Helpful Scripts

Descriptions and usage for both in-house and external short scripts that may appeal to a large number of PMI users.

*** About these scripts ***
All of the scripts in this category are installed at TGen North on the aspen cluster, and at NAU on the monsoon cluster (if a script you want isn't the...
Tue, Oct 31, 2017 at 10:04 AM
getNCBI
Usage The getNCBI script uses Entrez Direct (eDirect) to download information from the NCBI database. A basic query can be made to the database using the...
Fri, Oct 27, 2017 at 2:23 PM
snpDensityMatrix
Usage The snpDensityMatrix script is used to read files from a snp pipeline output directory and output an interactive web page based visualization of snp...
Fri, Aug 24, 2018 at 9:27 AM
renameSamples
Usage The renameSamples script can be used to rename various pieces of data in a document, or rename any number of files in a directory, depending on the...
Thu, Oct 26, 2017 at 1:30 PM
getAssemblyStats2
Usage The getAssemblyStats2 script reads all fasta files in a given directory and prints additional information about the fasta files into an output file...
Wed, Jul 19, 2017 at 3:11 PM
rename
Usage The rename script uses the perl substitution expression on a list of file names and directories in working directory. Command Line: renam...
Thu, Jul 13, 2017 at 2:02 PM
gbk2fasta
Usage The gbk2fasta script converts fasta files from GenBank format to FASTA format. More information on various genetic sequence formats may be found he...
Thu, Jul 13, 2017 at 2:02 PM
deleteFiles_new
Usage The deleteFiles_new script deletes all files and directories from the scratch drive older than 180 days that match a certain regular expression. Th...
Thu, Jul 13, 2017 at 2:02 PM
yield_approximation
Usage The yield_approximation script estimates the depth of coverage given a file name, read length, and estimated genome size. Command Line: y...
Thu, Jul 13, 2017 at 2:02 PM
getNumReads
Usage The getNumReads script reads all files in the working directory with regular expression *.bam, and for each bam file, prints the file name, the cou...
Thu, Jul 13, 2017 at 2:02 PM