* POC ** This is the phi6 genome: [[file:phi6 RefWT_from Lele.txt]] ** CSV file [[file:phi6 wt protein start stops.csv]] This is a CSV file with three columns: protein name, start nucleotide, ending nucleotide These numbers are inclusive. Everything else in the genome that’s not in at least one of those ranges (there’s one nucleotide overlaps between some reading frames) isn’t protein-coding. ** Standard genetic code [[file:Genetic-Code-Amino-Acid-Codon-Chart-sidebyside-03.png]] The standard genetic code that you’ve used for some of my class projects applies, we will be using the single capital letter abbreviations for amino acids. Because of this please use lowercase “a, c, g, t” for nucleotides. This is a chart that uses the DNA bases (no need to switch “u” to “t” in your head) and has the single letter amino acids. The three stop codons (taa, tag, tga) should all code for the same thing — could be “STOP” could be an asterisk… you can have some creative control here :-) ** Test As a test that our coordinates are correct, can you spit out the protein sequence from each of those proteins? Each will start with a M (one with a V, it’s an “alternate start codon) and should stop with a stop. Please send me that as a text file. If that works I’ll get you sample input and output for what we need the program to actually do have a nucleotide number and nucleotide inputted print out reference sequence nt at that number, the nt number, the inputted nucleotide (Tab) the name of the protein involved OR “noncoding” (Tab) Amino acid called by wild type sequence, the number in the protein that amino acid is, the amino acid called by the inputted nucleotide being in the sequence. Something like: input 7500g output: a7500g P7 S34T -- p7 is protein number from first email -- S is orig aa -- 34 is amino acid index inside p7 -- T is new aa -- say non-coding instead "P7 S34T" if P can't be calculated (sometimes the variant nucleotide will be in a protein-coding region but won’t change the called amino acid, this is normal and fine so we’ll 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 Sent: Friday, July 1, 2022 11:59 PM To: Siobain Duffy 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 Date: Friday, July 1, 2022 at 5:55 PM To: Mansha Seth-Pasricha 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 Sent: Friday, July 1, 2022 4:37 PM To: Siobain Duffy ; Mansha Pasricha 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 Date: Friday, July 1, 2022 at 3:52 PM To: Mansha Pasricha , Mansha Seth-Pasricha 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 Sent: Thursday, July 7, 2022 1:53 PM To: Siobain Duffy 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 Date: Thursday, July 7, 2022 at 12:42 PM To: Mansha Seth-Pasricha 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 ./codon2aa.pl 'phi6 RefWT_from Lele.txt' 'phi6 wt protein start stops.csv' #+end_src Full conversion: #+begin_src shell ./varscan2codon.pl 'phi6 RefWT_from Lele.txt' 'phi6 wt protein start stops.csv' t10-varscan.csv #+end_src Iter: #+name: iter #+begin_src shell :stdin mail-3-files 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 > $res echo file:$res done #+end_src #+call: iter() #+RESULTS: | file:E8A_Varscan.res.csv | | file:E8G_Varscan.res.csv | | file:E8K_Varscan.res.csv | | file:T9_Varscan.res.csv |