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@@ -0,0 +1 @@ +/HiNT-Package-2.2.8.tar.gz diff --git a/python-hint-package.spec b/python-hint-package.spec new file mode 100644 index 0000000..e4fb3f7 --- /dev/null +++ b/python-hint-package.spec @@ -0,0 +1,542 @@ +%global _empty_manifest_terminate_build 0 +Name: python-HiNT-Package +Version: 2.2.8 +Release: 1 +Summary: HiNT -- HiC for copy number vairations and translocations detection +License: MIT License +URL: https://github.com/suwangbio/HiNT_py3 +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/ff/a1/f1d40fad4546763d4df8b02aea3d07454d55a865c418c8163b1b124cbb6b/HiNT-Package-2.2.8.tar.gz +BuildArch: noarch + +Requires: python3-h5py +Requires: python3-numpy +Requires: python3-cooler +Requires: python3-pypairix +Requires: python3-pairtools +Requires: python3-scipy +Requires: python3-pandas +Requires: python3-scikit-learn +Requires: python3-multiprocess +Requires: python3-argparse +Requires: python3-pytabix + +%description +# HiNT +## A computational method for detecting copy number variations and translocations from Hi-C data + +## Summary +**HiNT** (**Hi**-C for copy **N**umber variation and **T**ranslocation detection), a computational method to detect CNVs and Translocations from Hi-C data. HiNT has three main components: **HiNT-PRE**, **HiNT-CNV**, and **HiNT-TL**. HiNT-PRE preprocesses Hi-C data and computes the contact matrix, which stores contact frequencies between any two genomic loci; both HiNT-CNV and HiNT-TL starts with HI-C contact matrix, predicts copy number segments, and inter-chromosomal translocations, respectively + +#### Overview of HiNT workflow: +<img src="https://github.com/suwangbio/HiNT/blob/master/images/HiNT_workflow.png" width="800"> + +## Installation + +### Dependencies +R and R packages + +1. [R >= 3.4](https://www.r-project.org/) +2. [mgcv](https://cran.r-project.org/web/packages/mgcv/index.html), [strucchange](https://cran.r-project.org/web/packages/strucchange/index.html), [doParallel](https://www.rdocumentation.org/packages/parallel/versions/3.4.1), [Cairo](https://cran.r-project.org/web/packages/Cairo/index.html), [foreach](https://cran.r-project.org/web/packages/optparse/index.html) + +Python and Python packages + +1. [python >= 3.5](https://www.python.org/) +2. [pyparix >= 0.3.0](https://github.com/4dn-dcic/pairix#pypairix), [cooler >= 0.7.4](https://github.com/mirnylab/cooler), [pairtools >= 0.2.2](https://github.com/mirnylab/pairtools), [numpy](https://www.scipy.org/install.html), [scipy](https://www.scipy.org/install.html), [pandas](https://pandas.pydata.org/), [sklearn](https://scikit-learn.org/stable/install.html), [multiprocessing](https://pypi.org/project/multiprocess/) + +Java and related tools (Optional: required when want to process Hi-C data with juicer tools) + +1. [Java (version >= 1.7)](https://www.java.com/en/download/) +2. [Juicer tools (1.8.9 is recommended)](https://github.com/aidenlab/juicer/wiki/Download) + +Perl + +1. [Perl (version >= 5)](https://www.perl.org/) + + +Other dependencies + +1. [samtools](http://www.htslib.org/doc/) (1.3.1+) +2. [BIC-seq2](http://www.math.pku.edu.cn/teachers/xirb/downloads/software/BICseq2/BICseq2/BICseq2-seg_v0.7.3.tar.gz) (0.7.3) ! This is optional: if you don't want to run HiNT-CNV, you don't need this package. [Download BICseq2, unzip it, and give the path of BICseq2-seg_v0.7.3 (/path/to/BICseq2-seg_v0.7.3)]. +3. [bwa](https://sourceforge.net/projects/bio-bwa/files/) (0.7.16+) ! This is optional: required only when your input is fastq +4. [tabix](https://sourceforge.net/projects/samtools/files/tabix/) (0.2.6) + +### Install HiNT + +* Method1: