| line |
true |
false |
branch |
|
306
|
0 |
0 |
unless $line =~ /scientific \s name/msx
|
|
330
|
0 |
0 |
if @{$taxids;} < 2
|
|
342
|
0 |
0 |
if keys %taxid_for < @{$taxids;}
|
|
410
|
0 |
0 |
unless $strain
|
|
415
|
0 |
0 |
if defined $strain_key and length $strain_key
|
|
481
|
0 |
0 |
unless @_
|
|
485
|
0 |
0 |
if ($_[0] =~ / [^A-Za-z0-9] /msx and $_[1] =~ / [A-Za-z0-9] /msx or $_[0] =~ / [A-Za-z0-9] /msx and $_[1] =~ / [^A-Za-z0-9] /msx)
|
|
490
|
0 |
0 |
if ($_[0] =~ / [A-Za-z0-9] /msx or $_[1] =~ / [A-Za-z0-9] /msx)
|
|
491
|
0 |
0 |
lc $_[0] eq lc $_[1] ? :
|
|
710
|
0 |
0 |
if $taxon_id
|
|
717
|
0 |
0 |
if ($taxon_id)
|
|
726
|
0 |
0 |
if @taxonomy
|
|
746
|
0 |
0 |
$levels ? :
|
|
752
|
0 |
0 |
unless $taxonomy[0]
|
|
753
|
0 |
0 |
unless @taxonomy
|
|
757
|
0 |
0 |
wantarray ? :
|
|
767
|
0 |
0 |
wantarray ? :
|
|
804
|
0 |
0 |
&looks_like_number($seq_ids[0]) ? :
|
|
827
|
0 |
0 |
@{$_;} ? :
|
|
854
|
0 |
0 |
unless $taxon
|
|
856
|
0 |
0 |
if $taxon_n / $n < $threshold
|
|
862
|
0 |
0 |
wantarray ? :
|
|
903
|
0 |
0 |
if $node->is_terminal
|
|
912
|
0 |
0 |
if @levels > @max_levels
|
|
947
|
0 |
0 |
if ($target_for{'collapse'} < $target_for{'name'})
|
|
979
|
0 |
0 |
if (not $is_named and $rank >= $target_for{'name'})
|
|
985
|
0 |
0 |
if ($rank == $target_for{'collapse'})
|
|
1055
|
0 |
0 |
if (@miss_gis)
|
|
1085
|
0 |
0 |
unless $report
|
|
1107
|
0 |
0 |
if (@miss_gis)
|
|
1110
|
0 |
0 |
if (++$attempt > $MAX_ATTEMPT)
|
|
1116
|
0 |
0 |
unless ($batch_size)
|
|
1157
|
0 |
0 |
if $line =~ /$Bio::MUST::Core::Taxonomy::EMPTY_LINE/ or $line =~ /$Bio::MUST::Core::Taxonomy::COMMENT_LINE/
|
|
1167
|
0 |
0 |
if ($idm)
|
|
1193
|
0 |
0 |
if $family
|
|
1400
|
0 |
0 |
if wantarray
|
|
1405
|
0 |
0 |
unless $got_taxon and $exp_taxon
|
|
1452
|
0 |
0 |
if $source eq "ncbi"
|
|
1455
|
0 |
0 |
if $source eq "gtdb"
|
|
1478
|
0 |
0 |
$gi_mapper ? :
|
|
1493
|
0 |
0 |
unless $ret_code == 200
|
|
1499
|
0 |
0 |
if ($target =~ /\A gi_taxid/msx) { }
|
|
1512
|
0 |
0 |
if -e $gcanamefile
|
|
1513
|
0 |
0 |
if -e $gcanodefile
|
|
1519
|
0 |
0 |
if (-r $gcanamefile and -r $gcanodefile)
|
|
1525
|
0 |
0 |
if -e $cachefile
|
|
1528
|
0 |
0 |
if ($gi_mapper)
|
|
1539
|
0 |
0 |
if (-r file($tax_dir, "names.dmp") and -r file($tax_dir, "nodes.dmp"))
|
|
1598
|
0 |
0 |
unless $ret_code == 200
|
|
1609
|
0 |
0 |
if $line =~ /$Bio::MUST::Core::Taxonomy::EMPTY_LINE/ or $line =~ /$Bio::MUST::Core::Taxonomy::COMMENT_LINE/
|
|
1616
|
0 |
0 |
if $tax->is_merged($taxon_id)
|
|
1618
|
0 |
0 |
if $tax->is_merged($species_taxon_id)
|
|
1622
|
0 |
0 |
if $tax->is_deleted($taxon_id)
|
|
1629
|
0 |
0 |
if ($species_taxon_id == $taxon_id)
|
|
1781
|
0 |
0 |
unless $ret_code == 200
|
|
1784
|
0 |
0 |
if ($target =~ /metadata/msx)
|
|
1797
|
0 |
0 |
if -e $new_arcfile
|
|
1798
|
0 |
0 |
if -e $new_bacfile
|
|
1803
|
0 |
0 |
if (-r $new_arcfile and -r $new_bacfile) { }
|
|
1814
|
0 |
0 |
if -e $prok_file
|
|
1822
|
0 |
0 |
$_ eq 'superkingdom' ? :
|
|
1863
|
0 |
0 |
unless ($tree_ref->{$taxon_id})
|
|
1869
|
0 |
0 |
$count_for{$taxon} > 1 ? :
|
|
1872
|
0 |
0 |
if $uniq_name
|
|
1876
|
0 |
0 |
if ($rank eq "species")
|
|
1879
|
0 |
0 |
if ($gca =~ /^GCF/msx)
|
|
1888
|
0 |
0 |
if (@taxonomy)
|
|
1915
|
0 |
0 |
if (-r $name_file and -r $node_file)
|
|
1919
|
0 |
0 |
if (-r $gcanamefile and -r $gcanodefile)
|
|
1938
|
0 |
0 |
if ($line =~ /^accession/msx)
|
|
1961
|
0 |
0 |
if ($gcas)
|
|
1972
|
0 |
0 |
unless $children_for
|