Problems with fastStructure

[DIANA LOPEZ]

Hi.

I´m trying to run fastStructure

python structure.py -K 10 --input=structure_tsv --output=prueba

but i obtained.

Traceback (most recent call last):
File "structure.py", line 3, in <module>
import fastStructure
File "admixprop.pxd", line 5, in init fastStructure (fastStructure.c:8424)
File "allelefreq.pxd", line 7, in init vars.admixprop (admixprop.c:5328)
ImportError: libgsl.so.0: cannot open shared object file: No such file or directory

Which may be happening?.

thanks in advance.

[Vikram Chhatre]

It appears you either don't have GNU Scientific Library or Python doesn't know where it is. Did you follow the tutorial for installation on Github pages?

V

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[DIANA LOPEZ]

Yes I am. I have repeated all the process 

Now Appears:

Traceback (most recent call last):

  File "structure.py", line 163, in <module>

    G = parse_bed.load(params['inputfile'])

  File "parse_bed.pyx", line 18, in parse_bed.load (parse_bed.c:1675)

    handle = open(file+'.fam','r')

Thanks in advance.

El viernes, 4 de abril de 2014 12:49:20 UTC+1, Vikram Chhatre escribió:

It appears you either don't have GNU Scientific Library or Python doesn't know where it is. Did you follow the tutorial for installation on Github pages?

V

On Friday, April 4, 2014, DIANA LOPEZ <dianal...@gmail.com> wrote:

Hi.

I´m trying to run fastStructure

python structure.py -K 10 --input=structure_tsv --output=prueba

but i obtained.

Traceback (most recent call last):
  File "structure.py", line 3, in <module>
    import fastStructure
  File "admixprop.pxd", line 5, in init fastStructure (fastStructure.c:8424)
  File "allelefreq.pxd", line 7, in init vars.admixprop (admixprop.c:5328)
ImportError: libgsl.so.0: cannot open shared object file: No such file or directory

Which may be happening?.

thanks in advance.

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[Vikram Chhatre]

Diana -

This is a different error from what you posted last time.

This error is related to parsing of the plink bed format data.  Anil may have some input for you on this matter.  In the meantime, you may want to make sure that your data is correctly formatted.

Vikram

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[DIANA LOPEZ]

Thanks.

I think this is my problem i don't sure about of the format of my data and if the instructions is Ok.

python structure.py -K 1 --input=structure_hyb --output=prueba 

or i need additional the numbers of individual or loci?

Thanks.

V

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[Vikram Chhatre]

The error has nothing to do with number of individuals or loci.  The program is unable to parse the bed format files correctly.  It assumes that you have three files in the current directory:

1. structure_hyb.bed

2. structure_hyb.bim

3. structure_hyb.fam

You can check the integrity of these files in PLINK.

V

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[DIANA LOPEZ]

Ok.

Now I understand my problem is that i have a file .txt that i obtained of stacks, but i don't had these files .bed .bim and .fam how i convert mi file txt to these it.

Thanks and sorry but i new with this program 

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[DIANA LOPEZ]

I continue to need to know how to transform my data in format .Txt to  .Bed .Fam and .Bim

Thanks

[臻]

use plink to create the binary files. 

[zeamne T]

Hi Diana,

I could be wrong.. but I think faststructure also has the option to use input files in the structure format, just that you have to remove the header of the locus names. I found this much easier to do than to use PLINK, because you first have to use PLINK-SEQ then PLINK...

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