Install using conda (highly recommended) + + ``` $ conda install -c su hint``` + + or + + ``` $ conda install hint``` + +* Method2: Install from PyPI using pip. + + ``` $ pip install HiNT-Packages``` + +* Method3: Install manually + 1. Install HiNT dependencies + 2. Download HiNT ```git clone https://github.com/parklab/HiNT.git``` + 3. Go to HiNT directory, install it by ```$ python setup.py install ``` + + *** Type ```$ hint``` to test if HiNT successfully installed + +* Method 4: Run HiNT in a Docker container (highly recommended) + + ``` $ docker pull suwangbio/hint``` + + ``` $ docker run suwangbio/hint hint``` + + See details of the usage on HiNT page at [docker hub](https://hub.docker.com/r/suwangbio/hint) + +### Download reference files used in HiNT [HERE](https://www.dropbox.com/sh/2ufsyu4wvrboxxp/AABk5-_Fwy7jdM_t0vIsgYf4a?dl=0) + +1. Download HiNT references [HERE](https://www.dropbox.com/sh/qas48d7409t2syz/AACk5G2ngZ0vylLXsLFZXif_a?dl=0). Only hg19, hg38 and mm10 are available currently. Unzip it ```$ unzip hg19.zip ``` +2. Download HiNT background matrices [HERE](https://www.dropbox.com/sh/fyxx9u5g5vn57ez/AAAx-DtByKaU6HvTYyEUvCzRa?dl=0). Only hg19, hg38 and mm10 are available currently. Unzip it ```$ unzip hg19.zip ``` +3. Download BWA index files [HERE](https://www.dropbox.com/sh/l004df4108s6d3c/AAB6qtS95mBK_MdDZYlo2V-pa?dl=0). Only hg19, hg38 and mm10 are available currently. Unzip it ```$ unzip hg19.zip ``` + +## Quick Start + +* Download the test datasets from [HERE](https://www.dropbox.com/sh/z1rceh8ddnsdtj7/AAC0VuDu48eh_RtzKHipztkLa?dl=0) + +### HiNT-PRE +HiNT pre: Preprocessing Hi-C data. HiNT pre does alignment, contact matrix creation and normalization in one command line. + +```$ hint pre -d /path/to/hic_1.fastq.gz,/path/to/hic_2.fastq.gz -i /path/to/bwaIndex/hg19/hg19.fa --refdir /path/to/refData/hg19 --informat fastq --outformat cooler -g hg19 -n test -o /path/to/outputdir --pairtoolspath /path/to/pairtools --samtoolspath /path/to/samtools --coolerpath /path/to/cooler``` + +```$ hint pre -d /path/to/test.bam --refdir /path/to/refData/hg19 --informat bam --outformat juicer -g hg19 -n test -o /path/to/outputdir --pairtoolspath /path/to/pairtools --samtoolspath /path/to/samtools --juicerpath /path/to/juicer_tools.1.8.9_jcuda.0.8.jar``` + +use ```$ which samtools ``` ```$ which pairtools ``` ```$ which cooler ``` to get the absolute path of these tools, and ```/path/to/juicer_tools.1.8.9_jcuda.0.8.jar``` should be the path where you store this file + +see details and more options + +```$ hint pre -h ``` + +### HiNT-CNV +HiNT cnv: prediction of copy number information, as well as segmentation from Hi-C. + +```$ hint cnv -m contactMatrix.cool -f cooler --refdir /path/to/refDir/hg19 -r 50 -g hg19 -n test -o /path/to/outputDir --bicseq /path/to/BICseq2-seg_v0.7.3 -e MboI``` + +```$ hint cnv -m /path/to/4DNFIS6HAUPP.mcool::/resolutions/50000 -f cooler --refdir /path/to/refDir/hg38 -r 50 -g hg38 -n HepG2 --bicseq /path/to/BICseq2-seg_v0.7.3 -e DpnII``` + +```$ hint cnv -m /path/to/4DNFICSTCJQZ.hic -f juicer --refdir /path/to/refDir/hg38 -r 50 -g hg38 -n HepG2 --bicseq /path/to/BICseq2-seg_v0.7.3 -e DpnII``` + +```$ hint cnv -m /path/to/4DNFICSTCJQZ.hic -f juicer --refdir /path/to/refDir/hg38 -r 50 -g hg38 -n HepG2 --bicseq /path/to/BICseq2-seg_v0.7.3 -e DpnII --doiter``` + +```/path/to/BICseq2-seg_v0.7.3``` should be the path where you store this package + +see details and more options + +```$ hint cnv -h ``` + +### HiNT-TL +HiNT tl: interchromosomal translocations and breakpoints detection from +Hi-C inter-chromosomal interaction matrices. + +```$ hint tl -m /path/to/data_1Mb.cool,/path/to/data_100kb.cool --chimeric /path/to/test_chimeric.sorted.pairsam.gz --refdir /path/to/refDir/hg19 --backdir /path/to/backgroundMatrices/hg19 --ppath /path/to/pairix -f cooler -g hg19 -n test -o /path/to/outputDir``` + +```$ hint tl -m /path/to/4DNFIS6HAUPP.mcool::/resolutions/1000000,/path/to/4DNFIS6HAUPP.mcool::/resolutions/100000 -f cooler --refdir /path/to/refDir/hg38 --backdir /path/to/backgroundMatrices/hg38 -g hg38 -n 4DNFICSTCJQZ -c 0.05 --ppath /path/to/pairix -p 12``` + +```$ hint tl -m /path/to/4DNFICSTCJQZ.hic -f juicer --refdir /path/to/refData/hg38 --backdir /path/to/backgroundMatrices/hg38 -g hg38 -n 4DNFICSTCJQZ -c 0.05 --ppath /path/to/pairix -p 12 -o HiNTtransl_juicerOUTPUT``` + +use ```$ which pairix ``` to get the absolute path of pairix + +see details and more options + +```$ hint tl -h ``` + +## Output of HiNT +### HiNT-PRE output +In the HiNT-PRE output directory, you will find + +1. ```jobname.bam``` aligned lossless file in bam format +2. ```jobname_merged_valid.pairs.gz``` reads pairs in pair format +3. ```jobname_chimeric.sorted.pairsam.gz``` ambiguous chimeric read pairs used for breakpoint detection in [pairsam](https://github.com/mirnylab/pairtools) format +4. ```jobname_valid.sorted.deduped.pairsam.gz``` valid read pairs used for Hi-C contact matrix creation in [pairsam](https://github.com/mirnylab/pairtools) format +5. ```jobname.mcool``` Hi-C contact matrix in [cool](https://github.com/mirnylab/cooler) format +6. ```jobname.hic``` Hi-C contact matrix in [hic](https://github.com/aidenlab/juicer) format + +### HiNT-CNV output +In the HiNT-CNV output directory, you will find + +1. ```jobname_GAMPoisson.pdf``` the GAM regression result +2. ```segmentation/jobname_bicsq_allchroms.txt``` CNV segments with log2 copy ratio and p-values in txt file +3. ```segmentation/jobname_resolution_CNV_segments.png``` figure to visualize CNV segments +4. ```segmentation/jobname_bicseq_allchroms.l2r.pdf``` figure to visualize log2 copy ration in each bin (bin size = resolution you set) +5. ```segmentation/other_files``` intermediate files used to run BIC-seq +6. ```jonname_dataForRegression/*``` data used for regression as well as residuals after removing Hi-C biases + +### HiNT-TL output +In the HiNT-TL output directory, you will find + +1. ```jobname_Translocation_IntegratedBP.txt``` the final integrated translocation breakpoint +2. ```jobname_chrompairs_rankProduct.txt``` rank product predicted potential translocated chromosome pairs +3. ```otherFolders``` intermediate files used to identify the translocation breakpoints + + + + +%package -n python3-HiNT-Package +Summary: HiNT -- HiC for copy number vairations and translocations detection +Provides: python-HiNT-Package +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-HiNT-Package +# HiNT +## A computational method for detecting copy number variations and translocations from Hi-C data + +## Summary +**HiNT** (**Hi**-C for copy **N**umber variation and **T**ranslocation detection), a computational method to detect CNVs and Translocations from Hi-C data. HiNT has three main components: **HiNT-PRE**, **HiNT-CNV**, and **HiNT-TL**. HiNT-PRE preprocesses Hi-C data and computes the contact matrix, which stores contact frequencies between any two genomic loci; both HiNT-CNV and HiNT-TL starts with HI-C contact matrix, predicts copy number segments, and inter-chromosomal translocations, respectively + +#### Overview of HiNT workflow: +<img src="https://github.com/suwangbio/HiNT/blob/master/images/HiNT_workflow.png" width="800"> + +## Installation + +### Dependencies +R and R packages + +1. [R >= 