4 # Downloads sequence for H. sapiens (human) from NCBI. This script was
5 # used to build the Bowtie index for H. sapiens 37.
7 # From README_CURRENT_BUILD:
8 # Organism: Homo sapiens (human)
9 # NCBI Build Number: 37
11 # Release date: 04 August 2009
40 CHRS_TO_INDEX=$BASE_CHRS
42 FTP_BASE=ftp://ftp.ncbi.nih.gov/genomes/H_sapiens
43 FTP_ASM_BASE=$FTP_BASE/Assembled_chromosomes
44 FTP_MT_BASE=$FTP_BASE/CHR_MT
48 if ! wget --version >/dev/null 2>/dev/null ; then
49 if ! curl --version >/dev/null 2>/dev/null ; then
50 echo "Please install wget or curl somewhere in your PATH"
53 curl -o `basename $1` $1
61 BOWTIE_BUILD_EXE=./bowtie-build
62 if [ ! -x "$BOWTIE_BUILD_EXE" ] ; then
63 if ! which bowtie-build ; then
64 echo "Could not find bowtie-build in current directory or in PATH"
67 BOWTIE_BUILD_EXE=`which bowtie-build`
72 BASE_NAME=hs_ref_GRCh37_
73 for c in $CHRS_TO_INDEX ; do
75 if [ ! -f $c.fa ] ; then
77 get ${FTP_ASM_BASE}/$F || (echo "Error getting $F" && exit 1)
78 gunzip $F || (echo "Error unzipping $F" && exit 1)
80 [ -n "$INPUTS" ] && INPUTS=$INPUTS,$c.fa
81 [ -z "$INPUTS" ] && INPUTS=$c.fa
84 # Special case: get mitochondrial DNA from its home
85 if [ ! -f hs_ref_chrMT.fa ] ; then
87 get ${FTP_MT_BASE}/$F || (echo "Error getting $F" && exit 1)
88 gunzip $F || (echo "Error unzipping $F" && exit 1)
91 INPUTS=$INPUTS,hs_ref_chrMT.fa
93 echo Running ${BOWTIE_BUILD_EXE} $* ${INPUTS} h_sapiens_37_asm
94 ${BOWTIE_BUILD_EXE} $* ${INPUTS} h_sapiens_37_asm
96 if [ "$?" = "0" ] ; then
97 echo "h_sapiens_37_asm index built:"
98 echo " h_sapiens_37_asm.1.ebwt h_sapiens_37_asm.2.ebwt"
99 echo " h_sapiens_37_asm.3.ebwt h_sapiens_37_asm.4.ebwt"
100 echo " h_sapiens_37_asm.rev.1.ebwt h_sapiens_37_asm.rev.2.ebwt"
101 echo "You may remove hs_ref_chr*.fa"
103 echo "Index building failed; see error message"