Stephen Kelly stevekm

## find_Rnw.sh
#!/bin/bash

# look in my /Users/ dir
# look for the .Rnw files
# suppress the permission denied messages with this:
# 2> /dev/null
# these are the files to search:
FILES=$(find /Users/username -type f -name "*.Rnw" 2> /dev/null)

# this is the pattern I want to find within the files

## ls_dir_only.sh
#!/bin/bash

ls -lF | grep /
# -F = adds '/' to the end of dirs in the list
# grep for this
# so simple!

## grep_all_files.sh
#!/bin/bash
grep -F Name_to_find *.md

# can also use -l to just return the file name

# find someone's email address

grep -F -e @ *.md | grep name_to_find

## plotPCAWithSampleNames.R
plotPCAWithSampleNames = function(x, intgroup="condition", ntop=500)
{
	library(RColorBrewer)
	library(genefilter)
	library(lattice)

	# pca
	rv = rowVars(assay(x))
	select = order(rv, decreasing=TRUE)[seq_len(min(ntop, length(rv)))]
	pca = prcomp(t(assay(x)[select,]))

## paste0_numbered_sample_names.R
paste0(rep("Sample",times=nrow(tmp_Table)),seq(1:nrow(tmp_Table)))
[1] "Sample1" "Sample2" "Sample3" "Sample4" "Sample5" "Sample6" "Sample7" "Sample8"

## find_grep_exec_xargs_example.sh
#!/bin/bash

# find all the shell scripts I have written that use the [ ] test function
# the [ needs to be escaped!

# using xargs
find ~/projects/ -type f -name "*.sh" -print0 | xargs -0 grep -l '\['

# using exec
find ~/projects/ -type f -name "*.sh" -exec grep -l '\[' {} \;

## jupyter_goes_here.txt
Had trouble getting iPython, Jupyter, installed after upgrading to El Capitan OS X 10.11
using default pip, packages were getting installed to

/Library/Python/2.7/site-packages/

when trying to run `jupyer notebook`, the notebook package was not being found, couldn't run
`> jupyter: 'notebook' is not a Jupyter command`

uninstalled all packages that were installed to that dir
example:

## .bashrc
# .bashrc

# Source global definitions
if [ -f /etc/bashrc ]; then
	. /etc/bashrc
fi

# User specific aliases and functions

### autocorrects cd misspellings, 'cd /sur/src/linus' >> 'cd /usr/src/linux' ###

## unzip_OS_X.sh
#!/bin/bash
# unzip all files in current directory
# extract into new directory of the same name
for i in *.zip; do echo $i; echo ${i%.zip}; mkdir ${i%.zip}; unzip ${i} -d ${i%.zip}; done

## find_ignore_dotfiles.sh
#!/bin/bash
# in OS X
find -E . \( ! -regex '.*/\..*' \)

# vanilla bash
find . \( ! -regex '.*/\..*' \) -type f -name "filename"
	#!/bin/bash

	# look in my /Users/ dir
	# look for the .Rnw files
	# suppress the permission denied messages with this:
	# 2> /dev/null
	# these are the files to search:
	FILES=$(find /Users/username -type f -name "*.Rnw" 2> /dev/null)

	# this is the pattern I want to find within the files
	#!/bin/bash

	ls -lF \| grep /
	# -F = adds '/' to the end of dirs in the list
	# grep for this
	# so simple!
	#!/bin/bash
	grep -F Name_to_find *.md

	# can also use -l to just return the file name

	# find someone's email address

	grep -F -e @ *.md \| grep name_to_find
	plotPCAWithSampleNames = function(x, intgroup="condition", ntop=500)
	{
	library(RColorBrewer)
	library(genefilter)
	library(lattice)

	# pca
	rv = rowVars(assay(x))
	select = order(rv, decreasing=TRUE)[seq_len(min(ntop, length(rv)))]
	pca = prcomp(t(assay(x)[select,]))
	paste0(rep("Sample",times=nrow(tmp_Table)),seq(1:nrow(tmp_Table)))
	[1] "Sample1" "Sample2" "Sample3" "Sample4" "Sample5" "Sample6" "Sample7" "Sample8"
	#!/bin/bash

	# find all the shell scripts I have written that use the [ ] test function
	# the [ needs to be escaped!

	# using xargs
	find ~/projects/ -type f -name "*.sh" -print0 \| xargs -0 grep -l '\['

	# using exec
	find ~/projects/ -type f -name "*.sh" -exec grep -l '\[' {} \;
	Had trouble getting iPython, Jupyter, installed after upgrading to El Capitan OS X 10.11
	using default pip, packages were getting installed to

	/Library/Python/2.7/site-packages/

	when trying to run `jupyer notebook`, the notebook package was not being found, couldn't run
	`> jupyter: 'notebook' is not a Jupyter command`

	uninstalled all packages that were installed to that dir
	example:
	# .bashrc

	# Source global definitions
	if [ -f /etc/bashrc ]; then
	. /etc/bashrc
	fi

	# User specific aliases and functions

	### autocorrects cd misspellings, 'cd /sur/src/linus' >> 'cd /usr/src/linux' ###
	#!/bin/bash
	# unzip all files in current directory
	# extract into new directory of the same name
	for i in *.zip; do echo $i; echo ${i%.zip}; mkdir ${i%.zip}; unzip ${i} -d ${i%.zip}; done
	#!/bin/bash
	# in OS X
	find -E . \( ! -regex './\..' \)

	# vanilla bash
	find . \( ! -regex './\..' \) -type f -name "filename"