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Top Forums Shell Programming and Scripting Run a program-print parameters to output file-replace op file contents with max 4th col Post 302760173 by Corona688 on Wednesday 23rd of January 2013 01:27:25 PM
Old 01-23-2013
Code:
while read CHROM START END NAME
do
        # Create the bed file
        program input2.bed -chrom=$CHROM -start=$START -end=$END ${CHROM}_${START}_${END}_op.bed

        # Replace column 1 with filename,
        # column 2 with the last column,
        # reduce it to 2 columns,
        # and print all lines.
        awk '{$1=F ; $2=$NF; NF=2 } 1' F="${CHROM}_${START}_${END}" ${CHROM}_${START}_${END}_op.bed > /tmp/$$
        cat /tmp/$$ > ${CHROM}_${START}_${END}_op.bed
done < input1.bed
# Remove temporary file
rm -f /tmp/$$

For 3 and 4, you start with 3 lines and end with 1 line. Is this intended? I've assumed it's not, that you want 3 lines out for 3 lines in.
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START 
TRANSACTION(7) SQL Commands START TRANSACTION(7) NAME
START TRANSACTION - start a transaction block SYNOPSIS
START TRANSACTION [ transaction_mode [, ...] ] where transaction_mode is one of: ISOLATION LEVEL { SERIALIZABLE | REPEATABLE READ | READ COMMITTED | READ UNCOMMITTED } READ WRITE | READ ONLY DESCRIPTION
This command begins a new transaction block. If the isolation level or read/write mode is specified, the new transaction has those charac- teristics, as if SET TRANSACTION [set_transaction(7)] was executed. This is the same as the BEGIN [begin(7)] command. PARAMETERS
Refer to SET TRANSACTION [set_transaction(7)] for information on the meaning of the parameters to this statement. COMPATIBILITY
In the standard, it is not necessary to issue START TRANSACTION to start a transaction block: any SQL command implicitly begins a block. PostgreSQL's behavior can be seen as implicitly issuing a COMMIT after each command that does not follow START TRANSACTION (or BEGIN), and it is therefore often called ``autocommit''. Other relational database systems might offer an autocommit feature as a convenience. The SQL standard requires commas between successive transaction_modes, but for historical reasons PostgreSQL allows the commas to be omit- ted. See also the compatibility section of SET TRANSACTION [set_transaction(7)]. SEE ALSO
BEGIN [begin(7)], COMMIT [commit(7)], ROLLBACK [rollback(7)], SAVEPOINT [savepoint(7)], SET TRANSACTION [set_transaction(7)] SQL - Language Statements 2010-05-14 START TRANSACTION(7)
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