python - Frequency of sequences in many files -

suppose have 50 files (in same folder), , each 1 contains character ">" @ beginning of search. examples:

file1.txt >organism1 >organism2 >organism3 >organism4 >organism5  file2.txt >organism3 >organism4 >organism5 >organism6 

my intention count frequency of each organism in each file , generate table. @ moment count each 1 file-by-file generate table:

table 1.           frequency organism1  1 organism2  1 organism3  2 organism4  2 organism5  2 organism6  1 

until now, can list file in folder can't open them make want.

    import sys     bio import seqio     import glob, os      os.chdir(sys.argv[1])      file_list = []      file in glob.glob("*.faa"):             if file not in file_list:                     file_list.append(file) # until here, perfect  f in file_list:         infile = open(f, 'r')         fasta = seqio.parse(infile, 'fasta')         seq = fasta.description  #.split("|")[2]         print seq 

the problem when try open files in file_list.

<generator object parse @ 0x7f76867c7a00> <generator object parse @ 0x7f76867c7a50> <generator object parse @ 0x7f76867c7a00> <generator object parse @ 0x7f76867c7a50> 

you're using seqio.parse() if seqio.read() won't work. seqio.parse() returns generator since produces multiple results file:

import sys import glob import os bio import seqio  os.chdir(sys.argv[1])  file_list = []  file in glob.glob("*.faa"):     if file not in file_list:         file_list.append(file)  file_name in file_list:     fasta in seqio.parse(file_name, 'fasta'):         description = fasta.description         print(description) 

this works in environment, python 3.6.0; biopython 1.69. in environment, code generates error:

attributeerror: 'generator' object has no attribute 'description' 

instead of producing output. see you're running python 2.7 biopython?

why filtering duplicates result of glob()?