labblouin.RegExpress module

Prosite pattern generator. Will turn an alignment into a regular expression

labblouin.RegExpress.check_if_is_align(dictionary_fasta)

will check the read fasta to see if is an alignment

labblouin.RegExpress.read_fasta(prefix)

Wll read the fasta, place sequences in a dictionary. Will break if not an alignment

labblouin.RegExpress.reg_express(fastas, l)

will create a matrix with the alignment, discard columns with gaps, and create a regular expression similar to prosite

labblouin.RegExpress.reg_express_col(col)

given a column of an alignment, return the string corresponding to the regular expression of such column

labblouin.RegExpress.strip_gaps(matrix)

given an alignment matrix, strip out the gap columns