scripts/make_d_melanogaster_fb5_22.sh

   1 #!/bin/sh
   2
   3 #
   4 # Downloads sequence for a D. melanogaster from flybase.  Currently set
   5 # to download 5.22, but F, REL, and IDX_NAME can be edited to reflect a
   6 # different version number.  (But note that you will usually also have
   7 # to change the date in REL.)
   8 #
   9
  10 GENOMES_MIRROR=ftp://ftp.flybase.net/genomes/Drosophila_melanogaster
  11 F=dmel-all-chromosome-r5.22.fasta
  12 REL=dmel_r5.22_FB2009_09
  13 IDX_NAME=d_melanogaster_fb5_22
  14
  15 get() {
  16         file=$1
  17         if ! wget --version >/dev/null 2>/dev/null ; then
  18                 if ! curl --version >/dev/null 2>/dev/null ; then
  19                         echo "Please install wget or curl somewhere in your PATH"
  20                         exit 1
  21                 fi
  22                 curl -o `basename $1` $1
  23                 return $?
  24         else
  25                 wget -O `basename $1` $1
  26                 return $?
  27         fi
  28 }
  29
  30 BOWTIE_BUILD_EXE=./bowtie-build
  31 if [ ! -x "$BOWTIE_BUILD_EXE" ] ; then
  32         if ! which bowtie-build ; then
  33                 echo "Could not find bowtie-build in current directory or in PATH"
  34                 exit 1
  35         else
  36                 BOWTIE_BUILD_EXE=`which bowtie-build`
  37         fi
  38 fi
  39
  40 if [ ! -f $F ] ; then
  41         FGZ=$F.gz
  42         get ${GENOMES_MIRROR}/$REL/fasta/$FGZ || (echo "Error getting $FGZ" && exit 1)
  43         gunzip $FGZ || (echo "Error unzipping $FGZ" && exit 1)
  44 fi
  45
  46 CMD="${BOWTIE_BUILD_EXE} $* $F $IDX_NAME"
  47 echo "Running $CMD"
  48 if $CMD ; then
  49         echo "$IDX_NAME index built; you may remove fasta files"
  50 else
  51         echo "Index building failed; see error message"
  52 fi