The pyp_io Module

pyp_io contains several procedures for writing structures to and reading them from disc (e.g. using pickle() to store and retrieve A and A-inverse). It also includes a set of functions used to render strings as HTML or plaintext for use in generating output files.

Module Contents

a_inverse_from_file(inputfile) ⇒ matrix [#]

a_inverse_from_file() uses the Python pickle system for persistent objects to read the inverse of a relationship matrix from a file.

inputfile
The name of the input file.
Returns:
The inverse of a numerator relationship matrix.

a_inverse_to_file(pedobj, ainv='') [#]

a_inverse_to_file() uses the Python pickle system for persistent objects to write the inverse of a relationship matrix to a file.

pedobj
A PyPedal pedigree object.
filetag
A descriptor prepended to output file names.

dissertation_pedigree_to_file(pedobj) [#]

dissertation_pedigree_to_file() takes a pedigree in 'asdxfg' format and writes is to a file.

pedobj
A PyPedal pedigree object.

dissertation_pedigree_to_pedig_format(pedobj) [#]

dissertation_pedigree_to_pedig_format() takes a pedigree in 'asdbxfg' format, formats it into the form used by Didier Boichard's 'pedig' suite of programs, and writes it to a file.

pedobj
A PyPedal pedigree object.

dissertation_pedigree_to_pedig_format_mask(pedobj) [#]

dissertation_pedigree_to_pedig_format_mask() Takes a pedigree in 'asdbxfg' format, formats it into the form used by Didier Boichard's 'pedig' suite of programs, and writes it to a file. THIS FUNCTION MASKS THE GENERATION ID WITH A FAKE BIRTH YEAR AND WRITES THE FAKE BIRTH YEAR TO THE FILE INSTEAD OF THE TRUE BIRTH YEAR. THIS IS AN ATTEMPT TO FOOL PEDIG TO GET f_e, f_a et al. BY GENERATION.

pedobj
A PyPedal pedigree object.

dissertation_pedigree_to_pedig_interest_format(pedobj) [#]

dissertation_pedigree_to_pedig_interest_format() takes a pedigree in 'asdbxfg' format, formats it into the form used by Didier Boichard's parente program for the studied individuals file.

pedobj
A PyPedal pedigree object.

pyp_file_footer(ofhandle, caller="Unknown PyPedal routine") [#]

pyp_file_footer()

ofhandle
A Python file handle.
caller
A string indicating the name of the calling routine.
Returns:
None

pyp_file_header(ofhandle, caller="Unknown PyPedal routine") [#]

pyp_file_header()

ofhandle
A Python file handle.
caller
A string indicating the name of the calling routine.
Returns:
None

renderTitle(title_string, title_level="1") [#]

renderTitle() ... Produced HTML output by default.