| line |
true |
false |
branch |
|
144
|
0 |
0 |
if ($path ne '') { } |
|
156
|
0 |
0 |
unless open my $fh, "< $path" |
|
158
|
0 |
0 |
if $line =~ /^\s*$/ or $line =~ /inclusion threshold/ |
|
161
|
0 |
0 |
if ($line =~ /^\#\s*((hmmscan)\.*)/) { } |
|
|
0 |
0 |
elsif ($line =~ /^\#\s*HMMER ([\d\.]+)\s+\(([^\)]+)\)/) { } |
|
|
0 |
0 |
elsif ($line =~ /^\#\s+target HMM database:\s+(\S+)/) { } |
|
|
0 |
0 |
elsif ($line =~ /^\#\squery sequence (file|database):\s+(.+)/) { } |
|
|
0 |
0 |
elsif ($line =~ /^Query\:\s+(\S+)/) { } |
|
198
|
0 |
0 |
if $line =~ m[//] |
|
199
|
0 |
0 |
if $line =~ /^\s*$/ |
|
201
|
0 |
0 |
if ($line =~ /^Domain annotation/) { } |
|
|
0 |
0 |
elsif ($in_hit_scores and not $line =~ /^\s+--/ and not $line =~ /inclusion_threshold/) { } |
|
|
0 |
0 |
elsif ($line =~ /^>>\s*(\S+)/) { } |
|
|
0 |
0 |
elsif ($in_domain_scores and $line =~ /Alignments for each/) { } |
|
|
0 |
0 |
elsif ($in_domain_scores and not $line =~ /^\s*[>\#-]/) { } |
|
|
0 |
0 |
elsif ($line =~ /^\s+E-value\s+score/) { } |
|
205
|
0 |
0 |
if ($line =~ /No hits detected/) |
|
227
|
0 |
0 |
unless $hit_acc |
|
229
|
0 |
0 |
unless exists $data->{'hits'}{$hit_acc} |
|
231
|
0 |
0 |
if ($line =~ /\[No individual domains that/) |
|
239
|
0 |
0 |
if ($c[1] eq 'targets' or $c[1] eq 'reported' or $c[1] eq 'Fwd') |
|
248
|
0 |
0 |
if ($b ne $a) |
|
275
|
0 |
0 |
if ($path ne '') { } |
|
281
|
0 |
0 |
unless open FH, "$path" |
|
290
|
0 |
0 |
unless (@lines) |
|
296
|
0 |
0 |
if ($lines[$i] =~ /^#\s*((hmmscan)\.*)/) |
|
307
|
0 |
0 |
if ($lines[$i] =~ /^#\s*target HMM database:\s+(\S+)/) { } |
|
|
0 |
0 |
elsif ($lines[$i] =~ /^#\s*query sequence (file|database):\s+(.+)/) { } |
|
313
|
0 |
0 |
if $i > @lines |
|
316
|
0 |
0 |
if ($lines[$i] =~ /^Query:\s+(\S+)/) |
|
322
|
0 |
0 |
if ($lines[$i] =~ /^Scores for/) { } |
|
|
0 |
0 |
elsif (not $lines[$i] =~ /No hits detected that satisfy reporting thresholds/i) { } |
|
327
|
0 |
0 |
if $lines[$i] =~ /inclusion threshold/g |
|
340
|
0 |
0 |
if $i > @lines |
|
343
|
0 |
0 |
if ($lines[$i] =~ /^Domain annotation for each model/) |
|
347
|
0 |
0 |
if (not $lines[$i] =~ /No targets detected that satisfy reporting thresholds/) { } |
|
348
|
0 |
0 |
if ($lines[$i] =~ />>/) |
|
353
|
0 |
0 |
if (not defined $data->{'hit'}{$hit_index}) { } |
|
384
|
0 |
0 |
if ($path ne '') { } |
|
391
|
0 |
0 |
unless open FH, "$path" |
|
403
|
0 |
0 |
unless (@lines) |
|
428
|
0 |
0 |
if ($lines[$i] =~ /^((hmmpfam|hmmsearch)\.*)/) |
|
445
|
0 |
0 |
if ($lines[$i] =~ /^HMM file:\s+(\S+)/) { } |
|
|
0 |
0 |
elsif ($lines[$i] =~ /^Sequence (file|database):\s+(.+)/) { } |
|
|
0 |
0 |
elsif ($lines[$i] =~ /^per-sequence score cutoff:\s+(.+)/) { } |
|
|
0 |
0 |
elsif ($lines[$i] =~ /^per-domain score cutoff:\s+(.+)/) { } |
|
|
0 |
0 |
elsif ($lines[$i] =~ /^per-sequence E-value cutoff:\s+(.+)/) { } |
|
|
0 |
0 |
elsif ($lines[$i] =~ /^per-domain E-value cutoff:\s+(.+)/) { } |
|
459
|
0 |
0 |
