jrherr

cat name.fasta |\ # identify file name
awk '/^>/ { if(i>0) printf("\n"); i++; printf("%s\t",$0); next;} {printf("%s",$0);} END { printf("\n");}' |\ # read data
perl -MList::Util -e 'print List::Util::shuffle <>' |\  # random sample of sequences with shuffle
head -n 50000 |\ # break fasta file into sections of 50000 sequences in length
awk '{printf("%s\n%s\n",$1,$2)}' > name_1.fasta  # write sequence output

jrherr

pip freeze --local | grep -v '^\-e' | cut -d = -f 1  | xargs pip install -U

jrherr

awk ‘/^>/{$0=”>”++i}1′ test.fna > test1.fna

jrherr

M <- matrix(c(1, 0, 0, 1), byrow = 1, nrow = 2)
df <- data.frame(A = 1)
df$B <- list(M)
df
#  A          B
#  1 1, 0, 0, 1

jrherr

Install Python

$ brew install readline sqlite gdbm
$ brew install python --universal --framework
$ python --version
Python 2.7

Symlinks...

jrherr

Here's the error I am getting with khmer install on Mac OSX Mavericks (OS X 10.9.4 (13E28)) install

```
./setup.py build_ext --inplace
running build_ext
bash -c cd third-party/zlib && ( test Makefile -nt configure || bash ./configure --static ) && make -f Makefile.pic PIC
make[1]: Nothing to be done for `PIC'.
bash -c cd third-party/bzip2 && make -f Makefile-libbz2_so all
#gcc -shared -Wl,-soname -Wl,libbz2.so.1.0 -o libbz2.so.1.0.6 blocksort.o huffman.o crctable.o randtable.o compress.o decompress.o bzlib.o
#gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -o bzip2-shared bzip2.c libbz2.so.1.0.6

jrherr

# A quick function to save a PBM (http://en.wikipedia.org/wiki/Netpbm_format)
# visualize *a lot* of missing data pretty quickly (outside of R).

writeMissingPBM <- function(x, file) {
  dims <- dim(x)
  x[] <- as.integer(is.na(x))
  con <- file(file, open="wt")
  writeLines(sprintf("P1\n%d %d", ncol(x), nrow(x)), con)
  write.table(x, file=con, sep=" ", col.names=FALSE, row.names=FALSE, quote=FALSE)
  close(con)

jrherr

Last login: Fri Oct 10 13:26:02 on ttys000
➜  ~  brew install gcc48 -dv                                                     
/usr/local/Library/brew.rb (Formulary::StandardLoader): loading /usr/local/Library/Taps/homebrew/homebrew-versions/gcc48.rb
/usr/local/Library/brew.rb (Formulary::StandardLoader): loading /usr/local/Library/Taps/homebrew/homebrew-versions/gmp4.rb
/usr/local/Library/brew.rb (Formulary::StandardLoader): loading /usr/local/Library/Taps/homebrew/homebrew-versions/libmpc08.rb
/usr/local/Library/brew.rb (Formulary::StandardLoader): loading /usr/local/Library/Taps/homebrew/homebrew-versions/mpfr2.rb
/usr/local/Library/brew.rb (Formulary::StandardLoader): loading /usr/local/Library/Taps/homebrew/homebrew-versions/cloog018.rb
/usr/local/Library/brew.rb (Formulary::StandardLoader): loading /usr/local/Library/Formula/pkg-config.rb
/usr/local/Library/brew.rb (Formulary::StandardLoader): loading /usr/local/Library/Taps/homebrew/homebrew-versions/isl011.rb
/usr/local/Library/Homebrew/build.rb (Formul

jrherr

sed -r "s/>NODE(_[0-9]+)_(.*)/>${input.name}\1 \2/g" $input > $output

jrherr

SAM and BAM filtering one-liners

@author: David Fredman, david.fredmanAAAAAA@gmail.com (sans poly-A tail)
@dependencies: http://sourceforge.net/projects/bamtools/ and http://samtools.sourceforge.net/

Please comment or extend with additional/faster/better solutions.

BWA mapping (using piping for minimal disk I/O)