sahilseth

split_tcga_barcode <- function(x, split.char="-"){
  tmp = strsplit(x, split.char)[[1]]
  
  # default values
  s.tss = "NA";
  s.participant = "NA";
  s.programcode = "NA";
  s.nucleic = "NA";
  s.portion = "NA";
  s.sampletype = "00";

sahilseth

# install this cool tools from Heng Li (https://github.com/lh3/bioawk)
brew install bioawk

# information regarding exit_code:
# - NA: not started yet

# show lines where job started and had errors
bioawk -tc hdr '{if($exit_code!=0 && $started=="TRUE") print $jobname, $cmd, $exit_code}' flow_details.txt

# show lines which did not start

sahilseth

find . -type f -printf "%f %s\n" |
  awk '{
      PARTSCOUNT=split( $1, FILEPARTS, "." );
      EXTENSION=PARTSCOUNT == 1 ? "NULL" : FILEPARTS[PARTSCOUNT];
      FILETYPE_MAP[EXTENSION]+=$2
    }
   END {
     for( FILETYPE in FILETYPE_MAP ) {
       print FILETYPE_MAP[FILETYPE], FILETYPE_MAP[FILETYPE]/10^6, FILETYPE;
      }

sahilseth

library(sendmailR)

send_mail <- function(msg="", subject, tos = c("[email protected]"), attachment}
    from <- sprintf("<abc@%s.inst.edu>", Sys.info()[4])
    
    if(missing(subject)) 
      subject <- paste("morning!")
      
    salute <- paste("Hello there\n I just ran the tracker on ")
    body <- c(salute, "\n", msg, "\n", mime_part(attachment))

sahilseth

# here is scratchpad on various steps which are helpful in using git submodules

# holy grail of details: https://git-scm.com/book/en/v2/Git-Tools-Submodules

# adding a submodule
git submodule add <URL>

# clone a repo with submodules
git clone --recursive <URL>

sahilseth

Do you want to display some code in a Keynote presentation?

It's easy. All you need is Homebrew installed.

First you need to install the program highlight.

brew install highlight
So you have a piece of code. For example some Python code. The take that snippet of code and save it to a file like code.py. Now all you need to do is run this:

highlight -O rtf code.py | pbcopy

sahilseth

# install this cool tools from Heng Li (https://github.com/lh3/bioawk)
brew install bioawk

# information regarding exit_code:
# - NA: not started yet

# show lines where job started and had errors
bioawk -tc hdr '{if($exit_code!=0 && $started=="TRUE") print $jobname, $cmd, $exit_code}' flow_details.txt

# show lines which did not start

sahilseth

# issue: http://stackoverflow.com/questions/10575679/bundle-update-fails-on-ffi

# install apple commandline tools:
xcode-select --install

sahilseth

fqs=$(find . -name '*.fastq')

for fq in $fqs; do
	echo "zipping $fq ...."
	gzip $fq
done

sahilseth

cd ~/Library/Containers/com.apple.iWork.Keynote/Data/Library/Application\ Support/User\ Templates/