Functions | |
| def | a_inverse_to_file |
| def | a_inverse_from_file |
| def | dissertation_pedigree_to_file |
| def | dissertation_pedigree_to_pedig_format |
| def | dissertation_pedigree_to_pedig_interest_format |
| def | dissertation_pedigree_to_pedig_format_mask |
| def | pyp_file_header |
| def | pyp_file_footer |
| def | renderTitle |
| def | renderBodyText |
| def | pickle_pedigree |
| def | unpickle_pedigree |
| def | summary_inbreeding |
| def | save_ijk |
| def | load_from_gedcom |
| def | save_from_gedcom |
| def | save_to_gedcom |
| def PyPedal::pyp_io::a_inverse_from_file | ( | inputfile | ) |
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. |
Use the Python pickle system for persistent objects to read the inverse of a relationship matrix from a file.
| def PyPedal::pyp_io::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. |
Use the Python pickle system for persistent objects to write the inverse of a relationship matrix to a file.
| def PyPedal::pyp_io::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_file() takes a pedigree in 'asdxfg' format and writes is to a file.
| def PyPedal::pyp_io::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() 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.
| def PyPedal::pyp_io::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_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.
| def PyPedal::pyp_io::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. |
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.
| def PyPedal::pyp_io::load_from_gedcom | ( | infilename, | ||
messages = 'verbose', |
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standalone = 1, |
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missing_sex = 'u', |
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missing_parent = 0, |
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missing_name = 'Unknown Name', |
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missing_byear = '0001', |
||||
debug = 0 | ||||
| ) |
load_from_gedcom() reads and parses pedigree data that conform to a subset of the GEDCOM 5.5 specification. Not all valid GEDCOM are supported; unsupported tags are ignored.
| infilename | The file to which the matrix should be written. | |
| messages | Controls output to the screen | |
| standalone | Uses logging if called by a NewPedigree method | |
| missing_sex | Value assigned to an animal with unknown sex | |
| missing_parent | Value assigned to unknown parents | |
| missing_name | Name assigned by default | |
| missing_byear | VAlue assigned to unknown birth years | |
| debug | Flag turning debugging messages on (1) and off (0) |
load_from_gedcom() reads and parses pedigree data that conform to a subset of the GEDCOM 5.5 specification. Not all valid GEDCOM are supported; unsupported tags are ignored.
| def PyPedal::pyp_io::pickle_pedigree | ( | pedobj, | ||
filename = '' | ||||
| ) |
pickle_pedigree() pickles a pedigree.
| pedobj | An instance of a PyPedal pedigree object. | |
| filename | The name of the file to which the pedigree object should be pickled (optional). |
pickle_pedigree() pickles a pedigree.
| def PyPedal::pyp_io::pyp_file_footer | ( | ofhandle, | ||
caller = "Unknown PyPedal routine" | ||||
| ) |
pyp_file_footer() writes a footer to a page of PyPedal output.
| ofhandle | A Python file handle. | |
| caller | A string indicating the name of the calling routine. |
pyp_file_footer() writes a footer to a page of PyPedal output.
| def PyPedal::pyp_io::pyp_file_header | ( | ofhandle, | ||
caller = "Unknown PyPedal routine" | ||||
| ) |
pyp_file_header() writes a header to a page of PyPedal output.
| ofhandle | A Python file handle. | |
| caller | A string indicating the name of the calling routine. |
pyp_file_header() writes a header to a page of PyPedal output.
| def PyPedal::pyp_io::renderBodyText | ( | text_string | ) |
renderBodyText() renders page contents (produces HTML output by default).
renderBodyText() renders page contents (produces HTML output by default).
| def PyPedal::pyp_io::renderTitle | ( | title_string, | ||
title_level = "1" | ||||
| ) |
renderTitle() renders page titles (produces HTML output by default).
renderTitle() renders page titles (produces HTML output by default).
| def PyPedal::pyp_io::save_from_gedcom | ( | outfilename, | ||
| assembled | ||||
| ) |
save_from_gedcom() takes pedigree data parsed by load_from_gedcom() and writes it to a text file in an ASD format that PyPedal can easily read.
| outfilename | The file to which the matrix should be written. | |
| fam2ids | Dictionary mapping family IDs to parents and offspring | |
| missing_parent | Value assigned to unknown parents | |
| id2name | Dictionary mapping IDs to names | |
| id2birth | Dictionary mapping IDs to birth years |
save_from_gedcom() takes pedigree data parsed by load_from_gedcom() and writes it to a text file in an ASD format that PyPedal can easily read.
| def PyPedal::pyp_io::save_ijk | ( | pedobj, | ||
| nrm_filename | ||||
| ) |
save_ijk() saves an NRM to a file in the form "animal A" "animal B" "rAB". @type pedobj: NewPedigree object @param pedobj: The pedigree to which the NRM is attached @type nrm_filename: string @param nrm_filename: The file to which the matrix should be written. @rtype: integer @return: A save status indicator (0: failed, 1: success).
| def PyPedal::pyp_io::save_to_gedcom | ( | pedobj, | ||
| outfilename | ||||
| ) |
save_to_gedcom() writes a PyPedal NewPedigree object to a file in GEDCOM 5.5 format.
| pedobj | An instance of a PyPedal NewPedigree object | |
| filename | The file to which the matrix should be written |
save_to_gedcom() writes a PyPedal NewPedigree object to a file in GEDCOM 5.5 format.
| def PyPedal::pyp_io::summary_inbreeding | ( | f_metadata | ) |
summary_inbreeding() returns a string representation of the data contained in the 'metadata' dictionary contained in the output dictionary returned by pyp_nrm/pyp_inbreeding().
| f_metadata | Dictionary of inbreeding metadata. |
summary_inbreeding() returns a string representation of the data contained in the 'metadata' dictionary contained in the output dictionary returned by pyp_nrm/pyp_inbreeding().
| def PyPedal::pyp_io::unpickle_pedigree | ( | filename = '' |
) |
unpickle_pedigree() reads a pickled pedigree in from a file and returns the unpacked pedigree object.
| filename | The name of the pickle file. |
unpickle_pedigree() reads a pickled pedigree in from a file and returns the unpacked pedigree object.
1.5.3