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remove R bindings + small corrections
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nicdemon committed Dec 11, 2024
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6 changes: 3 additions & 3 deletions README.md
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Expand Up @@ -8,7 +8,7 @@ Caribou was designed having these problems in mind. Therefore, it leverages mach

To do so, the workflow consists of 4 steps:
1. K-mers representation of genetic sequences
2. Bacterial sequences identification or host sequences exclusion
2. Bacterial sequences identification and host sequences exclusion
3. Top-down bacterial sequences classification
4. Output to user

Expand All @@ -19,7 +19,7 @@ To do so, the workflow consists of 4 steps:

**Analysis**

To use the Caribou pipeline for analysis, only a fasta file is required. It can either be gzipped or raw.
To use the Caribou pipeline for analysis, only a ``fasta`` file is required. It can either be gzipped or raw.

**Training**

Expand All @@ -41,6 +41,6 @@ For further information on how to install the package ses the [*installation* se
## Usage
The Caribou pipeline can be executed in it's entirety by supplying a config file from the linux command line.

Each step can also be executed by itself by using the corresponding scripts from the linux command line.
Each step can also be executed by itself using the corresponding scripts from the linux command line.

More details on scripts usage and options are discussed in the [*usage* section of the wiki](https://github.com/bioinfoUQAM/Caribou/wiki/Usage).
1 change: 0 additions & 1 deletion setup.cfg
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Expand Up @@ -35,7 +35,6 @@ scripts =
src/Caribou_extraction_train_cv.py
src/Caribou_classification_train_cv.py
src/Caribou_outputs.py
src/supplement/caribou.R
src/supplement/simulation.py
src/supplement/sklearn_tuning.py
data/subset_classes.py
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2 changes: 1 addition & 1 deletion src/Caribou_pipeline.py
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Expand Up @@ -9,7 +9,7 @@
from pathlib import Path
from outputs.out import Outputs
from data.build_data import build_load_save_data
from models.classification_old import ClassificationMethods
from models.classification import ClassificationMethods

__author__ = 'Nicolas de Montigny'

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70 changes: 0 additions & 70 deletions src/supplement/caribou.R

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