scripts/make_b_taurus_UMD3.sh

   1 #!/bin/sh
   2
   3 #
   4 # Builds an index from UMD Freeze 3.0 of the Bos Taurus (cow) genome.
   5 #
   6
   7 BASE_CHRS="\
   8 Chr1 \
   9 Chr2 \
  10 Chr3 \
  11 Chr4 \
  12 Chr5 \
  13 Chr6 \
  14 Chr7 \
  15 Chr8 \
  16 Chr9 \
  17 Chr10 \
  18 Chr11 \
  19 Chr12 \
  20 Chr13 \
  21 Chr14 \
  22 Chr15 \
  23 Chr16 \
  24 Chr17 \
  25 Chr18 \
  26 Chr19 \
  27 Chr20 \
  28 Chr21 \
  29 Chr22 \
  30 Chr23 \
  31 Chr24 \
  32 Chr25 \
  33 Chr26 \
  34 Chr27 \
  35 Chr28 \
  36 Chr29 \
  37 ChrX \
  38 ChrU \
  39 ChrY-contigs \
  40 ChrY-contigs.SHOTGUN_ONLY"
  41
  42 CHRS_TO_INDEX=$BASE_CHRS
  43
  44 get() {
  45         file=$1
  46         if ! wget --version >/dev/null 2>/dev/null ; then
  47                 if ! curl --version >/dev/null 2>/dev/null ; then
  48                         echo "Please install wget or curl somewhere in your PATH"
  49                         exit 1
  50                 fi
  51                 curl -o `basename $1` $1
  52                 return $?
  53         else
  54                 wget $1
  55                 return $?
  56         fi
  57 }
  58
  59 BOWTIE_BUILD_EXE=./bowtie-build
  60 if [ ! -x "$BOWTIE_BUILD_EXE" ] ; then
  61         if ! which bowtie-build ; then
  62                 echo "Could not find bowtie-build in current directory or in PATH"
  63                 exit 1
  64         else
  65                 BOWTIE_BUILD_EXE=`which bowtie-build`
  66         fi
  67 fi
  68
  69 FTP_BASE=ftp://ftp.cbcb.umd.edu/pub/data/Bos_taurus/Bos_taurus_UMD_3.0
  70 OUTPUT=b_taurus
  71
  72 INPUTS=
  73 for c in $CHRS_TO_INDEX ; do
  74         if [ ! -f ${c}.fa ] ; then
  75                 F=${c}.fa.gz
  76                 get ${FTP_BASE}/$F || (echo "Error getting $F" && exit 1)
  77                 gunzip $F || (echo "Error unzipping $F" && exit 1)
  78         fi
  79         [ -n "$INPUTS" ] && INPUTS=$INPUTS,${c}.fa
  80         [ -z "$INPUTS" ] && INPUTS=${c}.fa
  81 done
  82
  83 CMD="$BOWTIE_BUILD_EXE $* $INPUTS $OUTPUT"
  84 echo $CMD
  85 if $CMD ; then
  86         echo "$OUTPUT index built; you may remove fasta files"
  87 else
  88         echo "Index building failed; see error message"
  89 fi