ivy.sequtil module

ivy.sequtil.find_stop_codons(seq, pos=0)

Find stop codons within sequence (in reading frame)

Parameters:

• seq (str) – A sequence
• pos (int) – Starting position. Defaults to 0.

Yields:

tuple – The index where the stop codon starts and which stop codon was found.

ivy.sequtil.finditer(seq, substr, start=0)

Find substrings within a sequence

Parameters:

• seq (str) – A sequence.
• substr (str) – A subsequence to search for
• start (int) – Starting index. Defaults to 0

Yields:

int – Starting indicies of where the substr was found in seq

ivy.sequtil.gapidx(seq, gapchar=u'-')

For a sequence with gaps, calculate site positions without gaps

Parameters:

• seq (list) – Each element of the list is one character in a sequence.
• gapchar (str) – The character gaps are coded as. Defaults to ‘-‘

Returns:

An array where the first element corresponds to range(number of characters that are not gaps) and the second element is the indicies of all characters that are not gaps.

Return type:

array