csv file output in discoSNP

Question

[verissimoac]

Hi,

I've just downloaded discoSNP and am running the example data files. I've trying to run the ./discoSNP_to_csv.py following the directions in the manual. Although I get no error when executing the script, I get no .csv file but instead the info shows in my terminal. Besides, I get full sequence as well, and not just the four lines indicated in the manual. Seems like there is something missing in the python script? Or am I missing something?

Thanks for your help.

Ana

Answer 1

[pierre.peterlongo]

Hi Ana,

Thanks for your interest in discoSnp.

About the discoSNP_to_csv.py output: This scripts does not write files. Instead, as you mentioned it, it writes outputs in the terminal.

You can thus redirect this output into the file you want to create:

python discoSnp_to_csv.py ../discoRes_k_31_c_4_coherent.fa > my_file_name.csv

About the formatting. You're absolutely right. The current script separates fields using spaces ' ' while it should better use comma ','.

I updated a new version of this script on the discoSnp homepage: http://colibread.inria.fr/software/discosnp/

Best,

Pierre