LDBlockShow installation error
After using conda to install LDBlockShow, the above error occurred during use, prompting "Can't locate SVG.pm in @INC xxx /bin/ShowLDSVG line 24". The reason for this error is the lack of the SVG module of the Perl language. This note provides a method to solve problems during the installation and use of LDBlockShow.
Install LDBlockshow using conda
In Linux systems, first use conda to create a new environment, then activate the environment and run the installation command.
conda install -c bioconda ldblockshow
## Package Plan ##
environment location: /home/zhaojiwen/data_HD/miniconda3/envs/GWAS
added / updated specs:
- ldblockshow
The following packages will be downloaded:
package | build
---------------------------|-----------------
ldblockshow-1.40 | pl5262h9a82719_0 105 KB bioconda
openssl-3.0.12 | h7f8727e_0 5.2 MB http://mirrors.aliyun.com/anaconda/pkgs/main
perl-5.26.2 | h36c2ea0_1008 15.4 MB http://mirrors.aliyun.com/anaconda/cloud/conda-forge
perl-svg-2.84 | pl526_0 37 KB bioconda
------------------------------------------------------------
Total: 20.8 MB
The following NEW packages will be INSTALLED:
ldblockshow bioconda/linux-64::ldblockshow-1.40-pl5262h9a82719_0
perl anaconda/cloud/conda-forge/linux-64::perl-5.26.2-h36c2ea0_1008
perl-svg bioconda/linux-64::perl-svg-2.84-pl526_0
The following packages will be UPDATED:
openssl 3.0.11-h7f8727e_2 --> 3.0.12-h7f8727e_0
Proceed ([y]/n)?
Downloading and Extracting Packages
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
After the installation is completed, you can query it with the following command. If the following content is displayed, the installation is successful.
$ LDBlockShow
Usage: LDBlockShow -InVCF <in.vcf.gz> -OutPut <outPrefix> -Region chr1:10000-20000
-InVCF <str> Input SNP VCF Format
-OutPut <str> OutPut File of LD Blocks
-Region <str> In One Region to show LD info svg Figure
-SeleVar <int> Select statistic for deal. 1: D' 2: R^2 3/4:Both [1]
-SubPop <str> SubGroup Sample File List[ALLsample]
-BlockType <int> method to detect Block [beta] [1]
1. Block by PLINK (Gabriel method)
2. Solid Spine of LD RR/D' 3. Blockcut with self-defined RR/D'
4. FixBlock by input blocks files 5. No Block
-InGWAS <str> InPut GWAS Pvalue File(chr site Pvalue)
-InGFF <str> InPut GFF3 file to show Gene CDS and name
-BlockCut <float> 'Strong LD' cutoff and ratio for BlockType3[0.85:0.90]
-FixBlock <str> Input fixed block region
-MerMinSNPNum <int> merger color grids when SNPnumber over N[50]
-help Show more Parameters and help [hewm2008 v1.40]
Encountered an error when using LDBlockShow
Just after the installation is completed, if you use it directly, you may get a "Can't locate SVG.pm in @INC" error. You need to use cpan to install the SVG module.
Install CPAN
If perl and cpan are not installed in the system, you need to install cpan first. The method is as follows:
-
For Debian/Ubuntu systems:
bashCopy code
sudo apt-get install cpanminus
-
For Red Hat/CentOS systems:
bashCopy code
sudo yum install perl-App-cpanminus
After the installation is complete, use CPAN to install the SVG module as follows:
First, open a terminal and run the following command:
cpan
Then in the CPAN prompt, enter the following command to install theSVG module:
install SVG
CPAN will download, compile and install the SVG module and its dependencies.
cp lib/SVG/DOM.pm blib/lib/SVG/DOM.pm
cp lib/SVG/Extension.pm blib/lib/SVG/Extension.pm
cp lib/SVG/XML.pm blib/lib/SVG/XML.pm
cp lib/SVG/Element.pm blib/lib/SVG/Element.pm
cp lib/SVG.pm blib/lib/SVG.pm
The following prompt message will appear during the process:
After the installation is successful, the following information is displayed:
If you use the LDBlockShow command again at this time, the error message just now will not appear and you can use it normally.
How to use LDBlockShow
The required input file is in vcf format. After having the input file, run the following code to draw the LD inverted triangle heat map.
LDBlockShow -InVCF file.vcf \
-OutPut re5 -Region 1:49670000:50680000\
-OutPng -SeleVar 1
If you have GWAS data results and want to add the significance of the SNP site (small Manhattan plot) on the inverted triangle and above, just use the -InGWAS parameter directly.
The required GWAS example results are as follows:
$ head gwas.pvalue
chr11 24142640 0.00009
chr11 24142660 1.02e-9
chr11 24142669 1e-9
The execution command is as follows:
LDBlockShow -InVCF Test.vcf.gz \
-OutPut re2 -Region \
chr11:24100000:24200000 \
-InGWAS gwas.pvalue \
-OutPng -SeleVar 1
The above is a simple example of using LDBlockshow. For more information, please check the official help document.
参考资料：
https://github.com/hewm2008/LDBlockShow/blob/main/LDBlockShow_Manual_Chinese.pdf
https://blog.csdn.net/yijiaobani/article/details/127498536
https://anaconda.org/bioconda/ldblockshow
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