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| -rw-r--r-- | NOTES.org | 162 |
1 files changed, 16 insertions, 146 deletions
@@ -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 |