Query= M01757:19:000000000-A3WAT:1:1101:15902:2061 1:N:0:1

Length=53
                                                                      Score     E
Sequences producing significant alignments:                          (Bits)  Value

dbj|AP012555.1|  Mycobacterium avium subsp. hominissuis TH135 chr...  75.0    3e-11
gb|CP005928.1|  Mycobacterium avium subsp. paratuberculosis MAP4,...  75.0    3e-11
gb|CP000479.1|  Mycobacterium avium 104, complete genome              75.0    3e-11
gb|AE016958.1|  Mycobacterium avium subsp. paratuberculosis str. ...  75.0    3e-11


>dbj|AP012555.1| Mycobacterium avium subsp. hominissuis TH135 chromosomal DNA, 
complete genome
Length=4951217

 Score = 75.0 bits (40),  Expect = 3e-11
 Identities = 42/43 (98%), Gaps = 0/43 (0%)
 Strand=Plus/Plus

Query  7        CGGTGGGCAAGAAGGAACTCGAGAAGGACCCGCTGATGGGCAC  49
                |||||||||||||||||||||||||||||||| ||||||||||
Sbjct  1543504  CGGTGGGCAAGAAGGAACTCGAGAAGGACCCGGTGATGGGCAC  1543546



Lambda      K        H
    1.33    0.621     1.12 

Gapped
Lambda      K        H
    1.28    0.460    0.850 

Effective search space used: 1252612366488

Query= M01757:19:000000000-A3WAT:1:1101:16099:2064 1:N:0:1

Length=102


***** No hits found *****



Lambda      K        H
    1.33    0.621     1.12 

Gapped
Lambda      K        H
    1.28    0.460    0.850 

Effective search space used: 3701553444831



##</code><code>##

>M01757:19:000000000-A3WAT:1:1101:15902:2061 1:N:0:1
>M01757:19:000000000-A3WAT:1:1101:19601:5029 1:N:0:1
>M01757:19:000000000-A3WAT:1:1101:17448:5029 1:N:0:1 

##</code><code>##

# List of headers
# BLAST file
# Output file (BLAST format)

use strict;

# Specify I/O

my $headerfile = $ARGV[0];
my $blastfile = $ARGV[1];
my $outfile = $ARGV[2];


# open header file
open (HEADERFILE, $headerfile) or die "Cannot open header file\n";
# open blast file
open (BLASTFILE, $blastfile) or die "Cannot open BLAST file\n";
# open output file
open(OUTPUT, ">$outfile");

my $ender = "Query=";

while (my $headerline = <HEADERFILE> ) {
	chomp $headerline;
	my $headercut = substr $headerline, 1;
	
	while (my $blastline = <BLASTFILE>) { 
		if ($blastline =~ $headercut) {
			print $blastline;
			print OUTPUT $blastline;
			print until ( ($_ = <BLASTFILE>) =~ /$ender/i);
			print OUTPUT until ( ($_ = <BLASTFILE>) =~ /$ender/i);
			}
			}
		seek (BLASTFILE,0,0);
		}
	

exit; 

##</code><code>##

# List of headers
# BLAST file
# Output file (BLAST format)

use strict;

# Specify I/O
my $blastfile = $ARGV[0];
my $headerfile = $ARGV[1];
my $outfile = $ARGV[2];


# open blast file
open (BLASTFILE, $blastfile) or die "Cannot open BLAST file\n";
# open header file
open (HEADERFILE, $headerfile) or die "Cannot open header file\n";
# open output file
open(OUTPUT, ">$outfile");


my @headerline = <HEADERFILE>;
my $headerline = join ( '', @headerline);

while (my $blastline = <BLASTFILE> ) {
	my $blastcut = substr $blastline, 7;
	if ($headerline =~ /\Q$blastcut\E/) {
	print $blastcut;
	
	}
	}
exit;

##</code><code>##

# open blast file
open (BLASTFILE, $blastfile) or die "Cannot open BLAST file\n";
# open header file
open (HEADERFILE, $headerfile) or die "Cannot open header file\n";
# open output file
open(OUTPUT, ">$outfile");

my $ender = "Query=";
my @headerline = <HEADERFILE>;
my $headerline = join ( '', @headerline);

while (my $blastline = <BLASTFILE> ) {
	my $blastcut = substr $blastline, 7;
	if ($headerline =~ /\Q$blastcut\E/) {
	print $blastcut;
	print until ( ($_ = <BLASTFILE>) =~ /$ender/i);
	}
	}
exit;