polyA.converters package

Submodules

polyA.converters.cm_to_stockholm module

polyA.converters.cm_to_stockholm.convert(filename_cm: str, filename_out_sto: str, filename_out_matrix: str)

polyA.converters.cm_to_stockholm.get_alignment(alignment_array)

takes cm alignment split on newline and return string of chrom seq and subfam seq

polyA.converters.cm_to_stockholm.get_gap_penalties(file_contents)

returns gap_init and gap_ext

polyA.converters.cm_to_stockholm.get_info(info_array)

takes info line split by white space and assigns all info fields to variables

polyA.converters.cm_to_stockholm.get_score_matrix(file_contents)

grabs score matrix info from alignment file, puts it in correct format, returns string

polyA.converters.cm_to_stockholm.print_alignment(chrom_seq, subfam_seq, chrom, subfam, f_out_sto)

takes chrom and subfam names and chrom and subfam seqs and prints in stockholm format

polyA.converters.cm_to_stockholm.print_info(C, subfam, chrom, score, strand, start, stop, consensus_start, consensus_stop, flank, matrix_name, gap_init, gap_ext, f_out_sto)

prints all info in correct format for stockholm

polyA.converters.cm_to_stockholm.print_score_matrix(filename_out_matrix, score_matrix, matrix_name, background_freqs)

print score matrix to its own output file with extension “.matrix”

polyA.converters.cm_to_stockholm.read_file(filename_cm)

opens file and returns contents of file as one string

polyA.converters.rm_to_stockholm module

polyA.converters.rm_to_stockholm.convert(filename_rm: str, filename_out_sto: str, filename_out_matrix: str)

polyA.converters.rm_to_stockholm.get_alignment(alignment_array)

takes cm alignment split on newline and return string of chrom seq and subfam seq

polyA.converters.rm_to_stockholm.get_info(info_array)

takes info line split by white space and assigns all info fields to variables

polyA.converters.rm_to_stockholm.get_score_matrix(matrix_name)

grabs score matrix info from original matrix file, puts it in correct format, returns string

polyA.converters.rm_to_stockholm.print_alignment(chrom_seq, subfam_seq, chrom, subfam, f_out_sto)

takes chrom and subfam names and chrom and subfam seqs and prints in stockholm format

polyA.converters.rm_to_stockholm.print_info(C, subfam, chrom, score, strand, start, stop, consensus_start, consensus_stop, flank, matrix_name, f_out_sto)

prints all info in correct format for stockholm

polyA.converters.rm_to_stockholm.print_score_matrix(f_out_matrix, score_matrix, matrix_name)

print score matrix to its output file with extension “.matrix”

polyA.converters.rm_to_stockholm.read_file(filename_cm)

opens file and returns contents of file as one string

Module contents