grenaud/glactools

Need more details about program usepopsrootanc

congzhouczcz opened this issue · 4 comments

congzhouczcz commented

Hi ,
The commond line of program 'usepopsrootanc'
glactools usepopsrootanc [options]
What is the format of file ? the glac file contains root and ancestral samples?
Thanks!

congzhouczcz commented

What is the format of file 'pop to use as root' and 'pop to use as anc' ?
Thanks very much!

grenaud commented

Hello!
Suppose you have a file with the populations you want to use as outgroup and ancestor. In the case of hominin, it would be the chimp as outgroup and the Chimp/human ancestor as the ancestor. For example I would have the following

file1.acf.gz:

#ACF
#PG:union AltaiNean.acf.gz Denisova.acf.gz FrenchB.acf.gz YorubaB.acf.gz AustralianB.acf.gz 
#GITVERSION: 6e48e0efbfb131a6723830fa98f655a36da8c574
#DATE: 2019-12-02
#SQ	SN:1	LN:249250621
#SQ	SN:2	LN:243199373
#chr	coord	REF,ALT	root	anc	chimp	ChimpHumanAncestor
2	100022	A,N	0,0:0	0,0:0	1,0:0	1,0:0
2	100023	G,N	0,0:0	0,0:0	1,0:0	1,0:0
2	100024	A,N	0,0:0	0,0:0	1,0:0	1,0:0
2	100025	C,N	0,0:0	0,0:0	1,0:0	1,0:0
2	100026	A,N	0,0:0	0,0:0	1,0:0	1,0:0
2	100027	G,N	0,0:0	0,0:0	1,0:0	1,0:0
2	100028	A,N	0,0:0	0,0:0	1,0:0	1,0:0
2	100029	A,N	0,0:0	0,0:0	1,0:0	1,0:0
2	100030	C,N	0,0:0	0,0:0	1,0:0	1,0:0
2	100031	T,N	0,0:0	0,0:0	1,0:0	1,0:0
2	100032	T,N	0,0:0	0,0:0	1,0:0	1,0:0
2	100033	C,N	0,0:0	0,0:0	1,0:0	1,0:0
2	100034	A,N	0,0:0	0,0:0	1,0:0	1,0:0
2	100035	T,N	0,0:0	0,0:0	1,0:0	1,0:0
2	100036	T,N	0,0:0	0,0:0	1,0:0	1,0:0
2	100037	G,N	0,0:0	0,0:0	1,0:0	1,0:0

And I would have a second file without root and ancestral information:

file2.acf.gz:

#ACF
#PG:union AltaiNean.acf.gz Denisova.acf.gz FrenchB.acf.gz YorubaB.acf.gz AustralianB.acf.gz 
#GITVERSION: 6e48e0efbfb131a6723830fa98f655a36da8c574
#DATE: 2019-12-02
#SQ	SN:1	LN:249250621
#SQ	SN:2	LN:243199373
#chr	coord	REF,ALT	root	anc	AltaiNean	Denisova	FrenchB	YorubaB	AustralianB
2	100022	A,N	0,0:0	0,0:0	2,0:0	2,0:0	2,0:0	2,0:0	2,0:0
2	100023	G,N	0,0:0	0,0:0	2,0:0	2,0:0	2,0:0	2,0:0	2,0:0
2	100024	A,N	0,0:0	0,0:0	2,0:0	2,0:0	2,0:0	2,0:0	2,0:0
2	100025	C,N	0,0:0	0,0:0	2,0:0	2,0:0	2,0:0	2,0:0	2,0:0
2	100026	A,N	0,0:0	0,0:0	2,0:0	2,0:0	2,0:0	2,0:0	2,0:0
2	100027	G,N	0,0:0	0,0:0	2,0:0	2,0:0	2,0:0	2,0:0	2,0:0
2	100028	A,N	0,0:0	0,0:0	2,0:0	2,0:0	2,0:0	2,0:0	2,0:0
2	100029	A,N	0,0:0	0,0:0	2,0:0	2,0:0	2,0:0	2,0:0	2,0:0
2	100030	C,N	0,0:0	0,0:0	2,0:0	2,0:0	2,0:0	2,0:0	2,0:0
2	100031	T,N	0,0:0	0,0:0	2,0:0	2,0:0	2,0:0	2,0:0	2,0:0
2	100032	T,N	0,0:0	0,0:0	2,0:0	2,0:0	2,0:0	2,0:0	2,0:0
2	100033	C,N	0,0:0	0,0:0	2,0:0	2,0:0	2,0:0	2,0:0	2,0:0
2	100034	A,N	0,0:0	0,0:0	2,0:0	2,0:0	2,0:0	2,0:0	2,0:0
2	100035	T,N	0,0:0	0,0:0	2,0:0	2,0:0	2,0:0	2,0:0	2,0:0
2	100036	T,N	0,0:0	0,0:0	2,0:0	2,0:0	2,0:0	2,0:0	2,0:0
2	100037	G,N	0,0:0	0,0:0	2,0:0	2,0:0	2,0:0	2,0:0	2,0:0

First we will go into file1 and it take our two populations as our root and ancestor and put it into file3.acf.gz:

glactools usepopsrootanc file1.acf.gz chimp ChimpHumanAncestor > file3.acf.gz

file3.acf.gz will look like this:

#ACF
#PG:usepopsrootanc /tmp/temp.acf.gz chimp ChimpHumanAncestor 
#GITVERSION: 9d3e4107ea445a16737fb841e2181dabf31acac9
#DATE: 2020-04-02
#USEPOPASROOTANC: chimp chimp
#USEPOPASROOTANC#1
#	#ACF
#	#PG:union AltaiNean.acf.gz Denisova.acf.gz FrenchB.acf.gz YorubaB.acf.gz AustralianB.acf.gz 
#	#GITVERSION: 6e48e0efbfb131a6723830fa98f655a36da8c574
#	#DATE: 2019-12-02
#	#chr	coord	REF,ALT	root	anc	chimp	ChimpHumanAncestor
#SQ	SN:1	LN:249250621
#SQ	SN:2	LN:243199373
#chr	coord	REF,ALT	root	anc
2	100022	A,N	1,0:0	1,0:0
2	100023	G,N	1,0:0	1,0:0
2	100024	A,N	1,0:0	1,0:0
2	100025	C,N	1,0:0	1,0:0
2	100026	A,N	1,0:0	1,0:0
2	100027	G,N	1,0:0	1,0:0
2	100028	A,N	1,0:0	1,0:0
2	100029	A,N	1,0:0	1,0:0
2	100030	C,N	1,0:0	1,0:0
2	100031	T,N	1,0:0	1,0:0
2	100032	T,N	1,0:0	1,0:0
2	100033	C,N	1,0:0	1,0:0
2	100034	A,N	1,0:0	1,0:0
2	100035	T,N	1,0:0	1,0:0
2	100036	T,N	1,0:0	1,0:0
2	100037	G,N	1,0:0	1,0:0

Then you can use "replaceanc" to put the ancestral information into file2:

glactools replaceanc file2.acf.gz file3.acf.gz > file4.acf.gz

file4 should contain the same information as file to accept with the ancestral information of file1:

#ACF
#PG:replaceanc /tmp/temp2.acf.gz /tmp/file3.acf.gz 
#GITVERSION: 9d3e4107ea445a16737fb841e2181dabf31acac9
#DATE: 2020-04-02
#REPLACEANC:
#REPLACEANC#1
#	#ACF
#	#PG:union AltaiNean.acf.gz Denisova.acf.gz FrenchB.acf.gz YorubaB.acf.gz AustralianB.acf.gz 
#	#GITVERSION: 6e48e0efbfb131a6723830fa98f655a36da8c574
#	#DATE: 2019-12-02
#	#chr	coord	REF,ALT	root	anc	AltaiNean	Denisova	FrenchB	YorubaB	AustralianB
#REPLACEANC#2
#	#ACF
#	#PG:usepopsrootanc /tmp/temp.acf.gz chimp ChimpHumanAncestor 
#	#GITVERSION: 9d3e4107ea445a16737fb841e2181dabf31acac9
#	#DATE: 2020-04-02
#	#USEPOPASROOTANC: chimp chimp
#	#USEPOPASROOTANC#1
#	#	#ACF
#	#	#PG:union AltaiNean.acf.gz Denisova.acf.gz FrenchB.acf.gz YorubaB.acf.gz AustralianB.acf.gz 
#	#	#GITVERSION: 6e48e0efbfb131a6723830fa98f655a36da8c574
#	#	#DATE: 2019-12-02
#	#	#chr	coord	REF,ALT	root	anc	chimp	ChimpHumanAncestor
#	#chr	coord	REF,ALT	root	anc
#SQ	SN:1	LN:249250621
#SQ	SN:2	LN:243199373
#chr	coord	REF,ALT	root	anc	AltaiNean	Denisova	FrenchB	YorubaB	AustralianB
2	100022	A,N	1,0:0	1,0:0	2,0:0	2,0:0	2,0:0	2,0:0	2,0:0
2	100023	G,N	1,0:0	1,0:0	2,0:0	2,0:0	2,0:0	2,0:0	2,0:0
2	100024	A,N	1,0:0	1,0:0	2,0:0	2,0:0	2,0:0	2,0:0	2,0:0
2	100025	C,N	1,0:0	1,0:0	2,0:0	2,0:0	2,0:0	2,0:0	2,0:0
2	100026	A,N	1,0:0	1,0:0	2,0:0	2,0:0	2,0:0	2,0:0	2,0:0
2	100027	G,N	1,0:0	1,0:0	2,0:0	2,0:0	2,0:0	2,0:0	2,0:0
2	100028	A,N	1,0:0	1,0:0	2,0:0	2,0:0	2,0:0	2,0:0	2,0:0
2	100029	A,N	1,0:0	1,0:0	2,0:0	2,0:0	2,0:0	2,0:0	2,0:0
2	100030	C,N	1,0:0	1,0:0	2,0:0	2,0:0	2,0:0	2,0:0	2,0:0
2	100031	T,N	1,0:0	1,0:0	2,0:0	2,0:0	2,0:0	2,0:0	2,0:0
2	100032	T,N	1,0:0	1,0:0	2,0:0	2,0:0	2,0:0	2,0:0	2,0:0
2	100033	C,N	1,0:0	1,0:0	2,0:0	2,0:0	2,0:0	2,0:0	2,0:0
2	100034	A,N	1,0:0	1,0:0	2,0:0	2,0:0	2,0:0	2,0:0	2,0:0
2	100035	T,N	1,0:0	1,0:0	2,0:0	2,0:0	2,0:0	2,0:0	2,0:0
2	100036	T,N	1,0:0	1,0:0	2,0:0	2,0:0	2,0:0	2,0:0	2,0:0
2	100037	G,N	1,0:0	1,0:0	2,0:0	2,0:0	2,0:0	2,0:0	2,0:0

In this case I have created two superfluous files, depending on your level of comfort with Unix file descriptors, you can do the same process without creating intermediate files.

Hope this answers your questions, should I add this to the readme? let me know if I can close this issue.

grenaud commented

Is this fine? Can I close the issue?

congzhouczcz commented

Thank you very much, grenaud. I get it and now it works.
Thanks!