John McCallum 15 July 2016
- work out tidiest way to split up haplotypes from phased vcf in data.table for plotting haplotypes
John McCallum cfljam
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| <!DOCTYPE html> | |
| <html> | |
| <head> | |
| <meta charset="utf-8" /> | |
| <title>plotly</title> | |
| <script src="data:application/x-javascript;base64,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 |
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| <!DOCTYPE html> | |
| <html> | |
| <head> | |
| <meta charset="utf-8" /> | |
| <title>plotly</title> | |
| <script src="data:application/x-javascript;base64,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 |
cfljam
/ gist:f8ac3199b545423e5656c004fd0cfab0
Created
April 13, 2019 20:09
Remove Trailing ^M from Windows Text Files
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| ## Check the File | |
| cat -A myfile.csv | head | |
| ## File the File | |
| ### sed in-line | |
| sed -i 's/\r//g' myfile.csv | |
| ### tr | |
| tr -d '\r' < myfile.csv > tmp; mv tmp myfile.csv |
cfljam
/ gist:bf813edd04271fac43f0010d72cacd0c
Created
June 10, 2018 04:49
Check for file existence in BASH using a listfile
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| for FILE in $(cat my_FOF); do if [ -e $FILE ]; then echo $FILE "exists"; fi; done |
cfljam
/ HOWTO-ExploreTheOmegaPlusSoftware.ipynb
Created
June 22, 2017 09:18
Vignette for OmegaPlus Install and VCF Usage
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cfljam
/ gist:40b7e27fc4a5995f587b5406a438836a
Created
November 8, 2016 19:02
Convert Patman Primer Mapping Output to GFF
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| awk 'OFS="\t" {print $1,"patman","primer_binding_site",$3,$4,$6,$5,".","name="$2}' < inputFile |
cfljam
/ gist:8edada0f5723b1c1c9746ea00e67d1b1
Created
November 8, 2016 19:02
Convert Patman Primer Mapping Output to GFF
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| awk 'OFS="\t" {print $1,"patman","primer_binding_site",$3,$4,$6,$5,".","name="$2}' < inputFile |
cfljam
/ HOWTO Generate multiple graphs in IRKernel.ipynb
Created
July 14, 2016 07:33
HOWTO Generate multiple plots in a loop in IRKernel + Jupyter
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cfljam
/ gist:244aad08150c17f3378aef1796c59558
Created
June 17, 2016 02:19
Replace Tassel integer Chromsome ID in vcf file with "CHR"
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| sed 's/^\([0-9]\{1,2\}\)[[:space:]]/CHR\1\t/g' my.vcf |