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Commit aff51033 authored by Venkat Malladi's avatar Venkat Malladi
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Merge branch '55-CheckGenomeMapPeaks' into 'master'

Fix fasta file refernce and add check for correct genome version

Closes #55 and #56

See merge request !49
parents 6cf95be0 8ca60229
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...@@ -3,8 +3,15 @@ ...@@ -3,8 +3,15 @@
All notable changes to this project will be documented in this file. All notable changes to this project will be documented in this file.
## [Unreleased] ## [Unreleased]
## [publish_1.0.6 ] - 2019-05-31
### Added ### Added
- MIT LICENSE - MIT LICENSE
- Check for correct genome input
- Check for correct output for motif serach
### Fixed
- Path to reference fasta file
## [publish_1.0.5 ] - 2019-05-16 ## [publish_1.0.5 ] - 2019-05-16
### Fixed ### Fixed
......
...@@ -4,7 +4,7 @@ Copyright (c) 2019, University of Texas Southwestern Medical Center. ...@@ -4,7 +4,7 @@ Copyright (c) 2019, University of Texas Southwestern Medical Center.
All rights reserved. All rights reserved.
Contributors: Spencer D. Barnes, Holly Ruess, Beibei Chen, Venkat S. Malladi Contributors: Spencer D. Barnes, Holly Ruess, Jeremy A. Mathews, Beibei Chen, Venkat S. Malladi
Department: Bioinformatic Core Facility, Department of Bioinformatics Department: Bioinformatic Core Facility, Department of Bioinformatics
......
# **CHIPseq Manual** # **CHIPseq Manual**
## Version 1.0.5 ## Version 1.0.6
## May 16, 2019 ## May 31, 2019
# BICF ChIP-seq Pipeline # BICF ChIP-seq Pipeline
......
...@@ -52,6 +52,6 @@ ...@@ -52,6 +52,6 @@
* Ewels P., Magnusson M., Lundin S. and Käller M. 2016. MultiQC: Summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32(19): 3047–3048. doi:[10.1093/bioinformatics/btw354](https://dx.doi.org/10.1093/bioinformatics/btw354) * Ewels P., Magnusson M., Lundin S. and Käller M. 2016. MultiQC: Summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32(19): 3047–3048. doi:[10.1093/bioinformatics/btw354](https://dx.doi.org/10.1093/bioinformatics/btw354)
17. **BICF ChIP-seq Analysis Workflow**: 17. **BICF ChIP-seq Analysis Workflow**:
* Spencer D. Barnes, Holly Ruess, Beibei Chen, & Venkat S. Malladi. (2019). BICF ChIP-seq Analysis Workflow (publish_1.0.5). Zenodo. doi:[10.5281/zenodo.2648844](https://doi.org/10.5281/zenodo.2648844) * Spencer D. Barnes, Holly Ruess, Jeremy A. Mathews, Beibei Chen, & Venkat S. Malladi. (2019). BICF ChIP-seq Analysis Workflow (publish_1.0.5). Zenodo. doi:[10.5281/zenodo.2648844](https://doi.org/10.5281/zenodo.2648844)
Please cite in publications: Pipeline was developed by BICF from funding provided by **Cancer Prevention and Research Institute of Texas (RP150596)**. Please cite in publications: Pipeline was developed by BICF from funding provided by **Cancer Prevention and Research Institute of Texas (RP150596)**.
...@@ -34,7 +34,7 @@ if (params.astrocyte) { ...@@ -34,7 +34,7 @@ if (params.astrocyte) {
referenceLocation = "/project/shared/bicf_workflow_ref" referenceLocation = "/project/shared/bicf_workflow_ref"
params.bwaIndex = "$referenceLocation/$params.genome" params.bwaIndex = "$referenceLocation/$params.genome"
params.chromSizes = "$referenceLocation/$params.genome/genomefile.txt" params.chromSizes = "$referenceLocation/$params.genome/genomefile.txt"
params.fasta = "$referenceLocation/$params.genome/genome.fa.txt" params.fasta = "$referenceLocation/$params.genome/genome.fa"
if (params.genome == 'GRCh37' || params.genome == 'GRCh38') { if (params.genome == 'GRCh37' || params.genome == 'GRCh38') {
params.genomeSize = 'hs' params.genomeSize = 'hs'
} else if (params.genome == 'GRCm38') { } else if (params.genome == 'GRCm38') {
......
#!/bin/Rscript #!/bin/Rscript
/* #*
* -------------------------------------------------------------------------- #* --------------------------------------------------------------------------
* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md) #* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
* -------------------------------------------------------------------------- #* --------------------------------------------------------------------------
*/ #*
# Load libraries # Load libraries
library("ChIPseeker") library("ChIPseeker")
......
#!/bin/Rscript #!/bin/Rscript
/* #*
* -------------------------------------------------------------------------- #* --------------------------------------------------------------------------
* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md) #* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
* -------------------------------------------------------------------------- #* --------------------------------------------------------------------------
*/ #*
# Load libraries # Load libraries
library("DiffBind") library("DiffBind")
......
...@@ -218,6 +218,13 @@ def main(): ...@@ -218,6 +218,13 @@ def main():
shlex.split("samtools flagstat %s" % (bam_filename)), shlex.split("samtools flagstat %s" % (bam_filename)),
stdout=temp_file) stdout=temp_file)
#Genome/Bad fastq File Check
file_check = open(bam_mapstats_filename).readlines()
percent = file_check[4].split('(')[1]
percent = percent.split('%')[0]
if float(percent) < 10:
raise Exception ('Mapped Genes too low: Check for correct Genotype')
# Remove sai files # Remove sai files
for sai_file in sai: for sai_file in sai:
os.remove(sai_file) os.remove(sai_file)
......
...@@ -21,7 +21,7 @@ def test_limited_peaks_singleend(): ...@@ -21,7 +21,7 @@ def test_limited_peaks_singleend():
def test_motif_search_singleend(): def test_motif_search_singleend():
assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC_memechip', 'ENCSR238SGC.fa')) assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC_memechip', 'ENCSR238SGC.fa'))
assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC_memechip', 'index.html')) assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC_memechip', 'index.html'))
assert os.path.getsize(os.path.join(test_output_path, 'ENCSR238SGC_memechip', 'ENCSR238SGC.fa')) > 0
@pytest.mark.singleskip_true @pytest.mark.singleskip_true
def test_motif_search_singleend(): def test_motif_search_singleend():
...@@ -39,3 +39,4 @@ def test_limited_peaks_pairedend(): ...@@ -39,3 +39,4 @@ def test_limited_peaks_pairedend():
def test_motif_search_pairedend(): def test_motif_search_pairedend():
assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA_memechip', 'ENCSR729LGA.fa')) assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA_memechip', 'ENCSR729LGA.fa'))
assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA_memechip', 'index.html')) assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA_memechip', 'index.html'))
assert os.path.getsize(os.path.join(test_output_path, 'ENCSR729LGA_memechip', 'ENCSR729LGA.fa')) > 0
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