notes: remove old emails

1 files changed, 16 insertions, 146 deletions

diff --git a/NOTES.org b/NOTES.org
index b75fcb1..d580272 100644
--- a/NOTES.org
+++ b/NOTES.org
@@ -1,5 +1,4 @@
 * POC
-
 ** This is the phi6 genome:
 [[file:phi6 RefWT_from Lele.txt]]
 
@@ -48,144 +47,6 @@ see, for example, “S34S”
 Thanks!
 SD
 
-* mail 2
-
-Here's data from Mansha -- I can help reformat as you wish. I will come and talk to you about it after shopping and getting dinner started...
-SD
-
-
--------------------------------------------------------------------------------------------------------------------------
-From: Mansha Seth-Pasricha <mansha@sebs.rutgers.edu>
-Sent: Friday, July 1, 2022 11:59 PM
-To: Siobain Duffy <duffy@sebs.rutgers.edu>
-Subject: Re: Brian's ready for variant calls
-
-Sounds good. For 1 lineage there will be 13 text files. So sending 1 for starters- T10 ancestor. But the excel file has all 13 lineages- T10 and
-evolved pops. Please use the middle sheet “v.v. Low stringency” for the data in the excel file. I could not name the sheet as freq 0.01, so it’s a
-strange name.
-
-
-
-Thanks,
-
-Mansha
-
-
-
-From: Siobain Duffy <duffy@sebs.rutgers.edu>
-Date: Friday, July 1, 2022 at 5:55 PM
-To: Mansha Seth-Pasricha <mansha@sebs.rutgers.edu>
-Subject: Re: Brian's ready for variant calls
-
-send both  excel and text file for one set of lineages and we can see which works better?
-
--------------------------------------------------------------------------------------------------------------------------
-
-From: Mansha Seth-Pasricha <mansha@sebs.rutgers.edu>
-Sent: Friday, July 1, 2022 4:37 PM
-To: Siobain Duffy <duffy@sebs.rutgers.edu>; Mansha Pasricha <mansha.pasricha@gmail.com>
-Subject: Re: Brian's ready for variant calls
-
-
-
-That’s awesome. Does he need the excel files with the variants organized per ancestor and evolved pops (the ones I’ve been showing you) or
-the txt formats of the SNP output from varscan?
-
-
-
-As far UCSC goes, if we decide to go that route, we’ll basically be submitting it as a reference file with annotated ORF’s. Something like they
-already have for human genome/other organismal genomes that folks BLAT against. I think we can still hold on to this thought.
-
-
-
-Thanks,
-
-Mansha
-
-
-
-
-
-
-
-From: Siobain Duffy <duffy@sebs.rutgers.edu>
-Date: Friday, July 1, 2022 at 3:52 PM
-To: Mansha Pasricha <mansha.pasricha@gmail.com>, Mansha Seth-Pasricha <mansha@sebs.rutgers.edu>
-Subject: Brian's ready for variant calls
-
-He's got the phi6 concatenated genome parsed properly, and if you give me your data I can return your amino acid (or called as intergenic)
-changes returned over the weekend.
-
-
-
-I know you're jazzed about the idea of the UCSC browser for phi6, but minimally you can use Brian's calls as something to check against?
-
-SD
-
-[[file:1T_copy_trimmed_WTRef_bow_sorted.bam.snp]]
-
-[[file:T10_Varscan_copy.xlsx]]
-
-[[file:t10-varscan.csv]]
-
-* Mail 3
-You've made Mansha very very happy.  4 other files to similarly treat 🙂
-
-
--------------------------------------------------------------------------------------------------------------------------
-From: Mansha Seth-Pasricha <mansha@sebs.rutgers.edu>
-Sent: Thursday, July 7, 2022 1:53 PM
-To: Siobain Duffy <duffy@sebs.rutgers.edu>
-Subject: Re: T10 varscan results!
-
-Yes! Yes! Yes!! In case you can’t tell, I am jumping with joy. Thanks so much to Brian.
-
-
-
-Here you go on the other 4. Same thing- look in the low stringency tab.
-
-
-
-I found a visualizing software that aligns seqs and draws out the comparisons. I’ll see how/if I can get that to work.
-
-
-
-
-
-Thanks,
-
-Mansha
-
-
-
-
-
-From: Siobain Duffy <duffy@sebs.rutgers.edu>
-Date: Thursday, July 7, 2022 at 12:42 PM
-To: Mansha Seth-Pasricha <mansha@sebs.rutgers.edu>
-Subject: T10 varscan results!
-
-Want to send more excel files? Brian understands how to interpret them now.
-
-SD
-
-[[file:E8A_Varscan.xlsx]]
-[[file:E8G_Varscan.xlsx]]
-[[file:E8K_Varscan.xlsx]]
-[[file:T9_Varscan.xlsx]]
-
-[[file:E8A_Varscan.csv]]
-[[file:E8G_Varscan.csv]]
-[[file:E8K_Varscan.csv]]
-[[file:T9_Varscan.csv]]
-
-#+name: mail-3-files
-| E8A_Varscan.csv |
-| E8G_Varscan.csv |
-| E8K_Varscan.csv |
-| T9_Varscan.csv  |
-
-
 * Sample runs
 Protein runs:
 #+begin_src shell
@@ -200,7 +61,7 @@ Full conversion:
 
 Iter:
 #+name: iter
-#+begin_src shell :stdin mail-3-files
+#+begin_src shell :stdin e8k-redo
   for i in $(cat); do
       res=$(basename $i .csv).res.csv
       ./varscan2codon.pl 'phi6 RefWT_from Lele.txt' 'phi6 wt protein start stops.csv' $i > $res
@@ -208,10 +69,19 @@ Iter:
   done
 #+end_src
 
-#+call: iter()
+#+RESULTS: iter
+: file:E8K_lowStrin.res.csv
+
+todo directory:
+#+name: todo-directory
+#+begin_src shell
+  mkdir -p to-send
+  for i in todo/*.csv; do
+      res=to-send/$(basename "$i" .csv).res.csv
+      guix shell --pure -m manifest.scm -- ./varscan2codon.pl 'phi6 RefWT_from Lele.txt' 'phi6 wt protein start stops.csv' "$i" > "$res"
+      echo $res
+  done
+#+end_src
 
-#+RESULTS:
-| file:E8A_Varscan.res.csv |
-| file:E8G_Varscan.res.csv |
-| file:E8K_Varscan.res.csv |
-| file:T9_Varscan.res.csv  |
+#+RESULTS: todo-directory
+: to-send/jan4_samplevariation.res.csv