Branch Coverage

blib/lib/Bio/Tools/Run/StandAloneBlastPlus.pm
Criterion Covered Total %
branch 0 192 0.0


line true false branch
522 0 0 if ($db_name)
523 0 0 unless $db_name =~ m[^[a-z0-9_/:.+-]+$]i
526 0 0 if ($db_dir) { }
527 0 0 unless -d $db_dir
538 0 0 if ($db_name)
540 0 0 unless $f
545 0 0 if ('File::Spec'->file_name_is_absolute($db_name)) { }
546 0 0 unless not $d or -d $d
550 0 0 if $db_dir
554 0 0 unless not $d or -d $d
559 0 0 if ($masker)
560 0 0 unless grep /^$masker$/, keys %AVAILABLE_MASKERS
565 0 0 if ($program_dir) { }
0 0 elsif ($ENV{'BLASTPLUSDIR'}) { }
566 0 0 unless -d $program_dir
577 0 0 if $db_make_args
578 0 0 if $mask_make_args
589 0 0 if (defined $self->check_db and $self->check_db == 0 and not $self->is_remote)
590 0 0 unless $create or $overwrite
592 0 0 unless ($self->db)
594 0 0 unless ($self->db_data)
602 0 0 if ($self->db_dir) { }
691 0 0 if $fac
697 0 0 if $fac
719 0 0 if $self->check_db and not $self->overwrite
721 0 0 unless $self->db_data
729 0 0 $testio->next_seq->alphabet =~ /.na/ ? :
745 0 0 if $usr_db_args
755 0 0 if (%usr_args)
763 0 0 if ($self->mask_file) { }
0 0 elsif ($self->masker and $self->mask_data) { }
769 0 0 unless $db_args{'-mask_data'}
808 0 0 unless $data
810 0 0 unless $masker
813 0 0 if $usr_make_args
814 0 0 unless (grep /^$masker$/, keys %AVAILABLE_MASKERS)
817 0 0 if ($self->check_db($data)) { }
818 0 0 unless ($masker eq 'segmasker')
821 0 0 unless ($self->db_info($data)->{'_db_type'} eq $AVAILABLE_MASKERS{$masker})
832 0 0 if ($s->alphabet =~ /.na/) { }
0 0 elsif ($s->alphabet =~ /protein/) { }
841 0 0 unless ($type eq $AVAILABLE_MASKERS{$masker})
864 0 0 if (%usr_args)
870 0 0 if (/dustmasker/)
879 0 0 if (/windowmasker/)
881 0 0 if ($mask_db)
882 0 0 unless ($self->check_db($mask_db))
896 0 0 unless $status
901 0 0 if ($mask_db)
910 0 0 if (/segmasker/)
924 0 0 $status ? :
942 0 0 unless ($db)
946 0 0 if ($self->is_remote)
950 0 0 if ($db eq $self->db and $self->{'_db_info'})
960 0 0 if ($self->factory->stderr =~ /No alias or index file found/)
969 0 0 if (/Database: (.*)/)
973 0 0 if (/([0-9,]+) sequences; ([0-9,]+) total/)
980 0 0 if (/Date: (.*?)\s+Longest sequence: ([0-9,]+)/)
986 0 0 if (/Algorithm ID/)
989 0 0 if (/\s*([0-9]+)\s+([a-z0-9_]+)\s+(.*)/i) { }
1004 0 0 if (-e $db . '.psq') { }
0 0 elsif (-e $db . '.nsq') { }
1013 0 0 if ($db eq $self->db)
1035 0 0 unless ref($args) =~ /^ARRAY|HASH$/
1037 0 0 if (ref $args eq 'HASH')
1041 0 0 if @$args % 2
1062 0 0 unless ref($args) =~ /^ARRAY|HASH$/
1064 0 0 if (ref $args eq 'HASH')
1068 0 0 if @$args % 2
1093 0 0 if ($db) { }
1101 0 0 if ($db_path)
1109 0 0 if $self->factory->stderr =~ /No alias or index file found/
1130 0 0 if @_
1152 0 0 unless (ref $_)
1154 0 0 unless -e $data
1156 0 0 unless $guesser->guess eq 'fasta'
1162 0 0 if (ref $_ eq 'ARRAY' and ref $data->[0] and $data->[0]->isa('Bio::Seq') || $data->[0]->isa('Bio::PrimarySeq'))
1170 0 0 unless my $fasio = 'Bio::SeqIO'->new(-'file', ">$fname", -'format', 'fasta')
1184 0 0 if (ref $_)
1186 0 0 if ($fmt eq 'fasta') { }
1198 0 0 unless my $fasio = 'Bio::SeqIO'->new(-'file', ">$fname", -'format', 'fasta')
1201 0 0 if ($data->isa('Bio::AlignIO')) { }
0 0 elsif ($data->isa('Bio::SeqIO')) { }
0 0 elsif ($data->isa('Bio::Align::AlignI')) { }
0 0 elsif ($data->isa('Bio::Seq') or $data->isa('Bio::PrimarySeq')) { }
1272 0 0 unless length $d
1290 0 0 unless $self->{'_cleanup_list'}
1293 0 0 if (exists $self->{'_results'}{'_file'})
1299 0 0 if ($self_file ne '' and $_ =~ /$self_file$/)
1303 0 0 if (/(\.[a-z0-9_]+)+$/i)
1308 0 0 if (-e $_ . '.psq') { }
0 0 elsif (-e $_ . '.nsq') { }
1354 0 0 if (grep /^$method$/, @Bio::Tools::Run::StandAloneBlastPlus::BlastMethods)
1355 0 0 if $self->is_remote
1358 0 0 if ($self->factory and $self->factory->can($method))
1361 0 0 if ($self->db_info and grep /^$method$/, keys %{$self->db_info;})