creating a list of genes in python

Question

[arshad1292]

Hello,

I have a .csv file that contains columns called, geneid, log2FoldChange, pvalue, padj and symbol etc. I have gene symbols under the symbol column as shown in the attached screenshot .

I want to generate a volcano plot and for that I want to create a list called let's say picked1 that contains selected 5 gene symbols (CLK1, HMOX1, SAT1, TUFT1, RHOB).

How can I create that in python? I tried the following:

picked1 = ('CLK1', 'HMOX1', 'SAT1', 'TUFT1', 'RHOB')

In the above example, it does create a list but it's not reading from the .csv file. I want it to read it from the .csv file and whenever I call pikced1 it should pick these 5 symbols from the .csv file and tell me "log2FoldChange" values of these 5 genes.

Could anyone please guide me how should I create this list so it's linked to .csv file?

Many thanks in advance!

Answer 1

[iraun]

Not sure if I am following the question but... First you have to read the file:

df = pd.read_csv("input.csv")

Then you create the list with the genes of interest:

picked = ['CLK1', 'HMOX1', 'SAT1', 'TUFT1', 'RHOB']

Then you select those rows of the input file whose symbol column value is included in picked list, and you return log2FoldChange:

print(df[df['symbol'].isin(picked)]['log2FoldChange'])

Answer 2

[M.O.L.S]

• open the file.
• Append the contents to a list.
• Make your picked one list.
• split the line based on semicolons get your gene symbol and your log fold change.
• filter all values based on the ones in your picked1 list.
• close the file.

• make your volcano plot?

  enter code here

   infile = open("biostars.csv", "r")
  
   my_list = []
    for line in infile:
            my_list.append(line)
  
    lfc = []
    symb = []
  
    picked1 = ['CLK1', 'HMOX1', 'SAT1', 'TUFT1', 'RHOB']
  
    for line in my_list:
        individual_rows = line[:-2].split(";")
        log_fold_change = individual_rows[2]
        lfc.append(log_fold_change)
  
    symbol = individual_rows[-1]
    symb.append(symbol).  
  
   for val, gene in zip(lfc, symb):
       if gene in picked1:
       print(gene, val)
  
    infile.close()
  

Perhaps you could do something like that to make your volcano plot using the gene and lfc values in a list.