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Merge pull request #12 from USDA-ARS-GBRU/iss1
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imporving GTF file handling
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@arivers
arivers authored May 17, 2022
2 parents b38747f + 0022c9f commit 8f43866
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1 change: 1 addition & 0 deletions README.md
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Expand Up @@ -215,6 +215,7 @@ Most pools require amplification before cloning to convert the ssDNA to dsDNA an
* [Addgene: Guide to Using Pooled Libraries](https://www.addgene.org/guides/pooled-libraries/)

<h4 style="color: #003087">Pooled CRISPR Data Analysis</h4>

After the experiment, the cells are collected and DNA is isolated. The target sequence is then amplified and adaptors for high-throughput sequencing added. Several data analysis pipelines have been developed to identify target sequences over-represented or under-represented in the pool. The manuscript by Wang et al. (2019) provides a protocol for using a high-quality tool with these capabilities.


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2 changes: 1 addition & 1 deletion bioconda.recipe/guidemaker/meta.yaml
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Expand Up @@ -66,4 +66,4 @@ extra:
- ravinpoudel
identifiers:
- biotools:GuideMaker
- doi:10.5281/zenodo.4849258
- doi:10.5281/zenodo.4849258
1 change: 0 additions & 1 deletion conda.recipe/meta.yaml
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{% set data = load_setup_py_data() %}

package:
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243 changes: 128 additions & 115 deletions coverage.xml
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2 changes: 1 addition & 1 deletion guidemaker/cli.py
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Expand Up @@ -191,7 +191,7 @@ def main(arglist: list = None):
target_bed_df=tf_df)
logger.info("Identify genomic features")
anno.get_annotation_features()
logger.info("Total number of CDS/locus in the input genome: %d" % anno.locuslen())
logger.info("Total number of %s in the input genome: %d" % anno.locuslen())
logger.info("Find genomic features closest the guides")
anno._get_nearby_features()
logger.info("Select guides that start between +%s and -%s of a feature start" %
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