John McCallum cfljam
cfljam
/ Designing CAPS Markers.ipynb
Last active
December 19, 2015 03:49
iPython Notebook describing basic use of the Python PCR Design Tools
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| ##remove non-printing characters from a file | |
| cat file | tr -dc "[:alnum:][:space:][:punct:]" |
cfljam
/ using_PCR_design_python_tools_1.ipynb
Created
September 30, 2013 02:36
Designing HRM primer sets
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cfljam
/ using_PCR_design_python_tools_1.ipynb
Created
September 30, 2013 03:50
Designing HRM primer sets
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cfljam
/ gist:7036413
Created
October 18, 2013 04:15
install a python package to $HOME when you dont have root access
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| pip install --install-option="--prefix=$HOME/local" package-name | |
| export PYTHONPATH=$PYTHONPATH:~/local/lib/python2.6/site-packages/ |
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| sed 's/\(>\w*\)\s*.*/\1/' |
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| ##To reveal non-printing characters | |
| cat -v my_file | |
| ##To remove | |
| cat my_file | col -v > new_file |
cfljam
/ ipcress_tabular2gff
Last active
December 30, 2015 17:59
parse hits in ipcress output into simple columnar form and parse this into gff
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| awk '/^ipcress:/, split($2,HIT,":"){print HIT[1],$3,$4,$5,$6,$7,$8,$9,$10,$11}' |
cfljam
/ Exploring Vcf analysis with PyVCF .ipynb
Created
January 28, 2014 17:41
Using PyVcf to parse vcf format variant data
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cfljam
/ Exploring use of vcftools for VCF parsing.ipynb
Created
January 30, 2014 19:03
Using vcftools for VCF parsing
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