When I was using BioPerl to parse the blast results, I found that it can parse the blast(2.2.21) result but not the blast+(2.2.25+) result(all were in the default format).

The parser.pl code:

#!/usr/bin/perl
use strict;
use Bio::SearchIO;

my $fi     = $ARGV[0];
my $format = $ARGV[1];
my $in     = new Bio::SearchIO(
    -format => "$format",
    -file   => "$fi"
);

print "#Query\tHit\tScore\tBits\tEvalue\n";
while ( my $result = $in->next_result ) {
    while ( my $hit = $result->next_hit ) {
        while ( my $hsp = $hit->next_hsp ) {
            print $result->query_name, "\t", $hit->name, "\t",
              $hsp->score, "\t", $hsp->bits, "\t", $hsp->evalue, "\n";
        }
    }
}

The result of parsing blast (it is OK):

> #Query    Hit    Score    Bits    Evalue
first    gi|195972856|ref|NM_001130955.1|    21    42.1    2e-04
first    gi|195972854|ref|NM_015318.3|    21    42.1    2e-04
second    gi|261878474|ref|NM_001166295.1|    21    42.1    2e-04
second    gi|261878472|ref|NM_001166294.1|    21    42.1    2e-04
second    gi|261878551|ref|NM_001166417.1|    21    42.1    2e-04
second    gi|261878470|ref|NM_001166293.1|    21    42.1    2e-04
second    gi|261878468|ref|NM_014021.3|    21    42.1    2e-04
third    gi|115392135|ref|NM_007249.4|    21    42.1    2e-04

The result of parsing blast+ (No output except the header):

> #Query    Hit    Score    Bits    Evalue

================================================================

According to BioPerl's wiki (NCBI-BLAST parsing problems), XML format is recommended. But I found that Bioperl has problems in parsing blast or blast+ results in XML format.

The parser.pl is the same; The result of parsing blast in XML format (I have three queries, but it print the first one only!):

> #Query    Hit    Score    Bits    Evalue
first    gi|195972856|ref|NM_001130955.1|    21    42.1223    0.000184141
first    gi|195972854|ref|NM_015318.3|    21    42.1223    0.000184141
first    gi|261878474|ref|NM_001166295.1|    21    42.1223    0.000184141
first    gi|261878472|ref|NM_001166294.1|    21    42.1223    0.000184141
first    gi|261878551|ref|NM_001166417.1|    21    42.1223    0.000184141
first    gi|261878470|ref|NM_001166293.1|    21    42.1223    0.000184141
first    gi|261878468|ref|NM_014021.3|    21    42.1223    0.000184141
first    gi|115392135|ref|NM_007249.4|    21    42.1223    0.000184141

The result of parsing blast+ in XML format (Besides the same problem, it can not get the query id properly!):

> #Query    Hit    Score    Bits    Evalue
Query_1    gi|195972856|ref|NM_001130955.1|    42    39.1570490084919       0.000615407041092949
Query_1    gi|195972854|ref|NM_015318.3|    42    39.1570490084919     0.000615407041092949
Query_1    gi|261878474|ref|NM_001166295.1|    42    39.1570490084919    0.000615407041092949
Query_1    gi|261878472|ref|NM_001166294.1|    42    39.1570490084919    0.000615407041092949
Query_1    gi|261878551|ref|NM_001166417.1|    42    39.1570490084919    0.000615407041092949
Query_1    gi|261878470|ref|NM_001166293.1|    42    39.1570490084919    0.000615407041092949
Query_1    gi|261878468|ref|NM_014021.3|    42    39.1570490084919    0.000615407041092949
Query_1    gi|115392135|ref|NM_007249.4|    42    39.1570490084919    0.000615407041092949

Does anybody meet the same problems? What is the problem? How to solve it?