file written')
Update
As I said in the comment, this can be done much faster by only reading the protein files once. In order to be able to do this and format the output the way you want, the test results of each ligand in each file must be stored in a data structure, created incrementally as each file is read, and then tested several times, only to be written out. all-in-one, after everything is done. A simple list of lists is suitable for this purpose and has been used in the implementation below.
The trade-off uses more memory than reading and re-reading protein files. Since disk IO is often one of the slowest things on a computer, the potentially big performance gains for a slight increase in code complexity is probably worth it.
Here is the code showing this alternate version:
import csv
import os
receptors = ['crystal_1', 'modeller_1', 'moe_1',
'nci5_modeller0000_1', 'nci5_modeller0001_1',
'nci5_modeller0002_1', 'nci5_modeller0003_1',
'nci5_modeller0004_1', 'nci5_modeller0005_1',
'nci5_modeller0006_1', 'nci5_modeller0007_1',
'nci5_modeller0008_1', 'nci5_modeller0009_1',
'nci5_modeller0010_1', 'nci5_modeller0011_1',
'nci5_moe0000_1', 'nci5_moe0001_1', 'nci5_moe0002_1',
'nci5_moe0003_1', 'nci5_moe0004_1', 'nci5_moe0005_1',
'nci5_moe0006_1', 'nci5_moe0007_1', 'nci5_moe0008_1',
'nci5_moe0009_1', 'nci5_moe0010_1', 'nci5_moe0011_1',
'nci5_moe0012_1', 'nci5_moe0013_1', 'nci5_moe0014_1']
# initialize list of lists holding each ligand and its presence in each receptor
with open('potentiation.txt') as experiment:
ligands = [[ligand] for ligand in (line.rstrip() for line in experiment)]
for protein in receptors:
with open(protein + '.txt') as protein_file:
protein_file_data = protein_file.read()
for row in ligands:
# determine if this ligand (row[0]) appears in protein data
row.append('Found' if row[0] in protein_file_data else 'Not Found')
with open('output.csv', 'wb') as outfile:
csv_writer = csv.writer(outfile, delimiter='\t')
csv_writer.writerow(['Ligand'] + receptors) # header row
csv_writer.writerows(ligands)
print('output.csv file written')
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You can save your result in lists (one list for ligand, one for proteins), after adding "Protein" and the "Ligand" value to the corresponding list (at index 0). After that, it is easy to save the text file.
To save, you open the file to write and transform the list in line:
my_string = " ".join(map(str, lst))
and then save my_string (And do this for each list)
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