head -n 1 another_document > result && grep -v '>' query_document | grep -F -f - another_document >> result

head -n 1 other.tsv > result
sort -t '    ' -k1,1 other.tsv | join  -t '    ' -1 1 -2 1 <(grep -v ">" file.fa | sort -u ) - >> result

Put the FASTA sequences into a hash table, and print out rows from the matrix file if the motif field element is defined in the hash table:

#!/usr/bin/env perl

use strict;
use warnings;

my $fastaFn = $ARGV[0];
my $masterFn = $ARGV[1];

my $seqsRef;
my $header;
my $sequence;

open FASTA, "< $fastaFn" or die "could not open FASTA file\n";
while (<FASTA>) {
    chomp;
    if (/>/) {
        $header = $_;
        $header =~ s/^>//;
    }
    else {
        $sequence = $_;
        $seqsRef->{$sequence} = $header;
    }
}
close FASTA;

open MASTER, "< $masterFn" or die "could not open master file for filtering\n";
my $ln = <MASTER>;
print STDOUT "$ln\n";
while (<MASTER>) {
    chomp;
    my @elems = split("\t", $_);
    my $motif = $elems[0];
    if (defined $seqsRef->{$motif}) {
        print STDOUT "$_\n";
    }
}
close MASTER;

To use it:

$ filter.pl myQuerySeqs.fa myDataMatrix.mtx > myFilteredMatrix.mtx

The file myQuerySeqs.fa is your FASTA file. The myDataMatrix.mtx file is the "master" matrix file that you want to filter on sequences from the FASTA file. Output is sent to myFilteredMatrix.mtx.

This should be fairly fast, if memory-intensive, because hash table lookups are in constant time.

Not the most elegant, but this should do it (unless your Fasta file is too big for memory?)

from Bio import SeqIO
tags=[]
for seq_record in SeqIO.parse("in.fas", "fasta"):
    if str(seq_record.seq) not in tags:
        tags.append(str(seq_record.seq))


for tag in tags:
    with open("2.txt","rU") as f:
        for line in f:
            line=line.rstrip()
            if tag in line:
                print line

I am not sure how big are your files but if R can handle them, then you can use :

require("Biostrings")
sequence_data<<-read.DNAStringSet("file1.fasta")
motifs<-read.table("file2.txt",header=T)
tab3<-subset(motifs, motifs$motif%in%as.character(sequence_data))

> tab3
         motif MZQ1 MZQ3 MZQ4 MZQ5 MZQ6 MZQ7 MZQ8 MZQ2
2        AAAAAAAAAAAAACAGTTGGCATG    0    0    0    0    0    1    0    0
3 AAAAAAAAAAAAACCGAGTACCGTTCACGCC    0    0    0    0    0    1    0    0
4           AAAAAAAAAAAAACCTTGAAC    0    0    0    0    0    0    0    1

 #!/usr/bin/perl -w
print"Enter REFERENCE file: ";
chomp($file=<STDIN>);
open(FH,$file);
@org_det=<FH>;
print"Enter QUERY file: ";
$hspfile=<STDIN>;
open(FH1,$hspfile);
@hsporg=<FH1>;
print "enter output file : ";
$OUT = <STDIN>;
chomp($OUT);
open(OUT1,">$OUT");

foreach(@hsporg)
{
    @org=split('\t',$_);
    chomp($org=$_);
    foreach(@org_det)
    {
        @orginfo=split('\t',$_);
        if($org=~$orginfo[0])

        {
            print OUT1 "$_";
        }
            }
    }
close FH;
close FH1;
close OUT1;