gwLee's study

gene_name1
gene_name2
gene_name3
gene_name4

import glob,sys
from Bio import SeqIO

list_file = sys.argv[1]
db_file = sys.argv[2]
output_file = sys.argv[3]

lists = []
for x in open(list_file):
        lists.append(x.strip())

if len(lists) > 1:
        lists.sort()
        last = lists[-1]
        for i in range(len(lists)-2,-1,-1):
                if last == lists[i]:
                        del lists[i]
                else:
                        last=lists[i]

db = SeqIO.parse(open(db_file), format='fasta')
ow = open(output+'.txt','w')

for rec in db:
        name = rec.description
        seq = rec.seq.tostring()
        for x in lists:
                if name.strip() == x.strip() or (name.strip()).find(x.strip()) != -1:
                        if name[:1] == '>':
                                ow.write(name+'\n'+seq+'\n')
                        else:
                                ow.write('>'+name+'\n'+seq+'\n')
ow.close()

from sets import Set
from itertools import groupby
import os,re,glob

#KOG data -> memory
kog_dic = {}
for line in open('kog'):
  if line.find('KOG') != -1:
       kls = line.split()
       cat = kls[0]
       nam = kls[1]
       kog_dic[nam]=cat


#fasta files -> list file
for seq_file in glob.glob('*.fa'):
  name = seq_file.split('.')[0]
 
  ow = open(name+'.list','w')
  for line in open(seq_file):
       if line.find('>') != -1:
           if line.find('>>') != -1:
               ow.write((line.split()[0])[2:]+'\n')
           else:
               ow.write((line.split()[0])[1:]+'\n')
      
ow.close()


for list_file in glob.glob('*.list'): # list files
  name = list_file.split('.')[0]
  ow = open(name+'.result.txt','w') # save files
 
  for c_name in open(list_file):
       c_name1 = (c_name.replace('\n','')).replace('>','')

       check = 0
       tmp_func,tmp_result = [],[]

       for open_file in glob.glob(name+'*.fa.out.txt'): # blastpgp files
           for line in open(open_file):
               ls = line.split()

               c_name2 = ls[0]
               c_func = ls[1]
               c_valu = ls[-2]

               if c_name1 == c_name2 and check == 0:
                   check = 1
                   if float(c_valu) < float(1):
                       tmp_func.append(c_func.split(':')[-1])
                   else:
                       pass

               check = 0

          
           tmp_result = [(len(list(g)),k) for k, g in groupby(sorted(tmp_func))]

           tmp_result.sort()
           if len(tmp_result) != 0:
               result_func = (tmp_result.pop())[1]
           else:
               result_func = 'None'
 
           try:
               ow.write(c_name1+'\t'+result_func+'\t'+kog_dic[result_func]+'\n')
           except:
               ow.write(c_name1+'\tNone\tNone\n')