3.4](https://www.r-project.org/) +2. [mgcv](https://cran.r-project.org/web/packages/mgcv/index.html), [strucchange](https://cran.r-project.org/web/packages/strucchange/index.html), [doParallel](https://www.rdocumentation.org/packages/parallel/versions/3.4.1), [Cairo](https://cran.r-project.org/web/packages/Cairo/index.html), [foreach](https://cran.r-project.org/web/packages/optparse/index.html) + +Python and Python packages + +1. [python >= 3.5](https://www.python.org/) +2. [pyparix >= 0.3.0](https://github.com/4dn-dcic/pairix#pypairix), [cooler >= 0.7.4](https://github.com/mirnylab/cooler), [pairtools >= 0.2.2](https://github.com/mirnylab/pairtools), [numpy](https://www.scipy.org/install.html), [scipy](https://www.scipy.org/install.html), [pandas](https://pandas.pydata.org/), [sklearn](https://scikit-learn.org/stable/install.html), [multiprocessing](https://pypi.org/project/multiprocess/) + +Java and related tools (Optional: required when want to process Hi-C data with juicer tools) + +1. [Java (version >= 1.7)](https://www.java.com/en/download/) +2. [Juicer tools (1.8.9 is recommended)](https://github.com/aidenlab/juicer/wiki/Download) + +Perl + +1. [Perl (version >= 5)](https://www.perl.org/) + + +Other dependencies + +1. [samtools](http://www.htslib.org/doc/) (1.3.1+) +2. [BIC-seq2](http://www.math.pku.edu.cn/teachers/xirb/downloads/software/BICseq2/BICseq2/BICseq2-seg_v0.7.3.tar.gz) (0.7.3) ! This is optional: if you don't want to run HiNT-CNV, you don't need this package. [Download BICseq2, unzip it, and give the path of BICseq2-seg_v0.7.3 (/path/to/BICseq2-seg_v0.7.3)]. +3. [bwa](https://sourceforge.net/projects/bio-bwa/files/) (0.7.16+) ! This is optional: required only when your input is fastq +4. [tabix](https://sourceforge.net/projects/samtools/files/tabix/) (0.2.6) + +### Install HiNT + +* Method1: Install using conda (highly recommended) + + ``` $ conda install -c su hint``` + + or + + ``` $ conda install hint``` + +* Method2: Install from PyPI using pip. + + ``` $ pip install HiNT-Packages``` + +* Method3: Install manually + 1. Install HiNT dependencies + 2. Download HiNT ```git clone https://github.com/parklab/HiNT.git``` + 3. Go to HiNT directory, install it by ```$ python setup.py install ``` + + *** Type ```$ hint``` to test if HiNT successfully installed + +* Method 4: Run HiNT in a Docker container (highly recommended) + + ``` $ docker pull suwangbio/hint``` + + ``` $ docker run suwangbio/hint hint``` + + See details of the usage on HiNT page at [docker hub](https://hub.docker.com/r/suwangbio/hint) + +### Download reference files used in HiNT [HERE](https://www.dropbox.com/sh/2ufsyu4wvrboxxp/AABk5-_Fwy7jdM_t0vIsgYf4a?dl=0) + +1. Download HiNT references [HERE](https://www.dropbox.com/sh/qas48d7409t2syz/AACk5G2ngZ0vylLXsLFZXif_a?dl=0). Only hg19, hg38 and mm10 are available currently. Unzip it ```$ unzip hg19.zip ``` +2. Download HiNT background matrices [HERE](https://www.dropbox.com/sh/fyxx9u5g5vn57ez/AAAx-DtByKaU6HvTYyEUvCzRa?dl=0). Only hg19, hg38 and mm10 are available currently. Unzip it ```$ unzip hg19.zip ``` +3. Download BWA index files [HERE](https://www.dropbox.com/sh/l004df4108s6d3c/AAB6qtS95mBK_MdDZYlo2V-pa?dl=0). Only hg19, hg38 and mm10 are available currently. Unzip it ```$ unzip hg19.zip ``` + +## Quick Start + +* Download the test datasets from [HERE](https://www.dropbox.com/sh/z1rceh8ddnsdtj7/AAC0VuDu48eh_RtzKHipztkLa?dl=0) + +### HiNT-PRE +HiNT pre: Preprocessing Hi-C data. HiNT pre does alignment, contact matrix creation and normalization in one command line. + +```$ hint pre -d /path/to/hic_1.fastq.gz,/path/to/hic_2.fastq.gz -i /path/to/bwaIndex/hg19/hg19.fa --refdir /path/to/refData/hg19 --informat fastq --outformat cooler -g hg19 -n test -o /path/to/outputdir --pairtoolspath /path/to/pairtools --samtoolspath /path/to/samtools --coolerpath /path/to/cooler``` + +```$ hint pre -d /path/to/test.bam --refdir /path/to/refData/hg19 --informat bam --outformat juicer -g hg19 -n test -o /path/to/outputdir --pairtoolspath /path/to/pairtools --samtoolspath /path/to/samtools --juicerpath /path/to/juicer_tools.1.8.9_jcuda.0.8.jar``` + +use ```$ which samtools ``` ```$ which pairtools ``` ```$ which cooler ``` to get the absolute path of these tools, and ```/path/to/juicer_tools.1.8.9_jcuda.0.8.jar``` should be the path where you store this file + +see details and more options + +```$ hint pre -h ``` + +### HiNT-CNV +HiNT cnv: prediction of copy number information, as well as segmentation from Hi-C. + +```$ hint cnv -m contactMatrix.cool -f cooler --refdir /path/to/refDir/hg19 -r 50 -g hg19 -n test -o /path/to/outputDir --bicseq /path/to/BICseq2-seg_v0.7.3 -e MboI``` + +```$ hint cnv -m /path/to/4DNFIS6HAUPP.mcool::/resolutions/50000 -f cooler --refdir /path/to/refDir/hg38 -r 50 -g hg38 -n HepG2 --bicseq /path/to/BICseq2-seg_v0.7.3 -e DpnII``` + +```$ hint cnv -m /path/to/4DNFICSTCJQZ.hic -f juicer --refdir /path/to/refDir/hg38 -r 50 -g hg38 -n HepG2 --bicseq /path/to/BICseq2-seg_v0.7.3 -e DpnII``` + +```$ hint cnv -m /path/to/4DNFICSTCJQZ.hic -f juicer --refdir /path/to/refDir/hg38 -r 50 -g hg38 -n HepG2 --bicseq /path/to/BICseq2-seg_v0.7.3 -e DpnII --doiter``` + +```/path/to/BICseq2-seg_v0.7.3``` should be the path where you store this package + +see details and more options + +```$ hint cnv -h ``` + +### HiNT-TL +HiNT tl: interchromosomal translocations and breakpoints detection from +Hi-C inter-chromosomal interaction matrices. + +```$ hint tl -m /path/to/data_1Mb.cool,/path/to/data_100kb.cool --chimeric /path/to/test_chimeric.sorted.pairsam.gz --refdir /path/to/refDir/hg19 --backdir /path/to/backgroundMatrices/hg19 --ppath /path/to/pairix -f cooler -g hg19 -n test -o /path/to/outputDir``` + +```$ hint tl -m /path/to/4DNFIS6HAUPP.mcool::/resolutions/1000000,/path/to/4DNFIS6HAUPP.mcool::/resolutions/100000 -f cooler --refdir /path/to/refDir/hg38 --backdir /path/to/backgroundMatrices/hg38 -g hg38 -n 4DNFICSTCJQZ -c 0.05 --ppath /path/to/pairix -p 12``` + +```$ hint tl -m /path/to/4DNFICSTCJQZ.hic -f juicer --refdir /path/to/refData/hg38 --backdir /path/to/backgroundMatrices/hg38 -g hg38 -n 4DNFICSTCJQZ -c 0.05 --ppath /path/to/pairix -p 12 -o HiNTtransl_juicerOUTPUT``` + +use ```$ which pairix ``` to get the absolute path of pairix + +see details and more options + +```$ hint tl -h ``` + +## Output of HiNT +### HiNT-PRE output +In the HiNT-PRE output directory, you will find + +1. ```jobname.bam``` aligned lossless file in bam format +2. ```jobname_merged_valid.pairs.gz``` reads pairs in pair format +3. ```jobname_chimeric.sorted.pairsam.gz``` ambiguous chimeric read pairs used for breakpoint detection in [pairsam](https://github.com/mirnylab/pairtools) format +4. ```jobname_valid.sorted.deduped.pairsam.gz``` valid read pairs used for Hi-C contact matrix creation in [pairsam](https://github.com/mirnylab/pairtools) format +5. ```jobname.mcool``` Hi-C contact matrix in [cool](https://github.com/mirnylab/cooler) format +6. ```jobname.hic``` Hi-C contact matrix in [hic](https://github.com/aidenlab/juicer) format + +### HiNT-CNV output +In the HiNT-CNV output directory, you will find + +1. ```jobname_GAMPoisson.pdf``` the GAM regression result +2. ```segmentation/jobname_bicsq_allchroms.txt``` CNV segments with log2 copy ratio and p-values in txt file +3. ```segmentation/jobname_resolution_CNV_segments.png``` figure to visualize CNV segments +4. ```segmentation/jobname_bicseq_allchroms.l2r.pdf``` figure to visualize log2 copy ration in each bin (bin size = resolution you set) +5. ```segmentation/other_files``` intermediate files used to run BIC-seq +6. ```jonname_dataForRegression/*``` data used for regression as well as residuals after removing Hi-C biases + +### HiNT-TL output +In the HiNT-TL output directory, you will find + +1. ```jobname_Translocation_IntegratedBP.txt``` the final integrated translocation breakpoint +2. ```jobname_chrompairs_rankProduct.txt``` rank product predicted potential translocated chromosome pairs +3. ```otherFolders``` intermediate files used to identify the translocation breakpoints + + + + +%package help +Summary: Development documents and examples for HiNT-Package +Provides: python3-HiNT-Package-doc +%description help +# HiNT +## A computational method for detecting copy number variations and translocations from Hi-C data + +## Summary +**HiNT** (**Hi**-C for copy **N**umber variation and **T**ranslocation detection), a computational method to detect CNVs and Translocations from Hi-C data. HiNT has three main components: **HiNT-PRE**, **HiNT-CNV**, and **HiNT-TL**. HiNT-PRE preprocesses Hi-C data and computes the contact matrix, which stores contact frequencies between any two genomic loci; both HiNT-CNV and HiNT-TL starts with HI-C contact matrix, predicts copy number segments, and inter-chromosomal translocations, respectively + +#### Overview of HiNT workflow: +<img src="https://github.com/suwangbio/HiNT/blob/master/images/HiNT_workflow.png" width="800"> + +## Installation + +### Dependencies +R and R packages + +1. [R >= 3.4](https://www.r-project.org/) +2. [mgcv](https://cran.r-project.org/web/packages/mgcv/index.html), [strucchange](https://cran.r-project.org/web/packages/strucchange/index.html), [doParallel](https://www.rdocumentation.org/packages/parallel/versions/3.4.1), [Cairo](https://cran.r-project.org/web/packages/Cairo/index.html), [foreach](https://cran.r-project.org/web/packages/optparse/index.html) + +Python and Python packages + +1. [python >= 3.5](https://www.python.org/) +2. [pyparix >= 0.3.0](https://github.com/4dn-dcic/pairix#pypairix), [cooler >= 0.7.4](https://github.com/mirnylab/cooler), [pairtools >= 0.2.2](https://github.com/mirnylab/pairtools), [numpy](https://www.scipy.org/install.html), [scipy](https://www.scipy.org/install.html), [pandas](https://pandas.pydata.org/), [sklearn](https://scikit-learn.org/stable/install.html), [multiprocessing](https://pypi.org/project/multiprocess/) + +Java and related tools (Optional: required when want to process Hi-C data with juicer tools) + +1. [Java (version >= 1.7)](https://www.java.com/en/download/) +2. [Juicer tools (1.8.9 is recommended)](https://github.com/aidenlab/juicer/wiki/Download) + +Perl + +1. [Perl (version >= 5)](https://www.perl.org/) + + +Other dependencies + +1. [samtools](http://www.htslib.org/doc/) (1.3.1+) +2. [BIC-seq2](http://www.math.pku.edu.cn/teachers/xirb/downloads/software/BICseq2/BICseq2/BICseq2-seg_v0.7.3.tar.gz) (0.7.3) ! This is optional: if you don't want to run HiNT-CNV, you don't need this package. [Download BICseq2, unzip it, and give the path of BICseq2-seg_v0.7.3 (/path/to/BICseq2-seg_v0.7.3)]. +3. [bwa](https://sourceforge.net/projects/bio-bwa/files/) (0.7.16+) ! This is optional: required only when your input is fastq +4. [tabix](https://sourceforge.net/projects/samtools/files/tabix/) (0.2.6) + +### Install HiNT + +* Method1: Install using conda (highly recommended) + + ``` $ conda install -c su hint``` + + or + + ``` $ conda install hint``` + +* Method2: Install from PyPI using pip. + + ``` $ pip install HiNT-Packages``` + +* Method3: Install manually + 1. Install HiNT dependencies + 2. Download HiNT ```git clone https://github.com/parklab/HiNT.git``` + 3. Go to HiNT directory, install it by ```$ python setup.py install ``` + + *** Type ```$ hint``` to test if HiNT successfully installed + +* Method 4: Run HiNT in a Docker container (highly recommended) + + ``` $ docker pull suwangbio/hint``` + + ``` $ docker run suwangbio/hint hint``` + + See details of the usage on HiNT page at [docker hub](https://hub.docker.com/r/suwangbio/hint) + +### Download reference files used in HiNT [HERE](https://www.dropbox.com/sh/2ufsyu4wvrboxxp/AABk5-_Fwy7jdM_t0vIsgYf4a?dl=0) + +1. Download HiNT references [HERE](https://www.dropbox.com/sh/qas48d7409t2syz/AACk5G2ngZ0vylLXsLFZXif_a?dl=0). Only hg19, hg38 and mm10 are available currently. Unzip it ```$ unzip hg19.zip ``` +2. Download HiNT background matrices [HERE](https://www.dropbox.com/sh/fyxx9u5g5vn57ez/AAAx-DtByKaU6HvTYyEUvCzRa?dl=0). Only hg19, hg38 and mm10 are available currently. Unzip it ```$ unzip hg19.zip ``` +3. Download BWA index files [HERE](https://www.dropbox.com/sh/l004df4108s6d3c/AAB6qtS95mBK_MdDZYlo2V-pa?dl=0). Only hg19, hg38 and mm10 are available currently. Unzip it ```$ unzip hg19.zip ``` + +## Quick Start + +* Download the test datasets from [HERE](https://www.dropbox.com/sh/z1rceh8ddnsdtj7/AAC0VuDu48eh_RtzKHipztkLa?dl=0) + +### HiNT-PRE +HiNT pre: Preprocessing Hi-C data. HiNT pre does alignment, contact matrix creation and normalization in one command line. + +```$ hint pre -d /path/to/hic_1.fastq.gz,/path/to/hic_2.fastq.gz -i /path/to/bwaIndex/hg19/hg19.fa --refdir /path/to/refData/hg19 --informat fastq --outformat cooler -g hg19 -n test -o /path/to/outputdir --pairtoolspath /path/to/pairtools --samtoolspath /path/to/samtools --coolerpath /path/to/cooler``` + +```$ hint pre -d /path/to/test.bam --refdir /path/to/refData/hg19 --informat bam --outformat juicer -g hg19 -n test -o /path/to/outputdir --pairtoolspath /path/to/pairtools --samtoolspath /path/to/samtools --juicerpath /path/to/juicer_tools.1.8.9_jcuda.0.8.jar``` + +use ```$ which samtools ``` ```$ which pairtools ``` ```$ which cooler ``` to get the absolute path of these tools, and ```/path/to/juicer_tools.1.8.9_jcuda.0.8.jar``` should be the path where you store this file + +see details and more options + +```$ hint pre -h ``` + +### HiNT-CNV +HiNT cnv: prediction of copy number information, as well as segmentation from Hi-C. + +```$ hint cnv -m contactMatrix.cool -f cooler --refdir /path/to/refDir/hg19 -r 50 -g hg19 -n test -o /path/to/outputDir --bicseq /path/to/BICseq2-seg_v0.7.3 -e MboI``` + +```$ hint cnv -m /path/to/4DNFIS6HAUPP.mcool::/resolutions/50000 -f cooler --refdir /path/to/refDir/hg38 -r 50 -g hg38 -n HepG2 --bicseq /path/to/BICseq2-seg_v0.7.3 -e DpnII``` + +```$ hint cnv -m /path/to/4DNFICSTCJQZ.hic -f juicer --refdir /path/to/refDir/hg38 -r 50 -g hg38 -n HepG2 --bicseq /path/to/BICseq2-seg_v0.7.3 -e DpnII``` + +```$ hint cnv -m /path/to/4DNFICSTCJQZ.hic -f juicer --refdir /path/to/refDir/hg38 -r 50 -g hg38 -n HepG2 --bicseq /path/to/BICseq2-seg_v0.7.3 -e DpnII --doiter``` + +```/path/to/BICseq2-seg_v0.7.3``` should be the path where you store this package + +see details and more options + +```$ hint cnv -h ``` + +### HiNT-TL +HiNT tl: interchromosomal translocations and breakpoints detection from +Hi-C inter-chromosomal interaction matrices. + +```$ hint tl -m /path/to/data_1Mb.cool,/path/to/data_100kb.cool --chimeric /path/to/test_chimeric.sorted.pairsam.gz --refdir /path/to/refDir/hg19 --backdir /path/to/backgroundMatrices/hg19 --ppath /path/to/pairix -f cooler -g hg19 -n test -o /path/to/outputDir``` + +```$ hint tl -m /path/to/4DNFIS6HAUPP.mcool::/resolutions/1000000,/path/to/4DNFIS6HAUPP.mcool::/resolutions/100000 -f cooler --refdir /path/to/refDir/hg38 --backdir /path/to/backgroundMatrices/hg38 -g hg38 -n 4DNFICSTCJQZ -c 0.05 --ppath /path/to/pairix -p 12``` + +```$ hint tl -m /path/to/4DNFICSTCJQZ.hic -f juicer --refdir /path/to/refData/hg38 --backdir /path/to/backgroundMatrices/hg38 -g hg38 -n 4DNFICSTCJQZ -c 0.05 --ppath /path/to/pairix -p 12 -o HiNTtransl_juicerOUTPUT``` + +use ```$ which pairix ``` to get the absolute path of pairix + +see details and more options + +```$ hint tl -h ``` + +## Output of HiNT +### HiNT-PRE output +In the HiNT-PRE output directory, you will find + +1. ```jobname.bam``` aligned lossless file in bam format +2. ```jobname_merged_valid.pairs.gz``` reads pairs in pair format +3. ```jobname_chimeric.sorted.pairsam.gz``` ambiguous chimeric read pairs used for breakpoint detection in [pairsam](https://github.com/mirnylab/pairtools) format +4. ```jobname_valid.sorted.deduped.pairsam.gz``` valid read pairs used for Hi-C contact matrix creation in [pairsam](https://github.com/mirnylab/pairtools) format +5. ```jobname.mcool``` Hi-C contact matrix in [cool](https://github.com/mirnylab/cooler) format +6. ```jobname.hic``` Hi-C contact matrix in [hic](https://github.com/aidenlab/juicer) format + +### HiNT-CNV output +In the HiNT-CNV output directory, you will find + +1. ```jobname_GAMPoisson.pdf``` the GAM regression result +2. ```segmentation/jobname_bicsq_allchroms.txt``` CNV segments with log2 copy ratio and p-values in txt file +3. ```segmentation/jobname_resolution_CNV_segments.png``` figure to visualize CNV segments +4. ```segmentation/jobname_bicseq_allchroms.l2r.pdf``` figure to visualize log2 copy ration in each bin (bin size = resolution you set) +5. ```segmentation/other_files``` intermediate files used to run BIC-seq +6. ```jonname_dataForRegression/*``` data used for regression as well as residuals after removing Hi-C biases + +### HiNT-TL output +In the HiNT-TL output directory, you will find + +1. ```jobname_Translocation_IntegratedBP.txt``` the final integrated translocation breakpoint +2. ```jobname_chrompairs_rankProduct.txt``` rank product predicted potential translocated chromosome pairs +3. ```otherFolders``` intermediate files used to identify the translocation breakpoints + + + + +%prep +%autosetup -n HiNT-Package-2.2.8 + +%build +%py3_build + +%install +%py3_install +install -d -m755 %{buildroot}/%{_pkgdocdir} +if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi +if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi +if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi +if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi +pushd %{buildroot} +if [ -d usr/lib ]; then + find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/lib64 ]; then + find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/bin ]; then + find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/sbin ]; then + find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst +fi +touch doclist.lst +if [ -d usr/share/man ]; then + find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst +fi +popd +mv %{buildroot}/filelist.lst . +mv %{buildroot}/doclist.lst . + +%files -n python3-HiNT-Package -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Mon May 29 2023 Python_Bot <Python_Bot@openeuler.org> - 2.2.8-1 +- Package Spec generated @@ -0,0 +1 @@ +f95b22f554010fd4f14bbf56c7dab3cf HiNT-Package-2.2.8.tar.gz |