scripts/make_hg19.sh

   1 #!/bin/sh
   2
   3 #
   4 # Downloads sequence for the hg19 version of H. spiens (human) from
   5 # UCSC.
   6 #
   7 # Note that UCSC's hg19 build has three categories of compressed fasta
   8 # files:
   9 #
  10 # 1. The base files, named chr??.fa.gz
  11 # 2. The unplaced-sequence files, named chr??_gl??????_random.fa.gz
  12 # 3. The alternative-haplotype files, named chr??_?????_hap?.fa.gz
  13 #
  14 # By default, this script builds and index for just the base files,
  15 # since alignments to those sequences are the most useful.  To change
  16 # which categories are built by this script, edit the CHRS_TO_INDEX
  17 # variable below.
  18 #
  19
  20 BASE_CHRS="\
  21 chr1 \
  22 chr2 \
  23 chr3 \
  24 chr4 \
  25 chr5 \
  26 chr6 \
  27 chr7 \
  28 chr8 \
  29 chr9 \
  30 chr10 \
  31 chr11 \
  32 chr12 \
  33 chr13 \
  34 chr14 \
  35 chr15 \
  36 chr16 \
  37 chr17 \
  38 chr18 \
  39 chr19 \
  40 chr20 \
  41 chr21 \
  42 chr22 \
  43 chrX \
  44 chrY \
  45 chrM"
  46
  47 RANDOM_CHRS="\
  48 chr1_gl000191_random \
  49 chr1_gl000192_random \
  50 chr4_gl000193_random \
  51 chr4_gl000194_random \
  52 chr7_gl000195_random \
  53 chr8_gl000196_random \
  54 chr8_gl000197_random \
  55 chr9_gl000198_random \
  56 chr9_gl000199_random \
  57 chr9_gl000200_random \
  58 chr9_gl000201_random \
  59 chr11_gl000202_random \
  60 chr17_gl000203_random \
  61 chr17_gl000204_random \
  62 chr17_gl000205_random \
  63 chr17_gl000206_random \
  64 chr18_gl000207_random \
  65 chr19_gl000208_random \
  66 chr19_gl000209_random \
  67 chr21_gl000210_random \
  68 chrUn_gl000211 \
  69 chrUn_gl000212 \
  70 chrUn_gl000213 \
  71 chrUn_gl000214 \
  72 chrUn_gl000215 \
  73 chrUn_gl000216 \
  74 chrUn_gl000217 \
  75 chrUn_gl000218 \
  76 chrUn_gl000219 \
  77 chrUn_gl000220 \
  78 chrUn_gl000221 \
  79 chrUn_gl000222 \
  80 chrUn_gl000223 \
  81 chrUn_gl000224 \
  82 chrUn_gl000225 \
  83 chrUn_gl000226 \
  84 chrUn_gl000227 \
  85 chrUn_gl000228 \
  86 chrUn_gl000229 \
  87 chrUn_gl000230 \
  88 chrUn_gl000231 \
  89 chrUn_gl000232 \
  90 chrUn_gl000233 \
  91 chrUn_gl000234 \
  92 chrUn_gl000235 \
  93 chrUn_gl000236 \
  94 chrUn_gl000237 \
  95 chrUn_gl000238 \
  96 chrUn_gl000239 \
  97 chrUn_gl000240 \
  98 chrUn_gl000241 \
  99 chrUn_gl000242 \
 100 chrUn_gl000243 \
 101 chrUn_gl000244 \
 102 chrUn_gl000245 \
 103 chrUn_gl000246 \
 104 chrUn_gl000247 \
 105 chrUn_gl000248 \
 106 chrUn_gl000249"
 107
 108 ALT_HAP_CHRS="\
 109 chr4_ctg9_hap1 \
 110 chr6_apd_hap1 \
 111 chr6_cox_hap2 \
 112 chr6_dbb_hap3 \
 113 chr6_mann_hap4 \
 114 chr6_mcf_hap5 \
 115 chr6_qbl_hap6 \
 116 chr6_ssto_hap7 \
 117 chr17_ctg5_hap1"
 118
 119 CHRS_TO_INDEX=$BASE_CHRS
 120
 121 UCSC_HG19_BASE=ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes
 122
 123 get() {
 124         file=$1
 125         if ! wget --version >/dev/null 2>/dev/null ; then
 126                 if ! curl --version >/dev/null 2>/dev/null ; then
 127                         echo "Please install wget or curl somewhere in your PATH"
 128                         exit 1
 129                 fi
 130                 curl -o `basename $1` $1
 131                 return $?
 132         else
 133                 wget $1
 134                 return $?
 135         fi
 136 }
 137
 138 BOWTIE_BUILD_EXE=./bowtie-build
 139 if [ ! -x "$BOWTIE_BUILD_EXE" ] ; then
 140         if ! which bowtie-build ; then
 141                 echo "Could not find bowtie-build in current directory or in PATH"
 142                 exit 1
 143         else
 144                 BOWTIE_BUILD_EXE=`which bowtie-build`
 145         fi
 146 fi
 147
 148 INPUTS=
 149 for c in $CHRS_TO_INDEX ; do
 150         if [ ! -f ${c}.fa ] ; then
 151                 F=${c}.fa.gz
 152                 get ${UCSC_HG19_BASE}/$F || (echo "Error getting $F" && exit 1)
 153                 gunzip $F || (echo "Error unzipping $F" && exit 1)
 154         fi
 155         [ -n "$INPUTS" ] && INPUTS=$INPUTS,${c}.fa
 156         [ -z "$INPUTS" ] && INPUTS=${c}.fa
 157 done
 158
 159 CMD="${BOWTIE_BUILD_EXE} $* ${INPUTS} hg19"
 160 echo Running $CMD
 161 if $CMD ; then
 162         echo "hg19 index built; you may remove fasta files"
 163 else
 164         echo "Index building failed; see error message"
 165 fi