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comparison NGSrich_0.5.5/thirdparty/fetchChromSizes @ 0:89ad0a9cca52 default tip

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author pfrommolt
date Mon, 21 Nov 2011 08:12:19 -0500
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1 #!/bin/sh
2
3 # fetchChromSizes - script to grab chrom.sizes from UCSC via either of:
4 # mysql, wget or ftp
5
6 # "$Id: fetchChromSizes,v 1.2 2009/03/26 18:40:09 hiram Exp $"
7
8 usage() {
9 echo "usage: fetchChromSizes <db> > <db>.chrom.sizes"
10 echo " used to fetch chrom.sizes information from UCSC for the given <db>"
11 echo "<db> - name of UCSC database, e.g.: hg18, mm9, etc ..."
12 echo ""
13 echo "This script expects to find one of the following commands:"
14 echo " wget, mysql, or ftp in order to fetch information from UCSC."
15 echo "Route the output to the file <db>.chrom.sizes as indicated above."
16 echo ""
17 echo "Example: fetchChromSizes hg18 > hg18.chrom.sizes"
18 exit 255
19 }
20
21 DB=$1
22 export DB
23 if [ -z "${DB}" ]; then
24 usage
25 fi
26
27 WGET=`type wget 2> /dev/null | sed -e "s/.* is //"`
28 MYSQL=`type mysql 2> /dev/null | sed -e "s/.* is //"`
29 FTP=`type ftp 2> /dev/null | sed -e "s/.* is //"`
30
31 if [ -z "${WGET}" -a -z "${MYSQL}" -a -z "${FTP}" ]; then
32 echo "ERROR: can not find any of the commands: wget mysql or ftp"
33 usage
34 fi
35
36 DONE=0
37 export DONE
38 if [ -n "${MYSQL}" ]; then
39 echo "INFO: trying MySQL ${MYSQL} for database ${DB}" 1>&2
40 ${MYSQL} -N --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \
41 "SELECT chrom,size FROM chromInfo ORDER BY size DESC;" ${DB}
42 if [ $? -ne 0 ]; then
43 echo "WARNING: mysql command failed" 1>&2
44 else
45 DONE=1
46 fi
47 fi
48
49 if [ "${DONE}" -eq 1 ]; then
50 exit 0
51 fi
52
53 if [ -n "${WGET}" ]; then
54 echo "INFO: trying WGET ${WGET} for database ${DB}" 1>&2
55 tmpResult=chromInfoTemp.$$.gz
56 ${WGET} \
57 "ftp://hgdownload.cse.ucsc.edu/goldenPath/${DB}/database/chromInfo.txt.gz" \
58 -O ${tmpResult} 2> /dev/null
59 if [ $? -ne 0 -o ! -s "${tmpResult}" ]; then
60 echo "WARNING: wget command failed" 1>&2
61 rm -f "${tmpResult}"
62 else
63 zcat ${tmpResult} 2> /dev/null | cut -f1,2 | sort -k2nr
64 rm -f "${tmpResult}"
65 DONE=1
66 fi
67 fi
68
69 if [ "${DONE}" -eq 1 ]; then
70 exit 0
71 fi
72
73 if [ -n "${FTP}" ]; then
74 echo "INFO: trying FTP ${FTP} for database ${DB}" 1>&2
75 tmpFtpRsp=fetchTemp.$$
76 echo "user anonymous fetchChromSizes@" > ${tmpFtpRsp}
77 echo "cd goldenPath/${DB}/database" >> ${tmpFtpRsp}
78 echo "get chromInfo.txt.gz ${tmpResult}" >> ${tmpFtpRsp}
79 echo "bye" >> ${tmpFtpRsp}
80 ${FTP} -u -n -i hgdownload.cse.ucsc.edu < ${tmpFtpRsp} > /dev/null 2>&1
81 if [ $? -ne 0 -o ! -s "${tmpResult}" ]; then
82 echo "ERROR: ftp command failed" 1>&2
83 rm -f "${tmpFtpRsp}" "${tmpResult}"
84 else
85 zcat ${tmpResult} | cut -f1,2 | sort -k2nr
86 rm -f "${tmpFtpRsp}" "${tmpResult}"
87 DONE=1
88 fi
89 fi
90
91 if [ "${DONE}" -eq 0 ]; then
92 echo "ERROR: sorry, attempt to fetch chrom.sizes has failed ?" 1>&2
93 exit 255
94 fi