Index of /examples/perl/examples/advanced/ex06-bioperl

Name	Last modified	Size

Parent Directory		-
data_out/	2021-05-24 10:29	-
gene_anno.pl	2021-05-24 10:26	8.3K
gene_anno_cmd.out	2021-05-24 09:51	337
qlog/	2021-05-24 10:32	-
qsub/	2021-05-21 13:54	-

RCS Perl Example #6 - bioperl gene annotation

Directory Structure

gene_anno.pl - Perl script
gene_anno_cmd.out - the copy of screen output of execution of helloword.pl
../data_in/ - common data input directory stores the gene list file
../data_in/fanconi_genes.csv - gene list of interest
data_out/ - directory for store output result
data_out/fanconi_genes_anno.csv - gene annotation result
data_out/fanconi_genes_anno_from_qsub.csv - annotation output from qsub job
qlog/ - directory dedicated to store qsub job log
qsub/ - directory dedicated to put all qsub scripts
qsub/gene_anno.qsub - qsub script used to submit batch job

Notes

This is an advanced example using perl/5.28.1 and bioperl/1.7.2 module
provided to showcase how perl combines with other third party packages can achieve. Due to complicitity, comments are provided inside the script, rather than on the website.
In order to run this example, bioperl/1.7.2 and its dependancy perl/5.28.1 must be loaded first:


[ex06-bioperl]$ moulde load perl/5.28.1
[ex06-bioperl]$ module load bioperl/1.7.2
[ex06-bioperl]$ perl gene_anno.pl

The above command will output the annotation file in 'data_out/fanconi_genes_anno.csv'. And the command screen output is recorded in 'gene_anno_cmd.out'.
submit as job:


[ex06-bioperl]$ qsub qsub/gene_anno.qsub

After the job finished, there will be a gene_anno_job.oxxxx in qlog/ and an annotation file in 'data_out/genes_anno_from_job.csv'. This file shall be exactly same as 'data_out/fanconi_genes_anno.csv'.

Contact Information

Research Computing Services: help@scc.bu.edu

Note: RCS example programs are provided "as is" without any warranty of any kind. The user assumes the intire risk of quality, performance, and repai r of any defect. You are welcome to copy and modify any of the given examples for your own use.