Description
Locate header, blank and nonsequence-like supplied lines.
Sequence text, ambiguity codes and encoded quality scores describe different information. Literal alphabets and Phred transformations can be checked without identifying a molecule or proving calibrated sequencing accuracy; missingness and reporting encodings require explicit conventions.
Locate header, blank and nonsequence-like supplied lines.
When to use this tool
Use FASTA Non Sequence Label Gap when checking the stated sequence token, ambiguity, quality symbol or local trimming convention.
How to use the tool and how it works
- Enter lines, headerPrefix. Use the units and conventions below.
- Run the tool. Correct any format, range, or cross-field input error before interpreting the output.
- Read headerIndices, blankIndices, nonSequenceIndices. Use the output convention below.
Locate header, blank and nonsequence-like supplied lines. Require nonempty headerPrefix; mark literal prefix matches, exactly empty lines, and remaining nonempty lines outside ASCII letters, asterisk, dot and hyphen.1
| Input field | Meaning and units | Accepted input |
|---|---|---|
| lines | Lines | Required. Array of text; maximum UTF-16 length 8192; maximum items 256. |
| headerPrefix | Header Prefix | Required. Text; maximum UTF-16 length 8192. |
| Output field | Interpretation | Returned shape |
|---|---|---|
| headerIndices | Header Indices | Required. Array of safe integer; maximum items 256. |
| blankIndices | Blank Indices | Required. Array of safe integer; maximum items 256. |
| nonSequenceIndices | Non Sequence Indices | Required. Array of safe integer; maximum items 256. |
{
"input": {
"lines": [
">id",
"ACGT",
"",
"note 1"
],
"headerPrefix": ">"
},
"output": {
"headerIndices": [
0
],
"blankIndices": [
2
],
"nonSequenceIndices": [
3
]
}
}Limitations and assumptions
- Whitespace-only lines are not blank and alphabet checks are permissive; complete FASTA structure and sequence biology are not validated.
- Inputs must satisfy both the field types and the cross-field conditions above. Invalid input causes an error; a successful false flag or documented placeholder is a different result.
Alternative or Complementary methods
Use a complete format-aware sequence/quality workflow and the appropriate reference/genetic code; assess biological identity and quality calibration independently.
References
Similar or alternative tools
- FASTA Iupac Ambiguity Cardinality
Expand one uppercase IUPAC DNA ambiguity symbol.
- Protein Stop Symbol Terminal Policy
Check stop-symbol placement under a supplied terminal policy.