Try this python script:

import sys
from Bio import SeqIO
faFile = open(sys.argv[1],'r')
queries = set([strrecord.id) for record in SeqIO.parse(faFile,'fasta')])
hits = set([x.split()[0] for x in open(sys.argv[2],'r').read().strip().split('\n')])
noHits = queries - hits
print '\n'.join(noHits)

Save as noHits.py and run by:

python noHits.py queries.fasta blastx.tab.output > noHits.ids

This script basically just gets a list of query ids and list of hit ids. Then it prints out ids of any query id that's not in the hit id list.

It's basically like this:

export LC_ALL=C; comm -3 <(grep "^>" file.fasta | sort) <(cut -f1 blast.tsv | sort)

It might not work because blast may report shorter query sequence IDs than full headers. In this case, I would need to see a few headers and blast output lines so the first process substitution could be modified accordingly.

It works perfect;

ussage python python_script.py file1 file2

from __future__ import division
import sys
from Bio import SeqIO
import os

file1 = open(sys.argv[1],'r')
lista1 = []

for line in file1:
        line = line.rstrip('\n')
        lista1.append(line)
file1.close()

file2 = open(sys.argv[2],'r')
lista2 = []

for line in file2:
        line = line.rstrip('\n')
        lista2.append(line)
file2.close()

same = set(lista1).intersection(set(lista2))

file_out = open('some_output_file.txt', 'w')
for line in same:
    file_out.write(line)

file_out.close()