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HAPPE-0.1.4
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مشاهده بیشتر
تبلیغات ما
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مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشترتوضیحات
A tool to visualize the haplotype pattern and various information in excel.
| ویژگی | مقدار |
|---|---|
| سیستم عامل | OS Independent |
| نام فایل | HAPPE-0.1.4 |
| نام | HAPPE |
| نسخه کتابخانه | 0.1.4 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Cong Feng |
| ایمیل نویسنده | congfeng97@gmail.com |
| آدرس صفحه اصلی | - |
| آدرس اینترنتی | https://pypi.org/project/HAPPE/ |
| مجوز | - |
# HAPPE
A tool to visualize the haplotype pattern and various information in excel.
Please cite this paper when using HAPPE for your publications
> Cong Feng, Xingwei Wang, Shishi Wu, Weidong Ning, Bo Song, Jianbin Yan, and Shifeng Cheng. 2022. “HAPPE: A Tool for Population Haplotype Analysis and Visualization in Editable Excel Tables.” Frontiers in Plant Science 13 (July): 927407. https://doi.org/10.3389/fpls.2022.927407.
## Installing HAPPE
There easiest way to install `HAPPE` is to use pip3.
```sh
pip3 install HAPPE
```
or you can clone the project to your local directory and installing it with:
```sh
python3 setup.py install --record log.txt
#if u want to uninstall the package:
#cat log.txt | xargs rm -rf
```
then you should have the `HAPPE` command available.
```sh
$ HAPPE -h
usage: HAPPE [-h] -g CONFIG -v GZVCF [-k KEEP] [-r REGION]
[-s SNPLIST] -i INF -c COLOR [-I SNPINF] [-R REF]
[-F FUNCANN] [-f | -x | -n] [-D DEPTH] [-d DEPTHBIN]
-o OUTPUT
show haplotype patterns in excel file./fengcong@caas.cn
optional arguments:
-h, --help show this help message and exit
-g CONFIG, --config CONFIG
config file.[required]
-v GZVCF, --gzvcf GZVCF
gzvcf, bcftools indexed.use to annotation and get
ref/alt basepair.[required]
-k KEEP, --keep KEEP keep sample, if u wana plot a subset of
--gzvcf.[optional]
-r REGION, --region REGION
if u wana plot a subset of --gzvcf, u can use this
option. if u use this option , ucant use -s
option[optional]
-s SNPLIST, --snplist SNPLIST
snp id list(format:chr_pos). if u use this option , u
cant use -r option.[optional]
-w TREEWIDTH, --treewidth TREEWIDTH
How many columns do you want to occupy for this tree
topology.(default=1000)[optional]
-i INF, --inf INF the information of each sample.[required]
-c COLOR, --color COLOR
the color of each sample.[required]
-I SNPINF, --snpinf SNPINF
more information about SNP.[optional]
-R REF, --Ref REF change Reference and color system.[optional]
-F FUNCANN, --FuncAnn FUNCANN
functional annotation file.[optional]
-f, --functional only functional SNP
-x, --coding only coding region SNP
-n, --noncoding only noncoding region SNP
-D DEPTH, --Depth DEPTH
depth dir for each sample.[optional]
-d DEPTHBIN, --Depthbin DEPTHBIN
Depth bin size.[optional,default:50]
-o OUTPUT, --output OUTPUT
output prefix
```
## Preparing config file
```ini
[software]
bgzip=
bcftools=
tabix=
```
## Preparing the vcf file
1. The SNP/INDEL ID must be in the format :`Chromosome_position`.
2. Only bi-allelic remains in vcf file.
2. Compress `vcf` to `vcf.gz` using bgzip
3. Use `bcftools index` to create an index for the `vcf.gz` file.
## Preparing the depth information
if you want to integrate the depth information, you need to prepare the depth file as follows:
1. Create a directory for each sample with the name of the sample.
2. using `mosdepth` to calc the depth of each position for each sample.
```sh
#example
mosdepth -f ref.fa -Q 0 sample1/sample1.Q0 path/to/sample1.bam
```
## Usage
```sh
"-g CONFIG", required parameter, give the paths to bcftools, bgzip and tabix in the CONFIG file.
"-v GZVCF", required parameter, input vcf file.
"-k SAMPLELIST", required parameter, list of samples to be retained, one sample per line.
"-r REGION", optional parameter, the genomic region to be displayed, format: chromosome: start-end.
"-s VARIANTLIST", optional parameter, the list of variant IDs you need to keep, using this parameter you cannot use the -r parameter.
"-w TREEWIDTH", optional parameter, the width of the tree topology.
"-i INFORMATION", optional parameter, additional sample information, the first column must be the sample ID.
"-c COLOR", optional parameter, Specify the color of each sample, the first column is the sample id and the second column is the color hex code.
"-I VARINFORMATION", optional parameter, Additional variant annotation information, such as GWAS p-value. the first colum is the variant id and each column is the annotation information with header.
"-f", optional parameter, Only the variant that changes the amino acid is retained.( Requires that the input vcf file has been annotated with SnpEff.)
"-x", optional parameter, Only the variant in the CDS region is retained.( Requires that the input vcf file has been annotated with SnpEff.)
"-n"， optional parameter, Only the variant in the non-coding region is retained.( Requires that the input vcf file has been annotated with SnpEff.)
"-D DIRECTORY"， optional parameter, This directory contains the depth information for each sample calculated using mosdepth, one directory per sample.
"-d WINDOWSIZE", optional parameter, window size for calculate normalized depth.
"-o PREFIX"， required parameter, output prefix.
```
## example
```sh
HAPPE \
-g config.ini \
-v test.vcf.gz \
-r chr7A:71669854-71670886 \
-i 1000_Inf.txt \
-c 1000.pop.color \
-F FunctionalAnnotation_v1__HCgenes_v1.0.TAB \
-D path/to/depth_data/ \
-f \
-o test
## each file of the prameter
## -g config.ini
# [software]
# bgzip=path_to/bgzip
# bcftools=path_to/bcftools
# tabix=path_to/tabix
## -i 1000_Inf.txt
## Just make sure the first column is the sample name.
# Sample_ID ... ...
# sample1 ... ...
## -c 1000.pop.color
## Just make sure the first column is the sample name and the second column is color code.
# Sample_ID color
# sample1 FF0000
# ... ...
## -F FunctionalAnnotation_v1__HCgenes_v1.0.TAB
## just make sure the first column is the gene name , and the forth column is the functional annotation.
# Gene_name XXX XXX function ... ...
# gene1 XXX XXX func1 ... ...
## -D path/to/depth_data/
##Make sure that the files *mosdepth.summary.txt and *per-base.bed.gz are in the directory for each sample in this directory.
```
نیازمندی
| مقدار | نام |
|---|---|
| - | argparse |
| - | pandas |
| - | numpy |
| - | scipy |
| - | sklearn |
| - | openpyxl |
| - | ConfigParser |
| - | dynamicTreeCut |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.6 | Python |
نحوه نصب
نصب پکیج whl HAPPE-0.1.4:
pip install HAPPE-0.1.4.whl
نصب پکیج tar.gz HAPPE-0.1.4:
pip install HAPPE-0.1.4.tar.gz