match - find matches in two file using python -


i analyzing sequencing data , have few candidates genes need find functions.

after editing available human database , want compare candidate genes database , output function candidate gene.

i have basic python skills thought might me speed work finding functions of candidate genes.

so file1 contains candidate genes this

gene aqp7 rlim smco3 coasy hspa6

and database,file2.csv looks this:

gene   function  pdcd6  programmed cell death protein 6  cdc2   cell division cycle 2, g1 s , g2 m, isoform cra_a  cdc2   cell division cycle 2, g1 s , g2 m, isoform cra_a  cdc2   cell division cycle 2, g1 s , g2 m, isoform cra_a  cdc2   cell division cycle 2, g1 s , g2 m, isoform cra_a

desired output

 gene(from file1) ,function(matching file2)

i tried use code :

file1 = 'file1.csv' file2 = 'file2.csv' output = 'file3.txt'  open(file1) inf:     match = set(line.strip() line in inf)  open(file2) inf, open(output, 'w') outf:     line in inf:         if line.split(' ',1)[0] in match:             outf.write(line)

i blank page.

i tried using intersection function

with open('file1.csv', 'r') ref:     open('file2.csv','r') com:        open('common_genes_function','w') output:            same = set(ref).intersection(com)                 print same

not working also..

please otherwise need manually

i recommend using pandas merge function. however, requires clear separator between 'gene' , 'function'-column. in example, assume @ tab:

import pandas pd #open files pandas datasets file1 = pd.read_csv(filepath1, sep = '\t') file2 = pd.read_csv(filepath2, sep = '\t')  #merge files column 'gene' using 'inner', comes #with intersection of both datasets file3 = pd.merge(file1, file2, how = 'inner', on = ['gene'], suffixes = ['1','2']) file3.to_csv(filepath3, sep = ',')

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