| lib/Bio/BPWrapper/SeqManipulations.pm | |||
|---|---|---|---|
| Criterion | Covered | Total | % |
| condition | 8 | 47 | 17.0 |
| line | !l | l&&!r | l&&r | condition |
|---|---|---|---|---|
| 145 | 19 | 0 | 0 | defined $opts{'prefix'} and $opts{'prefix'} =~ /^$/ |
| 333 | 0 | 0 | 0 | $type eq "dna" and $mon =~ /[atcg]/i |
| 0 | 0 | 0 | $type eq "protein" and $mon =~ /[ACDEFGHIKLMNPQRSTVWY]/i | |
| 0 | 0 | 0 | $type eq "protein" and $mon =~ /\*\s*$/ | |
| 413 | 0 | 0 | 0 | $opts{'no-revcom'} and $fm < 0 |
| 1100 | 0 | 0 | 0 | not $see_aa and $mono[$i] eq "-" |
| line | l | !l | condition |
|---|---|---|---|
| 147 | 19 | 0 | shift @ARGV || 'STDIN' |
| 160 | 2 | 17 | $opts{'input'} // "fasta" |
| 165 | 1 | 18 | $opts{'output'} // "fasta" |
| 352 | 0 | 0 | $optStr || die("a file with old-tab-new needed\n") |
| 497 | 0 | 0 | $opts{'codon-info'} || 'need a codon usage file in CUTG GCG format' |
| 621 | 0 | 0 | $filename || die("file not found: $filename\n") |
| 643 | 0 | 0 | '<' . $cls_file || die("cdhit clstr file not found: $cls_file\n") |
| 724 | 0 | 0 | $value || die("can't find file $value\n") |
| 970 | 1 | 0 | $opts{'anonymize'} // die("Tried to use option 'prefix' without using option 'anonymize'. Exiting...\n") |
| 1006 | 7 | 0 | $out_format || 'fas' |
| line | l | !l&&r | !l&&!r | condition |
|---|---|---|---|---|
| 333 | 0 | 0 | 0 | $type eq "dna" and $mon =~ /[atcg]/i or $type eq "protein" and $mon =~ /[ACDEFGHIKLMNPQRSTVWY]/i |
| 0 | 0 | 0 | $type eq "dna" and $mon =~ /[atcg]/i or $type eq "protein" and $mon =~ /[ACDEFGHIKLMNPQRSTVWY]/i or $type eq "protein" and $mon =~ /\*\s*$/ | |
| 455 | 0 | 0 | 0 | $aas[$i] eq "*" or $i == $#aas |