scripts/make_h_sapiens_ncbi36.sh

   1 #!/bin/sh
   2
   3 #
   4 # Downloads sequence for H. sapiens (human) from NCBI.  This script was
   5 # used to build the Bowtie index for H. sapiens.
   6 #
   7 # From README_CURRENT_BUILD:
   8 #  Organism: Homo sapiens (human)
   9 #  NCBI Build Number: 36
  10 #  Version: 3
  11 #  Release date: 24 March 2008
  12 #
  13
  14 GENOMES_MIRROR=ftp://ftp.ncbi.nih.gov/genomes
  15 FILE_PATH=${GENOMES_MIRROR}/H_sapiens/ARCHIVE/BUILD.36.3/Assembled_chromosomes
  16
  17 BOWTIE_BUILD_EXE=./bowtie-build
  18 if [ ! -x "$BOWTIE_BUILD_EXE" ] ; then
  19         if ! which bowtie-build ; then
  20                 echo "Could not find bowtie-build in current directory or in PATH"
  21                 exit 1
  22         else
  23                 BOWTIE_BUILD_EXE=`which bowtie-build`
  24         fi
  25 fi
  26
  27 for c in 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y ; do
  28         if [ ! -f hs_ref_chr$c.fa ] ; then
  29                 if ! which wget > /dev/null ; then
  30                         echo wget not found, looking for curl...
  31                         if ! which curl > /dev/null ; then
  32                                 echo curl not found either, aborting...
  33                         else
  34                                 # Use curl
  35                                 curl ${FILE_PATH}/hs_ref_chr$c.fa.gz
  36                         fi
  37                 else
  38                         # Use wget
  39                         wget ${FILE_PATH}/hs_ref_chr$c.fa.gz
  40                 fi
  41                 gunzip hs_ref_chr$c.fa.gz
  42         fi
  43
  44         if [ ! -f hs_ref_chr$c.fa ] ; then
  45                 echo "Could not find hs_ref_chr$c.fa file!"
  46                 exit 2
  47         fi
  48 done
  49
  50 # Special case: get mitochondrial DNA from its home
  51 if [ ! -f hs_ref_chrMT.fa ] ; then
  52         if ! which wget > /dev/null ; then
  53                 echo wget not found, looking for curl...
  54                 if ! which curl > /dev/null ; then
  55                         echo curl not found either, aborting...
  56                 else
  57                         # Use curl
  58                         curl ${GENOMES_MIRROR}/H_sapiens/CHR_MT/hs_ref_chrMT.fa.gz
  59                 fi
  60         else
  61                 # Use wget
  62                 wget ${GENOMES_MIRROR}/H_sapiens/CHR_MT/hs_ref_chrMT.fa.gz
  63         fi
  64         gunzip hs_ref_chrMT.fa.gz
  65 fi
  66
  67 INPUTS=hs_ref_chr1.fa,hs_ref_chr2.fa,hs_ref_chr3.fa,hs_ref_chr4.fa,hs_ref_chr5.fa,hs_ref_chr6.fa,hs_ref_chr7.fa,hs_ref_chr8.fa,hs_ref_chr9.fa,hs_ref_chr10.fa,hs_ref_chr11.fa,hs_ref_chr12.fa,hs_ref_chr13.fa,hs_ref_chr14.fa,hs_ref_chr15.fa,hs_ref_chr16.fa,hs_ref_chr17.fa,hs_ref_chr18.fa,hs_ref_chr19.fa,hs_ref_chr20.fa,hs_ref_chr21.fa,hs_ref_chr22.fa,hs_ref_chrMT.fa,hs_ref_chrX.fa,hs_ref_chrY.fa
  68
  69 echo Running ${BOWTIE_BUILD_EXE} $* ${INPUTS} h_sapiens_asm
  70 ${BOWTIE_BUILD_EXE} $* ${INPUTS} h_sapiens_asm
  71
  72 if [ "$?" = "0" ] ; then
  73         echo "h_sapiens_asm index built:"
  74         echo "   h_sapiens_asm.1.ebwt h_sapiens_asm.2.ebwt"
  75         echo "   h_sapiens_asm.3.ebwt h_sapiens_asm.4.ebwt"
  76         echo "   h_sapiens_asm.rev.1.ebwt h_sapiens_asm.rev.2.ebwt"
  77         echo "You may remove hs_ref_chr*.fa"
  78 else
  79         echo "Index building failed; see error message"
  80 fi