Biotools

geneblocks.biotools.annotate_record(seqrecord, location='full', feature_type='feature', margin=0, **qualifiers)

Add a feature to a Biopython SeqRecord.

Parameters:

• seqrecord – The biopython seqrecord to be annotated.

• location – Either (start, end) or (start, end, strand). (strand defaults to +1)

• feature_type – The type associated with the feature

• margin – Number of extra bases added on each side of the given location.

• qualifiers – Dictionnary that will be the Biopython feature’s qualifiers attribute.

geneblocks.biotools.random_dna_sequence(length, probas=None, seed=None)

Return a random DNA sequence (“ATGGCGT…”) with the specified length.

Parameters:

• length – Length of the DNA sequence.

• proba – Frequencies for the different nucleotides, for instance probas={"A":0.2, "T":0.3, "G":0.3, "C":0.2}. If not specified, all nucleotides are equiprobable (p=0.25).

• seed – The seed to feed to the random number generator. When a seed is provided the random results depend deterministically on the seed, thus enabling reproducibility

geneblocks.biotools.sequences_differences(seq1, seq2)

Return the number of nucleotides that differ in the two sequences.

seq1, seq2 should be strings of DNA sequences e.g. “ATGCTGTGC”

geneblocks.biotools.sequences_differences_array(seq1, seq2)

Return an array [0, 0, 1, 0, …] with 1s for sequence differences.

seq1, seq2 should both be ATGC strings.