QURY: Contig103
SIZE: 264
GINO: 116055070
STID: unnamed protein product [Ostreococc...   
SCOR: 40   
EVAL: 0.003

QURY: Contig228
SIZE: 116
GINO: 162464429
NPNO: NP_001104917.1
STID: eucaryotic initiation factor7 [...   
SCOR: 34   
EVAL: 0.004

QURY: Contig1032
SIZE: 217
GINO: 168018663
NPNO: XP_001761865.1
STID: predicted protein [Physcomitrel...   
SCOR: 34 
EVAL: 2e-004

##</code><code>##

QURY: Heritiera_allseq.fna.Contig1032
SIZE: 217
GINO: 157349006</br>
STID: unnamed protein product [Vitis vini... 
SCOR: 59   
EVAL: 6e-015

##</code><code>##

#!/usr/bin/perl   
# the infile "query.txt" has multiple blast hits per each query
# the outfile needs to have the first blast hit with the Ref number or the best hit
# the second outfile "reflist.txt" is to get the ref numbers to do batch entrez
$infile = "query.txt"; #output of blast
open (IN, $infile) or die "can't open file: $!";

$outfile = "besthit.txt";
open (OUT, ">$outfile") or die "can't open file: $!";

$ofile = "reflist.txt";
open (NP, ">$ofile") or die "can't open file: $!";

while (<IN>) {
	if ($_ =~ /^Query/) {
		chomp;
		$query = $_;
		$query =~ s/^Query=\s//;
		
	}
	
	elsif ($_ =~ s/^\s+\((\d+)\sletters\)/$1/) {
		chomp;
		$length = $_;
		
	}
	
	elsif ($_ =~ /\|ref\|/) {
		chomp;
		$np = $_;
		until (/^\s+/) {
		$_ = <IN>;
		$line = join (" ", $line, $_);
		}
		# print OUT "$np\n";
		$id = substr $np, 0, 70;
		$score = substr $np, 70, 6;
		$score =~ s/^\s//;
		$evalue = substr $np, 76, 6;
		@id = split(/\|/, $id);
		$gino = $id[1];
		$npno = $id[3];
		$stid = $id[4];
		$stid =~ s/^\s//;
		print NP "$npno\n";
		print OUT "\nQURY: $query\n";
		print OUT "SIZE: $length\n";
		print OUT "GINO: $gino\n";
		print OUT "NPNO: $npno\n";
		print OUT "STID: $stid\n";
		print OUT "SCOR: $score\n";
		print OUT "EVAL: $evalue\n";
	} #elsif end

	elsif ($_ =~ /^gi/) {
		chomp;
		$np = $_;
		until (/^\s+/) {
		$_ = <IN>;
		$line = join (" ", $line, $_);
		}
		# print OUT "$np\n";
		$id = substr $np, 0, 70;
		$score = substr $np, 70, 6;
		$score =~ s/^\s//;
		$evalue = substr $np, 76, 6;
		@id = split(/\|/, $id);
		$gino = $id[1];
		$stid = $id[4];
		$stid =~ s/^\s//;
		print OUT "\nQURY: $query\n";
		print OUT "SIZE: $length\n";
		print OUT "GINO: $gino\n";
		print OUT "STID: $stid\n";
		print OUT "SCOR: $score\n";
		print OUT "EVAL: $evalue\n";
	} #elsif end
			
} #while end
close IN;
close OUT;
close NP;

</readmore>

##</code><code>##

Query= Contig103
         (264 letters)
                                                           Score    E
Sequences producing significant alignments:                      (bits) Value

gi|116055070|emb|CAL57466.1| unnamed protein product [Ostreococc...    40   0.003

  Database: All non-redundant GenBank CDS
  translations+PDB+SwissProt+PIR+PRF excluding environmental samples
S1: 41 (20.4 bits)
S2: 89 (38.9 bits)

Query= Contig228
         (116 letters)

Score    E
Sequences producing significant alignments:                      (bits) Value

gi|162464429|ref|NP_001104917.1| eucaryotic initiation factor7 [...    34   0.004
gi|164449261|gb|ABY56090.1| eukaryotic initiation factor iso4E [...    40   0.006
gi|170753|gb|AAA34296.1| initiation factor (iso)4F p28 subunit         33   0.007
gi|547713|sp|Q03389|IF4E2_WHEAT Eukaryotic translation initiatio...    33   0.007

  Database: All non-redundant GenBank CDS
  translations+PDB+SwissProt+PIR+PRF excluding environmental samples
  
S1: 41 (20.4 bits)
S2: 89 (38.9 bits)

Query= Contig1032
         (217 letters)

Score    E
Sequences producing significant alignments:                      (bits) Value

gi|157349006|emb|CAO24084.1| unnamed protein product [Vitis vini...    59   6e-015
gi|168018663|ref|XP_001761865.1| predicted protein [Physcomitrel...    34   2e-004
gi|168018829|ref|XP_001761948.1| predicted protein [Physcomitrel...    34   2e-004

  Database: All non-redundant GenBank CDS
  translations+PDB+SwissProt+PIR+PRF excluding environmental samples