%%bash
wget -q dereneaton.com/downloads/simRADs.zip
unzip simRADs.zip

%%bash
## I have pyRAD in my $PATH so that I can call it by simply typing pyRAD.
## If you haven't done this then you will need to type the full path to 
## the pyRAD script to execute it.

## call pyRAD with the (-n) option
pyRAD -n

%%bash
cat params.txt

%%bash
sed -i '/## 7. /c\2                   ## 7. N processors... ' params.txt
sed -i '/## 10. /c\.85                ## 10. lowered clust thresh... ' params.txt
sed -i '/## 14. /c\c85m4p3            ## 14. outprefix... ' params.txt
sed -i '/## 24./c\8                   ## 24. maxH raised ... ' params.txt
sed -i '/## 30./c\*                   ## 30. all output formats... ' params.txt

%%bash
cat params.txt

%%bash
less simRADs_R1.fastq.gz | head -n 12 | cut -c 1-90

%%bash
cat simRADs.barcodes

%%bash
pyRAD -p params.txt -s 1

%%bash
ls fastq/

%%bash
cat stats/s1.sorting.txt

%%bash
pyRAD -p params.txt -s 2

%%bash
ls edits/

%%bash
head -n 10 edits/1A0.edit | cut -c 1-80

%%bash
pyRAD -p params.txt -s 3

%%bash
less clust.85/1A0.clustS.gz | head -n 26 | cut -c 1-80

%%bash
head -n 40 stats/s3.clusters.txt

%%bash
pyRAD -p params.txt -s 4

%%bash
less stats/Pi_E_estimate.txt

%%bash
pyRAD -p params.txt -s 5

%%bash
less stats/s5.consens.txt

%%bash
pyRAD -p params.txt -s 6 

%%bash
pyRAD -p params.txt -s 7

%%bash
less stats/c85m4p3.stats

%%bash 
ls outfiles/

%%bash 
head -n 39 outfiles/c85m4p3.loci | cut -c 1-75

%%bash 
head -n 50 outfiles/c85m4p3.phy | cut -c 1-85

%%bash 
head -n 50 outfiles/c85m4p3.nex | cut -c 1-85

%%bash 
head -n 50 outfiles/c85m4p3.alleles| cut -c 1-85

%%bash 
head -n 50 outfiles/c85m4p3.str | cut -c 1-20

%%bash 
head -n 40 outfiles/c85m4p3.geno 

%%bash 
head -n 50 outfiles/c85m4p3.snps | cut -c 1-85

%%bash 
head -n 50 outfiles/c85m4p3.unlinked_snps | cut -c 1-85

%%bash 
## append group designations to the params file
echo "pop1 4 1A0,1B0,1C0,1D0 " >> params.txt
echo "pop2 4 2E0,2F0,2G0,2H0 " >> params.txt
echo "pop3 4 3* " >> params.txt

## view params file
cat params.txt

%%bash 
pyRAD -p params.txt -s 7

%%bash 
less outfiles/c85m4p3.treemix.gz | head -n 30

%%bash 
head -n 40 outfiles/c85m4p3.migrate | cut -c 1-85