if $i > @lines |
|
467
|
0 |
0 |
if ($lines[$i] =~ /^Query (?:HMM|sequence):\s+(.+)/) { } |
|
|
0 |
0 |
elsif ($lines[$i] =~ /^Accession:\s+(.+)/) { } |
|
|
0 |
0 |
elsif ($lines[$i] =~ /^Description:\s+(.+)/) { } |
|
477
|
0 |
0 |
if $i > @lines |
|
486
|
0 |
0 |
if ($lines[$i] =~ /^Scores for/) { } |
|
|
0 |
0 |
elsif (not $lines[$i] =~ /no hits above thresholds/i) { } |
|
488
|
0 |
0 |
if ($headers =~ /\bFr\b/) |
|
495
|
0 |
0 |
if ($find_frame) { } |
|
513
|
0 |
0 |
if $i > @lines |
|
521
|
0 |
0 |
if ($lines[$i] =~ /^Parsed for domains/) { } |
|
|
0 |
0 |
elsif (not $lines[$i] =~ /no hits above thresholds/) { } |
|
527
|
0 |
0 |
if ($find_frame) { } |
|
534
|
0 |
0 |
unless (defined $data->{'hit'}{$hit_index}) |
|
549
|
0 |
0 |
if $i > @lines |
|
552
|
0 |
0 |
if ($data->{'program'} =~ /hmmsearch/) |
|
556
|
0 |
0 |
if ($lines[$i] =~ /^Alignments of top-scoring domains/) |
|
568
|
0 |
0 |
if ($lines[$i] =~ /^(\S+): domain (\d+)/) |
|
572
|
0 |
0 |
if ($find_frame) |
|
573
|
0 |
0 |
if ($lines[$i] =~ /Fr = ([\-\d]+)/ or $lines[$i] =~ /\. frame ([\-\d]+)/) { } |
|
579
|
0 |
0 |
unless (defined $data->{'hit'}{$hit_index}) |
|
584
|
0 |
0 |
if ($lines[$i] =~ /\bRF\b/) |
|
598
|
0 |
0 |
if ($prot_seq =~ /\w+\s+(\d+|\-)\s+(\S+)\s+(\d+|\-)/) |
|
602
|
0 |
0 |
if $i > @lines |
|
611
|
0 |
0 |
if ($lines[$i] =~ /^\s+mu =\s+(-?\d+)/) { } |
|
|
0 |
0 |
elsif ($lines[$i] =~ /^\s+lambda =\s(-?\d+)/) { } |
|
|
0 |
0 |
elsif ($lines[$i] =~ /chi-sq statistic =\s(\d+)/) { } |
|
|
0 |
0 |
elsif ($lines[$i] =~ /Total sequences searched:\s*(\d+)/) { } |
|
|
0 |
0 |
elsif ($lines[$i] =~ /Whole sequence top hits/) { } |
|
|
0 |
0 |
elsif ($lines[$i] =~ /Domain top hits/) { } |
|
631
|
0 |
0 |
if $i > @lines |
|
662
|
0 |
0 |
if scalar keys %{$$h{'domains'};} == 0 |
|
667
|
0 |
0 |
if ($data->{'info'}{'program'} =~ /hmmsearch/) { } |
|
|
0 |
0 |
elsif ($data->{'info'}{'program'} =~ /hmmscan|hmmpfam/) { } |
|
671
|
0 |
0 |
$$HMM{$data->{'query'}}{'hmm_com_name'} ? : |
|
702
|
0 |
0 |
$HMM->{$hit}{'hmm_com_name'} ? : |
|
742
|
0 |
0 |
unless open my $OUT, ">$output_file" |
|
751
|
0 |
0 |
if ($data->{'hit'}{$hit}{'total_score'} >= $instructions->{'total_bit_cutoff'} and $data->{'hit'}{$hit}{'total_evalue'} <= $instructions->{'total_evalue_cutoff'}) |
|
758
|
0 |
0 |
if ($data->{'hit'}{$hit}{'domain'}{$domain}{'domain_score'} >= $instructions->{'domain_bit_cutoff'} and $data->{'hit'}{$hit}{'domain'}{$domain}{'domain_evalue'} <= $instructions->{'domain_evalue_cutoff'}) |
|
784
|
0 |
0 |
if (@hmma != @prota) |
|
797
|
0 |
0 |
if ($hmma[$i] ne '.') { } |
|
804
|
0 |
0 |
if $gap >= $DIST{$hmm_pos} |
|
829
|
0 |
0 |
if ($pos =~ /\d+/) { } |
|
851
|
0 |
0 |
if ($instructions->{'file_format'} eq 'mul') { } |
|
|
0 |
0 |
elsif ($instructions->{'file_format'} eq 'fasta' or $instructions->{'file_format'} eq 'fa') { } |
|
|
0 |
0 |
elsif ($instructions->{'file_format'} eq 'msf') { } |
|
919
|
0 |
0 |
if ($header_line == 0) |