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update new GuideCounter class name in README #68

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Jun 22, 2024
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update new GuideCounter class name in README #68

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913687c
mend
abearab Jun 19, 2024
b401953
add `GuideCounter` to README
abearab Jun 22, 2024
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10 changes: 5 additions & 5 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -59,15 +59,15 @@ A minor novelty here has enabled processing single, dual, or multiple sgRNA
CRISPR screens. Also, this approach can retain recombination events which can
occur in dual or higher order sgRNA CRISPR screens.

Currently, `Counter` class from the `ngs` module can process FASTQ files and generate counts for standard
Currently, `GuideCounter` class from the `ngs` module can process FASTQ files and generate counts for standard
CRISPR screens with [single](#dcas9-crisprai-single-sgrna-screens) or [dual](#crispri-dual-sgrna-screens)
guide design.

Here is a draft code to process FASTQ files and generate counts for an experiment with [CRISPRi-dual-sgRNA-screens](#crispri-dual-sgrna-screens):

```python
# Initialize the Counter object
counter = scp.Counter(cas_type = 'cas9', library_type = 'single_guide_design')
# Initialize the GuideCounter object
counter = scp.GuideCounter(cas_type = 'cas9', library_type = 'single_guide_design')

# Load the reference library
counter.load_library("<path-to-CRISPR-library-table>", sep = '\t', verbose = True, index_col=None)
Expand All @@ -90,7 +90,7 @@ Here is a draft code to process FASTQ files and generate counts for an experimen

```python
# Initialize the Counter object
counter = scp.Counter(cas_type = 'dCas9', library_type = 'dual_guide_design')
counter = scp.GuideCounter(cas_type = 'dCas9', library_type = 'dual_guide_design')

# Load the reference library
counter.load_library("<path-to-CRISPR-library-table>", sep = '\t', verbose = True, index_col=None)
Expand All @@ -108,7 +108,7 @@ counter.get_counts_matrix(
)
```

After this, you have `.counts_mat` calculated in the `Counter` object.
After this, you have `.counts_mat` calculated in the `GuideCounter` object.

___

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2 changes: 0 additions & 2 deletions screenpro/ngs/__init__.py
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Expand Up @@ -366,7 +366,6 @@ def build_counts_anndata(self, source='library', verbose=False):
X = self.counts_mat.T,
var = self._build_cas9_dual_guide_var_table(self.counts_mat, source='library')
)
adata.var['targetSource'] = 'library'

if source == 'recombinant':
counts_recombinants = {}
Expand All @@ -389,7 +388,6 @@ def build_counts_anndata(self, source='library', verbose=False):
var = var_table,
obs = adata.obs
)
adata.var['targetSource'] = 'recombinant'

if verbose: print('recombinant AnnData created.')

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