1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
|
#!/bin/sh
#
# Downloads sequence for H. sapiens (human) from NCBI. This script was
# used to build the Bowtie index for H. sapiens 37.
#
# From README_CURRENT_BUILD:
# Organism: Homo sapiens (human)
# NCBI Build Number: 37
# Version: 1
# Release date: 04 August 2009
#
BASE_CHRS="\
chr1 \
chr2 \
chr3 \
chr4 \
chr5 \
chr6 \
chr7 \
chr8 \
chr9 \
chr10 \
chr11 \
chr12 \
chr13 \
chr14 \
chr15 \
chr16 \
chr17 \
chr18 \
chr19 \
chr20 \
chr21 \
chr22 \
chrX \
chrY"
CHRS_TO_INDEX=$BASE_CHRS
FTP_BASE=ftp://ftp.ncbi.nih.gov/genomes/H_sapiens
FTP_ASM_BASE=$FTP_BASE/Assembled_chromosomes
FTP_MT_BASE=$FTP_BASE/CHR_MT
get() {
file=$1
if ! wget --version >/dev/null 2>/dev/null ; then
if ! curl --version >/dev/null 2>/dev/null ; then
echo "Please install wget or curl somewhere in your PATH"
exit 1
fi
curl -o `basename $1` $1
return $?
else
wget $1
return $?
fi
}
BOWTIE_BUILD_EXE=./bowtie-build
if [ ! -x "$BOWTIE_BUILD_EXE" ] ; then
if ! which bowtie-build ; then
echo "Could not find bowtie-build in current directory or in PATH"
exit 1
else
BOWTIE_BUILD_EXE=`which bowtie-build`
fi
fi
INPUTS=
BASE_NAME=hs_ref_GRCh37_
for c in $CHRS_TO_INDEX ; do
c=${BASE_NAME}${c}
if [ ! -f $c.fa ] ; then
F=$c.fa.gz
get ${FTP_ASM_BASE}/$F || (echo "Error getting $F" && exit 1)
gunzip $F || (echo "Error unzipping $F" && exit 1)
fi
[ -n "$INPUTS" ] && INPUTS=$INPUTS,$c.fa
[ -z "$INPUTS" ] && INPUTS=$c.fa
done
# Special case: get mitochondrial DNA from its home
if [ ! -f hs_ref_chrMT.fa ] ; then
F=hs_ref_chrMT.fa.gz
get ${FTP_MT_BASE}/$F || (echo "Error getting $F" && exit 1)
gunzip $F || (echo "Error unzipping $F" && exit 1)
fi
INPUTS=$INPUTS,hs_ref_chrMT.fa
echo Running ${BOWTIE_BUILD_EXE} $* ${INPUTS} h_sapiens_37_asm
${BOWTIE_BUILD_EXE} $* ${INPUTS} h_sapiens_37_asm
if [ "$?" = "0" ] ; then
echo "h_sapiens_37_asm index built:"
echo " h_sapiens_37_asm.1.ebwt h_sapiens_37_asm.2.ebwt"
echo " h_sapiens_37_asm.3.ebwt h_sapiens_37_asm.4.ebwt"
echo " h_sapiens_37_asm.rev.1.ebwt h_sapiens_37_asm.rev.2.ebwt"
echo "You may remove hs_ref_chr*.fa"
else
echo "Index building failed; see error message"
fi
|
