442 lines
9.5 KiB
Plaintext
442 lines
9.5 KiB
Plaintext
#! /bin/csh -f
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#
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# stealdata (St.Louis Version)
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#
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# Borrow data and files from a neighbouring cosmid database
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#
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# St.Louis version -
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# 1. prompts users for projects, versions, etc
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# 2. has to handle different reading/trace name conventions:
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#
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# Site Reading Trace
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# ------------ ---------- --------------------
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# Cambridge,UK <read> <read>.{SCF,ABI,ALF>
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# St.Louis <read>.seq <read>
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#
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#
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#
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# Change log:
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#
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# v1.2 Handle dap and bap databases
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# v1.3 Provide linking option
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# v1.4 Under no circumstances link sequence files
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# v1.5 Bug in option "l". Now works when databases have same name
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# v1.6 To work with new version of bap
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# v1.7 Variable report now set correctly
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# v1.7.s St.Louis Version
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# v1.8 bug in fudge
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#
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onintr abort
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#
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# set defaults here
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#
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# NOTE: "other" refers to the project you want to pinch data off
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# NOTE: db_type and other_db_type must be either "dap" or "bap"
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#
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echo -n "project name? (e.g. ZK1236)"
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set project = $<
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echo -n "project version (e.g. 0) "
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set version = $<
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echo -n "database type? (dap or bap) "
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set db_type = $<
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echo -n "other project directory? (e.g. ~rick/ZK353 or ~rick/ZK112/assembly) "
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set other_dir = $<
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echo -n "other project name? (e.g. ZK353) "
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set other_project = $<
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echo -n "other project version? (e.g. 0) "
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set other_version = $<
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echo -n "other database type? (dap or bap) "
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set other_db_type = $<
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#set project = F54G8
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#set version = 0
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#set db_type = dap
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#set other_dir = ~kt/ZC84
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#set other_project = ZC84
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#set other_version = 0
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#set other_db_type = bap
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#
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# available operations are:
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# r = report useful readings (response mailed)
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# s = "r" + copy useful sequences only
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# a = "r" + copy useful sequences AND traces
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# l = "r" + copy useful sequences and LINK traces
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# default = "s"
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#
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# set operation = "s"
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echo "Choose desired operation: "
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echo " Available operations are:"
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echo " r = report useful readings (response mailed)"
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echo " s = r + copy useful sequences only"
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echo " a = r + copy useful sequences AND traces"
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echo " l = r + copy useful sequences and LINK traces"
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set operation = $<
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#
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# other - DON'T TOUCH ... only used for England
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#
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set trace_suffixes = ALF,RES,SCF
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#
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# check defaults
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#
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if (! -e ${project}.SQ${version}) then
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echo Project ${project} version ${version} does not exist
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exit 1
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endif
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if (! -d ${other_dir}) then
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echo Directory ${other_dir} does not exist
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exit 1
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endif
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if (! -e ${other_dir}/${other_project}.SQ${other_version}) then
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echo Project ${other_dir}/${other_project} version ${other_version} does not exist
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exit 1
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endif
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#
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# Report file
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#
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set report = $cwd/_steal.rep.${project}
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set count = 0
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while ( -e $report )
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# echo Report file ${report} already exists...
