scripts/make_e_coli.sh

   1 #!/bin/sh
   2
   3 #
   4 # Downloads the sequence for a strain of e. coli from NCBI and builds a
   5 # Bowtie index for it
   6 #
   7
   8 GENOMES_MIRROR=ftp://ftp.ncbi.nlm.nih.gov/genomes
   9
  10 BOWTIE_BUILD_EXE=./bowtie-build
  11 if [ ! -x "$BOWTIE_BUILD_EXE" ] ; then
  12         if ! which bowtie-build ; then
  13                 echo "Could not find bowtie-build in current directory or in PATH"
  14                 exit 1
  15         else
  16                 BOWTIE_BUILD_EXE=`which bowtie-build`
  17         fi
  18 fi
  19
  20 if [ ! -f NC_008253.fna ] ; then
  21         if ! which wget > /dev/null ; then
  22                 echo wget not found, looking for curl...
  23                 if ! which curl > /dev/null ; then
  24                         echo curl not found either, aborting...
  25                 else
  26                         # Use curl
  27                         curl ${GENOMES_MIRROR}/Bacteria/Escherichia_coli_536/NC_008253.fna -o NC_008253.fna
  28                 fi
  29         else
  30                 # Use wget
  31                 wget ${GENOMES_MIRROR}/Bacteria/Escherichia_coli_536/NC_008253.fna
  32         fi
  33 fi
  34
  35 if [ ! -f NC_008253.fna ] ; then
  36         echo "Could not find NC_008253.fna file!"
  37         exit 2
  38 fi
  39
  40 CMD="${BOWTIE_BUILD_EXE} $* -t 8 NC_008253.fna e_coli"
  41 echo $CMD
  42 if $CMD ; then
  43         echo "e_coli index built; you may remove fasta files"
  44 else
  45         echo "Index building failed; see error message"
  46 fi