AFLP data file input

[Sabine Dietz]

Hi Structure group:
I have gone through the googlegroup postings, and I know this issue is not a new one. I am running STRUCTURE 2.3.4 on a Mac. I have AFLP data, saved in the format STRUCTURE requires (attached AP.txt). I have used different text editors to eliminate any possible hidden codes. I use the first line, recessive alleles, and have the populations coded with an integer. 46 ind, 280 loci, missing value -1. Every time I try creating a new project, I get the same anser:
Bad Format in Data Source: Data entries are more than expected (282) at line 2 (I only have 280 data points). I did tell the wizard that I have "individual ID for each individual" and that I have "putative population origin" for each individual.
Any suggestion?
Thanks.

--
Sabine Dietz
28 High Marsh Rd
Sackville NB
E4L 1K2

[Vikram Chhatre]

Please post your parameters here. What is the first line in the data
file? It contains only zeros. Also, there are three empty lines up
top. They may not be creating problems, but its best to not have any
empty lines at the top.

If you have 280 data points, depending upon whether you are setting
POPDATA and POPFLAG options, the program expects a different number of
columns.

If say, for example, you only have POPDATA=1, it expects 282 columns
(1 for ind name, 1 for pop location info, plus 280 data points).

HTH
V

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[Sabine]

Hi Vikram;
My first line is the line for recessive allele, the same as shown in the sample file for AFLP's. I am not sure where the three empty lines are from, I don't have any when opening the file in excel or in a text editor?

I am using the "new Project" wizard, and the options I have are for individuals (first column) and Population (second column) which gives me then 282 data points per row, for all 92 (for ploidy level set at 2) rows, and 280 data points (zeros) for row one.
Sabine

> structure-software+unsub...@googlegroups.com.

[Felipe Ventorim]

I don’t know if these advices gonna solve your problem, but when I ran my AFLPs data, I don’t put 0 (zero) in the two first columns in the first row, and I prefer used the Textpad (text editor) instead of Notepad. Other important fact is check if you put haploid data. 

Felipe

[Julie Hebert]

Felipe,

Check and see if this works. If so, what I did was add two tabs to your first line so that you have the correct number of columns, then switched it to ASCII and back to UNIX so that the end of the lines were the correct format. If it doesn't work, I suggest posting your params file and your extraparams if you have one. I highly recommend using Notepad++ because you can see all of the extra characters and easily convert between file types.

Julie

[Julie Hebert]

Oops, I meant to address it to Sabine. (Sorry about that.)

[Sabine]

Hi Julie - this in fact worked just fine! I appreciate your help. I will need to take more care with the text editors.
Sabine

[chitra nehra]

hii I have AFLP data file . I have to run this on structure softwere. I tried to convert this data into structure file by using PGD softwere but every time after successful translation there is blank notepad output file. If i direclty run this file on structure there is error shows Bad format in data source.
plz help me

[Emily CAMARGO ACOSTA]

HI, I have the same problem with the data. I made this basic matrix and still not get to enter the data. q I doing wrong? #indi: 4, ploidy:2,#loci :5,missing data:9
00000
g1 1 0 1 0 1
g1 1 0 1 0 1
g2 1 1 1 0 1
g2 1 1 1 0 1
g3 0 0 9 1 0
g3 0 0 9 1 0
g4 1 1 0 1 9
g4 1 1 0 1 9