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@ count ++
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set report = $cwd/_steal.rep.${project}.${count}
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end
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touch ${report}
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#
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# Output details of stealdata run
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#
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cat << EOF | tee -a ${report}
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Stealdata v1.8
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Borrow data from neighbouring cosmid database
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project = ${project}
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version = ${version}
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db_type = ${db_type}
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other_dir = ${other_dir}
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other_project = ${other_project}
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other_version = ${other_version}
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other_db_type = ${other_db_type}
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operation = ${operation}
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EOF
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switch ( ${operation} )
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case "r":
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echo " ( report only )" | tee -a ${report}
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breaksw
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case "s":
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echo " ( copy sequences only, report )" | tee -a ${report}
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breaksw
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case "a":
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echo " ( copy sequences and traces, report )" | tee -a ${report}
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breaksw
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case "l":
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echo " ( copy sequences and link traces, report )" | tee -a ${report}
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breaksw
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default:
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echo " ( unknown - report only )" | tee -a ${report}
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set operation = "r"
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breaksw
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endsw
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echo "" | tee -a ${report}
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#
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# create a temporary directory
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#
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echo Creating a temporary directory | tee -a ${report}
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set temp_dir = _steal.dir.${other_project}
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set count = 0
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while (-e ${temp_dir})
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echo Temporary directory ${temp_dir} already exists | tee -a ${report}
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@ count ++
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set temp_dir = _steal.dir.${other_project}.${count}
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end
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set home_dir = `pwd`
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mkdir ${temp_dir}
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#
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#consensus for database
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#
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set consensus = _steal.seq.${project}
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set count = 0
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while ( -e $consensus )
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echo Consensus file ${consensus} already exists | tee -a ${report}
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@ count ++
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set consensus = _steal.seq.${project}.${count}
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end
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#
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# determine consensus
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#
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echo Determining the consensus for project ${project} version ${version} | tee -a ${report}
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#
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# FUDGE!!!
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# The third question in option 8 (Calculate consensus)
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# has changed in the latest version of bap.
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# Was:
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# ? Make another consensus (y/n) (y)
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# Now is:
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# ? Staden format (y/n) (y) =
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#
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# Set fudge to reflect the appropriate choice
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#
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if ( ${db_type} == "bap" ) then
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set fudge = y
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else
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set fudge = n
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endif
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${db_type} << EOF > /dev/null
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y
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${project}
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${version}
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8
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${consensus}
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y
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${fudge}
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!
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EOF
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if ( $status ) then
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echo stealdata: failed to make consensus | tee -a ${report}
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goto abort
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endif
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#
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# move consensus to temp_dir
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#
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mv ${consensus} ${temp_dir}
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if ( $status ) then
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echo stealdata: failed to move consensus to temp_dir | tee -a ${report}
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goto abort
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endif
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#
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# copy other database to this directory
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#
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echo Copying project ${other_project} version ${other_version} | tee -a ${report}
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cd ${temp_dir}
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cp -i \
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${other_dir}/${other_project}.SQ${other_version} \
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${other_dir}/${other_project}.AR${other_version} \
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${other_dir}/${other_project}.RL${other_version} \
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${other_dir}/${other_project}.TG${other_version} \
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${other_dir}/${other_project}.CC${other_version} \
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.
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if ( $status ) then
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echo stealdata: failed to copy other database | tee -a ${report}
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goto abort
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endif
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#
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# file of file names in other database
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#
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set other_files = ${other_project}.all
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set other_useless = ${other_project}.useless
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set other_useful = ${other_project}.useful
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set other_new = ${other_project}.fn.$$
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#
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# extract gel readings
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#
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set option_extract = 32
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#
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# screen against vector
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#
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set option_screen = 18
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#
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echo Extracting gel readings from ${other_project} and | tee -a ${report}
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echo " screening against consensus from ${project}" | tee -a ${report}
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${other_db_type} << EOF > /dev/null
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y
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${other_project}
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${other_version}
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${option_extract}
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${other_files}
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n
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${option_screen}
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y
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${other_files}
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${other_useless}
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${consensus}
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30
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!
