offtracker 1.0.0__zip → 1.0.2__zip

{offtracker-1.0.0/offtracker.egg-info → offtracker-1.0.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: offtracker
-Version: 1.0.0
+Version: 1.0.2
 Summary: Track-seq data analysis
 Home-page: https://github.com/Lan-lab/offtracker
 Author: Runda Xu
@@ -26,7 +26,7 @@ Dependency
 ```bash
 # We recommend creating a new enviroment using mamba/conda to avoid compatibility problems
 # If you don't use mamba, just replace the code with conda 
-mamba create -n offtracker -c bioconda blast snakemake
+mamba create -n offtracker -c bioconda blast snakemake pybedtools
 ```
 
 
@@ -37,10 +37,11 @@ Installation
 # activate the environment
 conda activate offtracker
 
-# Download the offtracker from github:
-git clone https://github.com/Lan-lab/offtracker.git 
+# Direct installation with pip
+pip install offtracker
 
-# install
+# (Alternative) Download the offtracker from github
+git clone https://github.com/Lan-lab/offtracker.git 
 cd offtracker
 pip install .
 ```
@@ -78,8 +79,11 @@ offtracker_config.py -t 8 -g hg38 --blacklist hg38 \
 -r /Your_Path_To_Reference/hg38_genome.fa \
 -i /Your_Path_To_Reference/hg38_genome.chromap.index \
 -f /Your_Path_To_Fastq \
--o /Your_Path_To_Output \ # Default is outputting to /Your_Path_To_Fastq
---subfolder 0 # If different samples are in seperate folders, set this to 1
+-o /Your_Path_To_Output \ 
+--subfolder 0 
+
+# --subfolder: If different samples are in seperate folders, set this to 1
+# -o: Default is outputting to /Your_Path_To_Fastq
 
 # Run the snakemake program
 cd /Your_Path_To_Fastq
@@ -102,13 +106,17 @@ Analyzing the off-target sites
 ```bash
 # In this part, multiple samples in the same condition can be analyzed in a single run by pattern recogonization of sample names
 
-offtracker_analysis.py -g hg38 --name "HEK4" \ # the same as that in offtracker_candidates.py
---exp 'Cas9_HEK4.*293' \ # add one or multiple patterns of file name in regex
---control 'control' \ # add one or multiple patterns of file name in regex
+offtracker_analysis.py -g hg38 --name "HEK4" \
+--exp 'Cas9_HEK4.*293' \
+--control 'control' \
 --outname 'Cas9_HEK4_293' \
 -f /Your_Path_To_Output \
 --seqfolder /Your_Path_To_Candidates
 
+# --name: the same as that in offtracker_candidates.py
+# --exp/--control: add one or multiple patterns of file name in regex
+
+
 # This step will generate Trackseq_result_{outname}.csv
 # Intermediate files are saved in ./temp folder, which can be deleted 
 # Keeping the intermediate files can make the analysis faster if involving previously analyzed samples (e.g. using the same control samples for different analyses)

{offtracker-1.0.0 → offtracker-1.0.2}/README.md

@@ -14,7 +14,7 @@ Dependency
 ```bash
 # We recommend creating a new enviroment using mamba/conda to avoid compatibility problems
 # If you don't use mamba, just replace the code with conda 
-mamba create -n offtracker -c bioconda blast snakemake
+mamba create -n offtracker -c bioconda blast snakemake pybedtools
 ```
 
 
@@ -25,10 +25,11 @@ Installation
 # activate the environment
 conda activate offtracker
 
-# Download the offtracker from github:
-git clone https://github.com/Lan-lab/offtracker.git 
+# Direct installation with pip
+pip install offtracker
 
-# install
+# (Alternative) Download the offtracker from github
+git clone https://github.com/Lan-lab/offtracker.git 
 cd offtracker
 pip install .
 ```
@@ -66,8 +67,11 @@ offtracker_config.py -t 8 -g hg38 --blacklist hg38 \
 -r /Your_Path_To_Reference/hg38_genome.fa \
 -i /Your_Path_To_Reference/hg38_genome.chromap.index \
 -f /Your_Path_To_Fastq \
--o /Your_Path_To_Output \ # Default is outputting to /Your_Path_To_Fastq
---subfolder 0 # If different samples are in seperate folders, set this to 1
+-o /Your_Path_To_Output \ 
+--subfolder 0 
+
+# --subfolder: If different samples are in seperate folders, set this to 1
+# -o: Default is outputting to /Your_Path_To_Fastq
 
 # Run the snakemake program
 cd /Your_Path_To_Fastq
@@ -90,13 +94,17 @@ Analyzing the off-target sites
 ```bash
 # In this part, multiple samples in the same condition can be analyzed in a single run by pattern recogonization of sample names
 
