Script respository

This is my collection of various scripts (mostly bash and R) to automate simple repetive tasks.

Table of contents

• summary
• p2fdr
• calcContext
• collapseCSV
• ht
• lsfTophat
• seqimp2html
• seqimpSummarise
• dropbox
• csv2html
• dtCompare
• regExSelect

summary

Efficient script that reads a file and prints summary statistics (n, min, quartiles, max, median, mean).

Usage:

summary [-h] [-c column] filename
   -h     Print this help screen
   -c <1>        Column
   -m <1024>     Size of sort buffer (in MB)

p2fdr

Reads a tab separated file and uses the Benjamini and Hochberg method to calculate the FDR for the p-values in the specified column

Usage:

p2fdr [-h] [-H] [-m SIZE] -c <column> filename
   -h displays this help message
   -H ignores the first (header) row of the file
   -m use SIZE as main memory buffer for sort (default 100M).
   -c the number of the column with p-values
   Notice: this script doesn't support pipes or named pipes

calcContext.R

calcContext.R is an R function that reads an RNA secondary structure in vienna format and returns the structural context of each nucleotide. The output is a string of the same length of the input sequence where each character can take three values:

• p: paired nucleotide
• e: external nucleotide
• l: nucleotide is in a loop
• b: nucleotide is in a bulge

collapseCSV

This program reads a 2 fields tab separated files and using the first field as index it collapses the file putting the second field values all on the same line separated by commas. If the -s option is provided it sums up all the second field values having the same index. The input file must be sorted by the index.

ht

ht is a handy replacement for head that aligns columns in an orderly fashion. This script was written by Dennis Gascoigne at some point in 2010

lsfTophat

This script allows to run Tophat on an LSF system with a shared filesystem. It runs Tophat on a node using a temporary local folder to store output. Upon completion, it copies the output back to a user-specified path.

Usage:

usage: lsfTophat [-dnh] -p <params list> -o <out folder> -i <genome index> -f <fastq> -t <tophat binary>

This script makes your life easier when you have to run Tophat over LSF.
Tophat's output is stored in a temporary directory on the node (under /tmp) 
and upon colpletion the results are copied back to an output folder 
specified with the -o option.
If the -n option is specified the results are directly stored in the output
directory rather than in /tmp. This is useful if the tophat tmp data exceeds
the size available on /tmp.
OPTIONS:
   -h      Show this message
   -p      List of parameters to be passed to Tophat
   -o      Path where to save Tophat output (it's created if it doesn't exist)
   -i      Path to genome index
   -f      Path to Fastq file
   -t      Path to Tophat binary
   -d	   Dry run
   -n	   Write directly to the folder specified by -o

seqimp2html

Seqimp2html makes a folder with all QC plots from seqimp and an index.html file with links.

Usage:

seqimp2html <analysis_folder> <description.txt> <output_dir>
    <analysis folder>: path to the analysis folder created by SequenceImp
    <description.txt>: description file submitted to SequenceImp
    <output_dir>: path to the directory where to save output

seqimpSummarise

SeqimpSummarise reads a SeqIMP description files and produces a properly formatted summary table of counts. Usage:

seqimpSummarise <analysis_folder> <description.txt>
    <analysis folder>: path to the analysis folder created by SequenceImp
    <description.txt>: description file submitted to SequenceImp

dropbox

This script copies a file to an http-accessible folder, provides the URL pointing to it (and optionally a shortened URL) and optionally sends the the link via email. If the filename is not specified, the input is read from stdin and saved in the html folder Usage:

dropbox [-s] [-e <email>] [-h] [-u <url>] [-f <folder>] [-n] filename
Options:
  -s            Shorten the URL using Google APIs
  -e <email>    Email address to send the link to.
                Default: tleonardi@gmail.com
  -h            Print this help screen
  -u <URL>      Base URL of the http folder
                Default: http://www.ebi.ac.uk/~tl344/dropbox
  -f <folder>   Save the file in the specified http-accessible folder.
                Default: /homes/tl344/public_html/dropbox
  -n            Do not send an email
  -o <name>     Target file name
                Default: source filename or date-time.html if reading from stdin

csv2htm

This script creates an HTML table from a tab delimited file. Optionally, the table will use the DataTables JS library. The delimited input file can be provided as a filename argument or through stdin. Usage:

csv2htm [OPTIONS] input.csv
Options:
  -d       Specify delimiter to look for, instead of tab.
  --head   Treat first line as header, required for proper function of datatables
  --dt     Use Datables
  --help   Print this help message

dtCompare

This script allows the visual comparison of multiple bigWig files. It reads a set of matrices produced by deeptools and it generates multiple heatmaps in a single plot. It uses ggplot2 for plotting and allows various forms of sorting in the plots (see comments for the configuration parameters) Each input matrix can be generated with a command like this:

computeMatrix reference-point --referencePoint TSS --regionsFileName annotation.bed  --sortRegions "no" --outFileNameMatrix matrix.txt --scoreFileName path.to.bigWig --beforeRegionStartLength 1000 --afterRegionStartLength 1000 --binSize 10 --missingDataAsZero --outFileName outfile

regExSelect

This script for Adobe Illustrator selects text elements whose content matches a regular expression.

The search applies only to the selected objects. If no objects are selected it searches the whole document.

Tested in Illustrator CS6