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EOF
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if ( $status ) then
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echo stealdata: failed to extact or screen readings | tee -a ${report}
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goto abort
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endif
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#
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# determine useful files in other project
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#
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echo Determining useful gel readings | tee -a ${report}
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# lfw added awk intermediary
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# need to get a .seq on the end of all of the filenames...the output
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# from dap/bap would have truncated names
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sort ${other_files} | tr -d ' ' | awk 'BEGIN{FS=".";}{ print $1"."$2".seq";}' > ${other_files}.nice
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sort ${other_useless} | tr -d ' ' | awk 'BEGIN{FS=".";}{ print $1"."$2".seq";}' > ${other_useless}.nice
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comm -23 ${other_files}.nice ${other_useless}.nice > ${other_useful}
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#
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# create report header
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#
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echo "" | tee -a ${report}
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echo Useful gel readings: | tee -a ${report}
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#
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# determine new files
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#
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touch ${other_new}
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set useful = 0
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foreach x ( `cat ${other_useful}` )
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if ( -e ../$x ) then
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echo $x | tee -a ${report}
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else
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echo $x "- NEW" | tee -a ${report}
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echo $x >> ${other_new}
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@ useful ++
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endif
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end
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if ( $useful == 0 ) then
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echo No new gel readings | tee -a ${report}
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goto done
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endif
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#
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# transfer sequences
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#
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if (${operation} == "s") then
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echo "" | tee -a ${report}
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echo "Transfering sequence files: " | tee -a ${report}
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foreach x ( `cat ${other_new}` )
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cp -i ${other_dir}/${x} ..
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echo ${other_dir}/${x} | tee -a ${report}
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end
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# file of file names
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mv ${other_new} ..
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echo "" | tee -a ${report}
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echo File of file names is ${other_new} | tee -a ${report}
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endif
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#
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# transfer sequences and traces
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#
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if (${operation} == "a") then
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echo "" | tee -a ${report}
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echo "Transfering sequence and trace files: " | tee -a ${report}
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# foreach x ( `cat ${other_new} | sed 's/.seq//g' ` )
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# change by lfw for our sequence file naming convention
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foreach x ( `cat ${other_new} | sed 's/.seq//g' ` )
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# copy sequence file
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cp -i ${other_dir}/${x} ..
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echo ${other_dir}/${x} | tee -a ${report}
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# foreach file ( ${other_dir}/${x}{${trace_suffixes}} )
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# change by lfw for our sequence file naming convention
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foreach file ( ${other_dir}/${x} )
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if (-e $file) then
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cp -i $file ..
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echo $file | tee -a ${report}
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endif
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end
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end
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# file of file names
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mv ${other_new} ..
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echo "" | tee -a ${report}
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echo File of file names is ${other_new} | tee -a ${report}
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endif
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#
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# transfer sequences and link traces
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#
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if (${operation} == "l") then
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echo "" | tee -a ${report}
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echo "Transfering sequence and trace files: " | tee -a ${report}
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#change by lfw so that it accomodates our sequence file names
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set files = `cat ${other_new} | sed 's/.seq//g' `
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pushd .. >& /dev/null
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foreach x ( $files )
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# copy sequence file
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cp -i ${other_dir}/${x} .
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echo ${other_dir}/${x} | tee -a ${report}
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# foreach file ( ${other_dir}/${x}{${trace_suffixes}} )
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# change by lfw so that it accomodates our sequence and trace file names
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foreach file ( ${other_dir}/${x} )
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# link to traces
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if (-e $file) then
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ln -s $file
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echo $file | tee -a ${report}
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endif
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end
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end
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popd >& /dev/null
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# file of file names
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mv ${other_new} ..
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echo "" | tee -a ${report}
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echo File of file names is ${other_new} | tee -a ${report}
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endif
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done:
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#
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# cleanup
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#
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echo Cleaning up | tee -a ${report}
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cd ..
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/bin/rm -r ${temp_dir}
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#
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# Finish up
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#
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echo "" | tee -a ${report}
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echo "Completed" | tee -a ${report}
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#
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# mail report
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#
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echo Mailing you a report
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mail `whoami` < ${report}
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exit 0
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#
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#
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#
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abort:
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echo stealdata aborted `date` | tee -a ${report}
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if ( $?home_dir ) then
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cd $home_dir
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echo Cleaning up | tee -a ${report}
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/bin/rm -r ${temp_dir}
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endif
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exit 1
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