-offtracker_analysis.py -g hg38 --name "HEK4" \ # the same as that in offtracker_candidates.py
---exp 'Cas9_HEK4.*293' \ # add one or multiple patterns of file name in regex
---control 'control' \ # add one or multiple patterns of file name in regex
+offtracker_analysis.py -g hg38 --name "HEK4" \
+--exp 'Cas9_HEK4.*293' \
+--control 'control' \
 --outname 'Cas9_HEK4_293' \
 -f /Your_Path_To_Output \
 --seqfolder /Your_Path_To_Candidates
 
+# --name: the same as that in offtracker_candidates.py
+# --exp/--control: add one or multiple patterns of file name in regex
+
+
 # This step will generate Trackseq_result_{outname}.csv
 # Intermediate files are saved in ./temp folder, which can be deleted 
 # Keeping the intermediate files can make the analysis faster if involving previously analyzed samples (e.g. using the same control samples for different analyses)

offtracker-1.0.2/offtracker/_version.py

@@ -0,0 +1 @@
+__version__ = "1.0.2"

{offtracker-1.0.0 → offtracker-1.0.2}/offtracker/mapping/Snakefile_Trackseq

@@ -11,7 +11,6 @@ name2 = nametype + '.' + suffix
 
 import os
 
-#所有的输出列表
 
 rule all:
     input:
@@ -174,20 +173,3 @@ rule bdg2bw_rv:
     shell:
         "{params.dir_script}/bedGraphToBigWig {input} {params.gl} {output}"
 
-#rule bwAdd:
-#    input:
-#        fw=os.path.join(output_dir,"{sample}.fw.scaled.bw"),
-#        rv=os.path.join(output_dir,"{sample}.rv.scaled.bw")
-#    threads:
-#        _threads
-#    output:
-#        os.path.join(output_dir,"{sample}." + BinSize + ".add.bdg")
-#    shell:
-#        """
-#        bigwigCompare --binSize {BinSize} -p {threads} --verbose -o {output} \
-#        --outFileFormat bedgraph \
-#        --bigwig1 {input.fw} \
-#        --bigwig2 {input.rv} \
-#        --operation add 
-#        """
-

{offtracker-1.0.0 → offtracker-1.0.2/offtracker.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: offtracker
-Version: 1.0.0
+Version: 1.0.2
 Summary: Track-seq data analysis
 Home-page: https://github.com/Lan-lab/offtracker
 Author: Runda Xu
@@ -26,7 +26,7 @@ Dependency
 ```bash
 # We recommend creating a new enviroment using mamba/conda to avoid compatibility problems
 # If you don't use mamba, just replace the code with conda 
-mamba create -n offtracker -c bioconda blast snakemake
+mamba create -n offtracker -c bioconda blast snakemake pybedtools
 ```
 
 
@@ -37,10 +37,11 @@ Installation
 # activate the environment
 conda activate offtracker
 
-# Download the offtracker from github:
-git clone https://github.com/Lan-lab/offtracker.git 
+# Direct installation with pip
+pip install offtracker
 
-# install
+# (Alternative) Download the offtracker from github
+git clone https://github.com/Lan-lab/offtracker.git 
 cd offtracker
 pip install .
 ```
@@ -78,8 +79,11 @@ offtracker_config.py -t 8 -g hg38 --blacklist hg38 \
 -r /Your_Path_To_Reference/hg38_genome.fa \
 -i /Your_Path_To_Reference/hg38_genome.chromap.index \
 -f /Your_Path_To_Fastq \
--o /Your_Path_To_Output \ # Default is outputting to /Your_Path_To_Fastq
---subfolder 0 # If different samples are in seperate folders, set this to 1
+-o /Your_Path_To_Output \ 
+--subfolder 0 
+
+# --subfolder: If different samples are in seperate folders, set this to 1
+# -o: Default is outputting to /Your_Path_To_Fastq
 
 # Run the snakemake program
 cd /Your_Path_To_Fastq
@@ -102,13 +106,17 @@ Analyzing the off-target sites
 ```bash
 # In this part, multiple samples in the same condition can be analyzed in a single run by pattern recogonization of sample names
 
-offtracker_analysis.py -g hg38 --name "HEK4" \ # the same as that in offtracker_candidates.py
---exp 'Cas9_HEK4.*293' \ # add one or multiple patterns of file name in regex
---control 'control' \ # add one or multiple patterns of file name in regex
+offtracker_analysis.py -g hg38 --name "HEK4" \
+--exp 'Cas9_HEK4.*293' \
+--control 'control' \
 --outname 'Cas9_HEK4_293' \
 -f /Your_Path_To_Output \
 --seqfolder /Your_Path_To_Candidates
 
+# --name: the same as that in offtracker_candidates.py
+# --exp/--control: add one or multiple patterns of file name in regex
+
+
 # This step will generate Trackseq_result_{outname}.csv
 # Intermediate files are saved in ./temp folder, which can be deleted 
 # Keeping the intermediate files can make the analysis faster if involving previously analyzed samples (e.g. using the same control samples for different analyses)

offtracker-1.0.0/offtracker/_version.py

@@ -1 +0,0 @@
-__version__ = "1.0.0"