PyPedal - BioHackersNet

[Python]으로 씌여진 Pedigree 분석 프로그램

http://pypedal.sourceforge.net/

PyPedal has been used to perform calculations on pedigrees as large as 600,000 animals and has been used in scientific research (Cole, Franke, and Leighton 2004; Cole 2007).

주요기능

Reading pedigree files in user-defined formats; 사용자정의 포맷으로 가계도 데이터 입력가능
Checking pedigree integrity (duplicate IDs, parents younger than offspring, etc.); 가계정보 체크기능
Generating summary information such as frequency of appearance in the pedigree file; 가계정보 요약기능
Reordering and renumbering of pedigree files. : 가계정보 재정렬 기능
Computation of the numerator relationship matrix (A) from a pedigree file using the tabular method; 가계 행렬 계산 기능
Inbreeding calculations for large pedigrees; 대형 가계를 위한 육종관련 계산 기능
Computation of average total and average individual coefficients of inbreeding and relationship; 육종관련 통계수치 계산 기능
Calculation of coefficients of partial inbreeding using an iterative tabulat method ( Lacy, Alaks, and Walsh 1996; Gulisija, Gianola, Weigel, and Toro 2006); iterative tabulat method를 이용한 partial inbreeding coefficients 계산기능
Calculation of coefficients of ancestral inbreeding using the methods of Ballou ( 1997) or Suwanlee et al. (2007); Ballou method 를 이용한 ancestral inbreeding coefficient 계산 기능
Decomposition of A into T and D such that A = T DT ;
Computation of the direct inverse of A (not accounting for inbreeding) using the method of Henderson ( 1976);
Computation of the direct inverse of A (accounting for inbreeding) using the method of Quaas ( 1976);
Storage of A and its inverse between user sessions as persistent Python objects using the pickle module to avoid unnecessary calculations;
Calculation of theoretical and actual effective population sizes;
Computation of effective founder number using the exact algorithm of Lacy ( 1989);
Computation of effective founder number using the approximate algorithm of Boichard et al. ( 1997);
Computation of effective ancestor number using the algorithms of Boichard et al. ( 1997);
Selection of subpedigrees containing all ancestors of an animal;
Identification of the common relatives of two animals;
Calculation of the inbreeding of offspring from a prospective mating;
Output to ASCII text files, including matrices, coefficients of inbreeding and relationship, and summary information;
Importation and exportation of GEDCOM 5.5 files;
Loading pedigrees from, and saving them to, MySQL, Postgres, and SQLite databases;
Simulation of pedigrees using an algorithm derived from that in Matvec 1.1a;

아래와 같은 확장이 필요하다.

(위 확장에서 볼수 있듯이, 다양한 네트워크 다이어그램들을 보여주는듯.)