Filtering larvae files that have been trimmed for adapters already filterd for context- now want to get 3x coverage

In [4]: 
#obtaining a filtered file with at least 3x coverage
!awk '{if ($8 >= 3) print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' </Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methratio_out_CG_M1.txt> /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methratio_out_CG3x_M1.txt
In [5]: 
#obtaining a filtered file with at least 3x coverage
!awk '{if ($8 >= 3) print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' </Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methratio_out_CG_M3.txt> /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methratio_out_CG3x_M3.txt
In [6]: 
#obtaining a filtered file with at least 3x coverage
!awk '{if ($8 >= 3) print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' </Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methratio_out_CG_T1D3.txt> /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methratio_out_CG3x_T1D3.txt
In [7]: 
#obtaining a filtered file with at least 3x coverage
!awk '{if ($8 >= 3) print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' </Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methratio_out_CG_T1D5.txt> /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methratio_out_CG3x_T1D5.txt
In [8]: 
#obtaining a filtered file with at least 3x coverage
!awk '{if ($8 >= 3) print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' </Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methratio_out_CG_T3D3.txt> /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methratio_out_CG3x_T3D3.txt
In [9]: 
#obtaining a filtered file with at least 3x coverage
!awk '{if ($8 >= 3) print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' </Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methratio_out_CG_T3D5.txt> /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methratio_out_CG3x_T3D5.txt
In [20]: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methratio_out_CG3x_M1.txt /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methratio_out_CG3x_M3.txt /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methratio_out_CG3x_T1D3.txt /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methratio_out_CG3x_T1D5.txt /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methratio_out_CG3x_T3D3.txt /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methratio_out_CG3x_T3D5.txt > /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/3xCoverage_concatenated.txt
In [21]: 
!head /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/3xCoverage_concatenated.txt

C12768 103 + TTCGT 0.167 6.00 1 6 6 6 0.030 0.564
C12768 119 + TTCGT 0.250 4.00 1 4 4 4 0.046 0.699
C12768 145 + TTCGT 0.000 3.00 0 3 3 3 0.000 0.562
C12806 56 + AACGA 0.000 4.00 0 4 4 4 0.000 0.490
C12806 76 + ATCGC 0.200 5.00 1 5 5 5 0.036 0.624
C12806 78 + CGCGT 0.200 5.00 1 5 5 5 0.036 0.624
C12806 105 + ATCGG 0.250 4.00 1 4 5 5 0.046 0.699
C12806 142 + ATCGG 0.375 8.00 3 8 8 8 0.137 0.694
C12924 19 + AACGA 0.000 4.00 0 4 4 4 0.000 0.490
C12924 30 + ATCGT 0.000 4.00 0 5 5 4 0.000 0.490
In []: 
#Uploaded this file to SQLshare (saved as 3xCoverage_concatenated.txt) and kept all unique entries

Run_Query_18F9C4B9.png

In [14]: 
!tr ',' "\t" </Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/AllUniqueLoci_3xCoverage.csv> /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/AllUniqueLoci_3xCoverage.txt
In [15]: 
!head /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/AllUniqueLoci_3xCoverage.txt

chr	pos
C12768	103

C12768	119

C12768	145

C12798	142

C12798	145

C12798	151

C12806	56

C12806	76

C12806	78
In [11]: 
!awk '{print $1,$2,$2+1}' </Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/AllUniqueLoci_3xCoverage.csv> /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/AllUniqueLoci_3xCoverage_startend.csv
In [12]: 
!tr ',' "\t" </Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/AllUniqueLoci_3xCoverage_startend.csv> /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/AllUniqueLoci_3xCoverage_final.txt
In [14]: 
#NOTEBOOK NAME
nb='FilteringAdapterTrimmed_3xcoverage'

#NOTEBOOK LOCATION
nbloc='/Users/claireolson/Dropbox/Lab\ \(1\)/IPython_nbs/Claire/'



#TIMESTAMP
date=!date +%m%d_%H%M
#LOCATION OF POST DIRECTORY
post='/Volumes/web/Mollusk/iPython_Posts/'
In [15]: 
cd {post}

[Errno 20] Not a directory: '/Volumes/web/Mollusk/iPython_Posts/'
/Users/claireolson/Dropbox/Lab (1)/IPython_nbs/Claire
In [16]: 
!ipython nbconvert {nbloc}{nb} --to html --template full --output {nb}{date}

[NbConvertApp] Using existing profile dir: u'/Users/claireolson/.ipython/profile_default'
[NbConvertApp] Converting notebook /Users/claireolson/Dropbox/Lab (1)/IPython_nbs/Claire/FilteringAdapterTrimmed_3xcoverage.ipynb to html
[NbConvertApp] Support files will be in FilteringAdapterTrimmed_3xcoverage[0412_1031]_files/
[NbConvertApp] Loaded template html_full.tpl
[NbConvertApp] Writing 201660 bytes to FilteringAdapterTrimmed_3xcoverage[0412_1031].html
In []: