https://github.com/tleonardi/scripts
Various scripts that make my everyday life easier
https://github.com/tleonardi/scripts
Last synced: 10 months ago
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Various scripts that make my everyday life easier
- Host: GitHub
- URL: https://github.com/tleonardi/scripts
- Owner: tleonardi
- Created: 2014-01-08T14:05:37.000Z (over 12 years ago)
- Default Branch: master
- Last Pushed: 2017-12-04T15:21:31.000Z (over 8 years ago)
- Last Synced: 2025-02-21T12:47:49.645Z (over 1 year ago)
- Language: Shell
- Size: 37.1 KB
- Stars: 1
- Watchers: 3
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# Script respository
This is my collection of various scripts (mostly bash and R) to automate simple repetive tasks.
## Table of contents
- [summary](#summary)
- [p2fdr](#p2fdr)
- [calcContext](#calccontextr)
- [collapseCSV](#collapsecsv)
- [ht](#ht)
- [lsfTophat](#lsftophat)
- [seqimp2html](#seqimp2html)
- [seqimpSummarise](#seqimpsummarise)
- [dropbox](#dropbox)
- [csv2html](#csv2htm)
- [dtCompare](#dtcompare)
- [regExSelect](#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 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 -o -i -f -t
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
: path to the analysis folder created by SequenceImp
: description file submitted to SequenceImp
: 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
: path to the analysis folder created by SequenceImp
: 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 ] [-h] [-u ] [-f ] [-n] filename
Options:
-s Shorten the URL using Google APIs
-e Email address to send the link to.
Default: tleonardi@gmail.com
-h Print this help screen
-u Base URL of the http folder
Default: http://www.ebi.ac.uk/~tl344/dropbox
-f Save the file in the specified http-accessible folder.
Default: /homes/tl344/public_html/dropbox
-n Do not send an email
-o 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