Byron J. Smith bsmith89

## python-day-2.ipynb

      
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                bsmith89
                / python-day-2.ipynb
            
            
              Created
              February 23, 2016 22:21
            
          
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## Makefile
# ====================
#  Project Makefile
# ====================
#  User Configuration {{{1
# ====================

# Major targets {{{2
.PHONY: figs res
figs:
# [Partially redacted]

## gapminder-analysis.ipynb

      
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                bsmith89
                / gapminder-analysis.ipynb
            
            
              Last active
              December 21, 2016 21:16
            
              
                Example analysis notebook and (*very*) rudimentary notes for a customized python-novice-gapminder. http://blog.byronjsmith.com/python-lesson-balance.html
              
          
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## 2017-01-22_hplc_method_comparison.ipynb

      
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                bsmith89
                / 2017-01-22_hplc_method_comparison.ipynb
            
            
              Last active
              January 22, 2017 20:00
            
              
                HPLC Calibration
              
          
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## contaminant-removal.sh
#!/usr/bin/env bash
# Remove pairs which hit the mouse reference.
#
# I haven't tested this script, but you should be able to use the commands in it
# to do your contaminant filtering.
# It would probably be best to feed in fully trimmed reads.  Otherwise you
# might want to use "local" mapping.
# See: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#end-to-end-alignment-versus-local-alignment

# Adapter trim and quality trim your HiSeq reads

## pull_from_remote.sh
#!/usr/bin/env bash
remote='<PROJECT_PATH_HERE>'

for path in $@
do
    dirname=$(dirname $path)
    basename=$(basename $path)
    mkdir -p "$dirname"

    # Use rsync --partial for restartable transfers.

## .gitattributes
*.ipynb	filter=dropoutput_jupyter
*.[tc]sv	diff=daff-csv
*.[tc]sv	merge=daff-csv

## ipynb_output_filter.py
#! /usr/bin/env python
"""From http://stackoverflow.com/a/20844506/1951857

To use::

    # Add the script to your path
    chmod +x path/to/this/ipynb_output_filter.py
    echo "*.ipynb    filter=dropoutput_ipynb" >> ~/.gitattributes
    git config --global core.attributesfile ~/.gitattributes
    git config --global filter.dropoutput_ipynb.clean ipynb_output_filter.py
	# ====================
	# Project Makefile
	# ====================
	# User Configuration {{{1
	# ====================

	# Major targets {{{2
	.PHONY: figs res
	figs:
	# [Partially redacted]
	#!/usr/bin/env bash
	# Remove pairs which hit the mouse reference.
	#
	# I haven't tested this script, but you should be able to use the commands in it
	# to do your contaminant filtering.
	# It would probably be best to feed in fully trimmed reads. Otherwise you
	# might want to use "local" mapping.
	# See: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#end-to-end-alignment-versus-local-alignment

	# Adapter trim and quality trim your HiSeq reads
	#!/usr/bin/env bash
	remote='<PROJECT_PATH_HERE>'

	for path in $@
	do
	dirname=$(dirname $path)
	basename=$(basename $path)
	mkdir -p "$dirname"

	# Use rsync --partial for restartable transfers.
	*.ipynb filter=dropoutput_jupyter
	*.[tc]sv diff=daff-csv
	*.[tc]sv merge=daff-csv
	#! /usr/bin/env python
	"""From http://stackoverflow.com/a/20844506/1951857

	To use::

	# Add the script to your path
	chmod +x path/to/this/ipynb_output_filter.py
	echo "*.ipynb filter=dropoutput_ipynb" >> ~/.gitattributes
	git config --global core.attributesfile ~/.gitattributes
	git config --global filter.dropoutput_ipynb.clean ipynb_output_filter.py