A small tool for parsing files in the pedigree (.ped) format. The parser will create a family object for each family found in the pedigree file and a individual object for each individual found. The tool can be used to access information from ped files or convert the data to madeline2 format for drawing pedigree trees. Also it is possible to create family objects and individual object and print the in ped and madeline formats.
pip install ped_parser
Parse a file with family info, this can be a .ped file, a .fam, a .txt(alternative ped style) file or another ped based alternative.
.ped and .fam always have 6 columns, these are
Family_ID - '.' or '0' for unknown
Individual_ID - '.' or '0' for unknown
Paternal_ID - '.' or '0' for unknown
Maternal_ID - '.' or '0' for unknown
Sex - '1'=male; '2'=female; ['other', '0', '.']=unknown
Phenotype - '1'=unaffected, '2'=affected, ['-9', '0', '.']= missing
The other types must specify the columns in the header. Header always start with '#'. These files always start with the ped columns described above.
The following column names will be treated with care, which means that they will be used when outputting a madeline type of file or makes accesable variables in the parser.
InheritanceModel - a ';'-separated list of expected inheritance models.
Choices are
['AR','AR_hom','AR_denovo','AR_hom_denovo','AR_hom_dn','AR_dn','AR_compound','AR_comp','AD','AD_dn','AD_denovo','X','X_dn','X_denovo','NA','Na','na','.']
A proband is the first affected member of a pedigree coming to medical attention. They are annotated with:
Proband - 'Yes', 'No', 'Unknown' or '.'
A consultand is an individual who has sought genetic counseling or testing.
Consultand - 'Yes', 'No', 'Unknown' or '.'
Alive - 'Yes', 'No', 'Unknown' or '.'
##Usage##
ped_parser can be used as a standalone command line tool to convert ped files and ped like files to json or madeline2 format. Or just to get information about the content of a pedigree file.
When installed, try:
ped_parser --help
for more information.
When parsing the .ped file the following will be checked:
- That the family bindings are consistent and that all mandatory values exist and have correct values. Exceptions are raised if the number of columns differ between individuals
- That mother and father have correct gender, if not an exception is raised
- If two individuals are siblings
- Identify all trios (or duos) found in the pedigree
##Alternative .ped files##
ped_parser does also support modified .ped files (some users want to store extra family and/or individual information in the pedigree file). In this case ped_parser will look at the first 6 columns and work as described above. In this case use:
ped_parser infile.ped --family_type alt
Madeline2 is an excellent tool to draw pedigrees but they use there own input formats. ped_parser can now produce madeline2 input files from ped files by using
ped_parser input.ped --to_madeline [-o output.txt]
The following columns will be added to the madeline file:
'FamilyID', 'IndividualID', 'Gender', 'Father', 'Mother', 'Affected', 'Proband', 'Consultand', 'Alive'
Since only the first six of these columns are the standard ped format columns ped parser allows for alternative pedigree files with the following rules:
ped_parser input.ped --to_json [-o output.txt]
This is a list with lists that represents families, families have dictionaries that represents individuals like
[
[
{
'family_id:family_id',
'id':individual_id,
'sex':gender_code,
'phenotype': phenotype_code,
'mother': mother_id,
'father': father_id
},
{
...
}
],
[
]
]Ped like objects can be created from within a python program and convert them to ped, json or madeline output like this
>from ped_parser import Individual, Family
>outfile = open('my_family.ped','a')
>my_individuals = []
>my_individuals.append(Individual(
'proband',
family='1',
mother='mother',
father='father',
sex='1',
phenotype='2'
)
)
>my_individuals.append(Individual(
'mother',
family='1',
mother='0',
father='0',
sex='2',
phenotype='1'
)
)
>my_individuals.append(Individual(
'father',
'family'='1',
'mother'='0',
'father'='0',
'sex'='1',
'phenotype'='1'
)
)
>my_family = Family(family_id='1')
>for individual in my_individuals:
my_family.add_individual(individual)
>my_family.to_ped(outfile)