Steven and I are trying to ID target loci (lineage-specific and developmentally different loci). This is a check to make sure we can obtain the same result¶

Starting with the methratio files, I am going to filter for context and coverage. Then I will create files containing columns for loci ID and methylation information¶

In [6]:

#Output for methratio file
methratio="/Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_methratio_files/"

#Location of output files
filtered="/Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/"

In [2]:

!grep "[A-Z][A-Z]CG[A-Z]" <{methratio}methratio_out_M1.txt> {filtered}methratio_out_M1_CG.txt

In [12]:

!awk '{if ($8 >= 3) print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' </Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/methratio_out_M1_CG.txt> /Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/methratio_out_CG3x_M1.txt

In [13]:

!awk '{print ($1"."$2),$5}' </Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/methratio_out_CG3x_M1.txt> /Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/SQL_M1.txt

In [38]:

!sed '/NA/d' {filtered}SQL_M1.txt > {filtered}M1.txt

In [39]:

!head {filtered}SQL_M1.txt

loci M1ratio
C12768.103 0.167
C12768.119 0.250
C12768.145 0.000
C12806.56 0.000
C12806.76 0.200
C12806.78 0.200
C12806.105 0.250
C12806.142 0.375
C12924.19 0.000

In [15]:

!grep "[A-Z][A-Z]CG[A-Z]" <{methratio}methratio_out_T1D3.txt> {filtered}methratio_out_T1D3_CG.txt

In [16]:

!awk '{if ($8 >= 3) print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' </Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/methratio_out_T1D3_CG.txt> /Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/methratio_out_CG3x_T1D3.txt

In [17]:

!awk '{print ($1"."$2),$5}' </Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/methratio_out_CG3x_T1D3.txt> /Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/SQL_T1D3.txt

In [40]:

!sed '/NA/d' {filtered}SQL_T1D3.txt > {filtered}T1D3.txt

In [41]:

!head {filtered}T1D3.txt

loci T1D3ratio
C12960.123 0.000
C13208.83 1.000
C13766.37 0.000
C13766.42 0.000
C13766.126 0.000
C13766.145 0.000
C13842.49 0.000
C13874.46 0.000
C13874.167 0.000

In [19]:

!grep "[A-Z][A-Z]CG[A-Z]" <{methratio}methratio_out_T1D5.txt> {filtered}methratio_out_T1D5_CG.txt

In [20]:

!awk '{if ($8 >= 3) print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' </Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/methratio_out_T1D5_CG.txt> /Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/methratio_out_CG3x_T1D5.txt

In [21]:

!awk '{print ($1"."$2),$5}' </Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/methratio_out_CG3x_T1D5.txt> /Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/SQL_T1D5.txt

In [42]:

!sed '/NA/d' {filtered}SQL_T1D5.txt > {filtered}T1D5.txt

In [43]:

!head {filtered}T1D5.txt

loci T1D5ratio
C12832.25 0.000
C12960.67 0.000
C12960.123 0.000
C13040.69 0.000
C13128.87 0.000
C13208.148 0.333
C13442.65 0.000
C13442.79 0.000
C13546.84 0.000

In [23]:

!grep "[A-Z][A-Z]CG[A-Z]" <{methratio}methratio_out_M3.txt> {filtered}methratio_out_M3_CG.txt

In [24]:

!awk '{if ($8 >= 3) print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' </Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/methratio_out_M3_CG.txt> /Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/methratio_out_CG3x_M3.txt

In [25]:

!awk '{print ($1"."$2),$5}' </Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/methratio_out_CG3x_M3.txt> /Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/SQL_M3.txt

In [45]:

!sed '/NA/d' {filtered}SQL_M3.txt > {filtered}M3.txt

In [46]:

!head {filtered}M3.txt

loci M3ratio
C12806.142 0.000
C12866.162 0.000
C12960.123 0.000
C12994.134 0.000
C13046.76 0.000
C13074.146 0.000
C13080.102 0.000
C13080.111 0.000
C13080.130 0.000

In [27]:

!grep "[A-Z][A-Z]CG[A-Z]" <{methratio}methratio_out_T3D3.txt> {filtered}methratio_out_T3D3_CG.txt

In [28]:

!awk '{if ($8 >= 3) print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' </Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/methratio_out_T3D3_CG.txt> /Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/methratio_out_CG3x_T3D3.txt

In [29]:

!awk '{print ($1"."$2),$5}' </Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/methratio_out_CG3x_T3D3.txt> /Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/SQL_T3D3.txt

In [49]:

!sed '/NA/d' {filtered}SQL_T3D3.txt > {filtered}T3D3.txt

In [50]:

!head {filtered}T3D3.txt

loci T3D3ratio
C12768.103 0.000
C12960.67 0.000
C12960.123 0.000
C12960.176 0.000
C12960.186 0.000
C13046.76 0.000
C13208.148 0.333
C13248.98 0.000
C13390.79 0.000

In [31]:

!grep "[A-Z][A-Z]CG[A-Z]" <{methratio}methratio_out_T3D5.txt> {filtered}methratio_out_T3D5_CG.txt

In [32]:

!awk '{if ($8 >= 3) print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' </Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/methratio_out_T3D5_CG.txt> /Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/methratio_out_CG3x_T3D5.txt

In [33]:

!awk '{print ($1"."$2),$5}' </Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/methratio_out_CG3x_T3D5.txt> /Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/SQL_T3D5.txt

In [51]:

!sed '/NA/d' {filtered}SQL_T3D5.txt > {filtered}T3D5.txt

In [52]:

!head {filtered}T3D5.txt

loci T3D5ratio
C12798.142 0.000
C12798.145 0.000
C12798.151 0.000
C12960.67 0.000
C12960.123 0.000
C12994.63 0.000
C12994.90 0.000
C13128.87 0.000
C13208.83 0.500

In [35]:

#NOTEBOOK NAME
nb='ID_Target_Loci_Check'

#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 [36]:

cd {post}

/Volumes/web/Mollusk/iPython_Posts

In [37]:

!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/ID_Target_Loci_Check.ipynb to html
[NbConvertApp] Support files will be in ID_Target_Loci_Check[0716_1422]_files/
[NbConvertApp] Loaded template html_full.tpl
[NbConvertApp] Writing 212983 bytes to ID_Target_Loci_Check[0716_1422].html