Comments (1)
The problems come from the format that is asked:
First, it asks for technical replicate files which end with _n.txt
, being n the number of technical replicate.
It is also related with how paths and file names are formed in the code. In lines such as:
These lines do not work if, instead of a directory, a single file is passed:
https://github.com/jcasadogp/bacterial_growth/blob/49c6309843c82d858494e0b2c66d5e1004c2653b/src/import_into_database/populate_db.py#L88-L89
From the previous lines we get the variable files_dir
. Here, it passes files_dir
as an argument to the .sh
file. It MUST be a directory; if not, the .sh
will give errors.
https://github.com/jcasadogp/bacterial_growth/blob/49c6309843c82d858494e0b2c66d5e1004c2653b/src/import_into_database/populate_db.py#L145-L146
from bacterial_growth.
Related Issues (10)
- Standardized ways to measure growth
- Biological replicates HOT 1
- Combination of user input parameters in --createInfoFile HOT 3
- test data set, example of how to run
- Antibiotic and carbon source data HOT 2
- Serial dilutions
- Displaying tables with BR, TR or perturbation id
- Missing values
- Plot one technical replicates
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