Sequence File Errors

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Sequence File Errors

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Multiple Sequences Detected

When a sequence file is imported that has multiple sequences, a "Multiple sequences detected" error message displays and the Upload button is disabled. When the file is validated in the Edit Sequence window, an "Error, Multiple sequences detected" message displays.

_STNext-ImportBiosequence-MultipleSequenceError.png

_STNext-ValidateBiosequence-MultipleSequenceError.png

Validation Errors

When a sequence file is imported and has one or more of the below error types, a "Validation Errors" message displays and the Upload button is inactive:

_STNext-ImportBiosequence-ValidationErrors.png

Click the Edit button, and then click the Validate button in the Edit Sequence window to display the error type and the line number where the error occurs.

_STNext-ImportBiosequence-ValidationErrors_EditButton.png

_STNext-ImportBiosequence-ValidationErrors-EditBiosequence-ValidateButton.png

Note: White space in a sequence is ignored; a line which contains only white space is treated as a break between sequence queries.

No Sequence Detected

The file contains no sequence data.

_STNext-ImportBiosequence-ValidationErrors-NoSequenceDetected.png

Invalid Characters

The sequence contains a character that is not allowed ("%" in the example below).

_STNext-BiosequenceValidation-InvalidCharacters.png

Valid characters:

A-Z a-z ( ) [ ] ? -
^ | + * .  

As part of a valid quantifier:

0-9 { } , -

Examples

  • AZAASCGATGAH valid
  • AACC(GG){4} valid
  • 11CC22 valid - first and last numeric values are removed prior to upload, leaving the valid characters "CC"
  • AA2CC invalid - numeric value "2" is not part of a quantifier
  • AZS%HJJJHYS invalid %
  • ACGT'SS' invalid apostrophes
  • ACCG=GHSTH invalid =
  • 1,2 invalid - first and last numeric values are removed prior to upload, leaving just a comma on the line
  • 1-2 valid - leading and trailing numbers are removed prior to upload, leaving the hyphen, which system views as a comment
  • 1,2- invalid - hyphen is at the end and will not be removed, also causes an invalid (negative) number error

The exception to the last rule is if the system determines that the line is a comment. Comments are defined as:

  • A line beginning with '<' or '>'
  • A line containing only:
    • _
    • =
    • :
  • A line only the containing the characters ':' and '.'

Invalid Number Pattern

The sequence contains a valid character that is outside of a quantifier ("1" in the example below).

STNext-BiosequenceValidation-InvalidNumberPattern.png

Unbalanced Parenthesis

The sequence contains a mismatched quantity of parenthesis or brackets (missing ")" in the example below).

_STNext-BiosequenceValidation-UnbalancedParenthesis.png

Examples

  • AACCG(AA){1,3} valid
  • AACCG(AA{1,3} invalid
  • AACCG(AA){1,3 invalid
  • AACCD[AA(AA) invalid

Invalid Quantifier

The sequence contains a quantity indicator (quantifier) that is not well formed ("{aa}" in the example below); only 0-9, ',' and '-"' should appear within curly brackets. Additionally ',' and ''-" are mutually exclusive and can only appear once in each set of curly brackets. Note: When "-" or "," are not part of a valid quantifier, they are treated as invalid characters.

_STNext-BiosequenceValidation-InvalidQuantifier.png

Examples

  • {1,2} valid - comma within valid quantifier
  • {,3} valid
  • {1,} valid
  • {2} valid
  • {1-3} valid
  • {-1} valid
  • {1-} valid
  • {AA} invalid
  • {1,2,3} invalid
  • {1,,3} invalid
  • {1A2} invalid
  • {1,-2} invalid - negative number
  • 1,2 invalid - first and last numeric values are removed prior to upload, leaving just a comma on the line
  • 1-2, invalid
  • 1,2, invalid
  • 1,2- invalid
  • AA1-2BB invalid - hyphen is in the middle of sequence, considered invalid character