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1 #!/bin/sh
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2
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3 # fetchChromSizes - script to grab chrom.sizes from UCSC via either of:
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4 # mysql, wget or ftp
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5
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6 # "$Id: fetchChromSizes,v 1.2 2009/03/26 18:40:09 hiram Exp $"
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7
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8 usage() {
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9 echo "usage: fetchChromSizes <db> > <db>.chrom.sizes"
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10 echo " used to fetch chrom.sizes information from UCSC for the given <db>"
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11 echo "<db> - name of UCSC database, e.g.: hg18, mm9, etc ..."
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12 echo ""
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13 echo "This script expects to find one of the following commands:"
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14 echo " wget, mysql, or ftp in order to fetch information from UCSC."
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15 echo "Route the output to the file <db>.chrom.sizes as indicated above."
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16 echo ""
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17 echo "Example: fetchChromSizes hg18 > hg18.chrom.sizes"
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18 exit 255
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19 }
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20
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21 DB=$1
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22 export DB
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23 if [ -z "${DB}" ]; then
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24 usage
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25 fi
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26
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27 WGET=`type wget 2> /dev/null | sed -e "s/.* is //"`
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28 MYSQL=`type mysql 2> /dev/null | sed -e "s/.* is //"`
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29 FTP=`type ftp 2> /dev/null | sed -e "s/.* is //"`
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30
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31 if [ -z "${WGET}" -a -z "${MYSQL}" -a -z "${FTP}" ]; then
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32 echo "ERROR: can not find any of the commands: wget mysql or ftp"
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33 usage
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34 fi
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35
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36 DONE=0
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37 export DONE
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38 if [ -n "${MYSQL}" ]; then
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39 echo "INFO: trying MySQL ${MYSQL} for database ${DB}" 1>&2
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40 ${MYSQL} -N --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \
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41 "SELECT chrom,size FROM chromInfo ORDER BY size DESC;" ${DB}
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42 if [ $? -ne 0 ]; then
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43 echo "WARNING: mysql command failed" 1>&2
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44 else
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45 DONE=1
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46 fi
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47 fi
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48
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49 if [ "${DONE}" -eq 1 ]; then
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50 exit 0
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51 fi
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52
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53 if [ -n "${WGET}" ]; then
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54 echo "INFO: trying WGET ${WGET} for database ${DB}" 1>&2
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55 tmpResult=chromInfoTemp.$$.gz
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56 ${WGET} \
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57 "ftp://hgdownload.cse.ucsc.edu/goldenPath/${DB}/database/chromInfo.txt.gz" \
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58 -O ${tmpResult} 2> /dev/null
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59 if [ $? -ne 0 -o ! -s "${tmpResult}" ]; then
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60 echo "WARNING: wget command failed" 1>&2
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61 rm -f "${tmpResult}"
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62 else
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63 zcat ${tmpResult} 2> /dev/null | cut -f1,2 | sort -k2nr
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64 rm -f "${tmpResult}"
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65 DONE=1
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66 fi
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67 fi
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68
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69 if [ "${DONE}" -eq 1 ]; then
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70 exit 0
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71 fi
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72
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73 if [ -n "${FTP}" ]; then
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74 echo "INFO: trying FTP ${FTP} for database ${DB}" 1>&2
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75 tmpFtpRsp=fetchTemp.$$
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76 echo "user anonymous fetchChromSizes@" > ${tmpFtpRsp}
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77 echo "cd goldenPath/${DB}/database" >> ${tmpFtpRsp}
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78 echo "get chromInfo.txt.gz ${tmpResult}" >> ${tmpFtpRsp}
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79 echo "bye" >> ${tmpFtpRsp}
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80 ${FTP} -u -n -i hgdownload.cse.ucsc.edu < ${tmpFtpRsp} > /dev/null 2>&1
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81 if [ $? -ne 0 -o ! -s "${tmpResult}" ]; then
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82 echo "ERROR: ftp command failed" 1>&2
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83 rm -f "${tmpFtpRsp}" "${tmpResult}"
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84 else
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85 zcat ${tmpResult} | cut -f1,2 | sort -k2nr
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86 rm -f "${tmpFtpRsp}" "${tmpResult}"
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87 DONE=1
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88 fi
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89 fi
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90
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91 if [ "${DONE}" -eq 0 ]; then
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92 echo "ERROR: sorry, attempt to fetch chrom.sizes has failed ?" 1>&2
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93 exit 255
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94 fi
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