Mercurial > repos > rnateam > rnacode
diff processMAF.sh @ 2:f9a7dc68d6cf draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit 3abc213e109bb564de7dee75d71d90eb1bf78c7e
| author | rnateam |
|---|---|
| date | Thu, 15 Nov 2018 01:15:35 -0500 |
| parents | 0554fa091710 |
| children |
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--- a/processMAF.sh Fri Apr 13 07:37:15 2018 -0400 +++ b/processMAF.sh Thu Nov 15 01:15:35 2018 -0500 @@ -133,7 +133,7 @@ last=0 if [[ ! -z "$tabular" ]]; then - echo -e "HSS #\tFrame\tLength\tFrom\tTo\tName\tStart\tEnd\tScore\tP" >> ${outfile:-/dev/stdout} + echo -e "HSS #\tStrand\tFrame\tLength\tFrom\tTo\tName\tStart\tEnd\tScore\tP" >> ${outfile:-/dev/stdout} fi tmpif=$(mktemp -p '.') @@ -151,8 +151,7 @@ if [[ "$line" =~ ^# ]]; then echo -n > ${tmpif} elif [[ "$line" =~ ^$ ]]; then - run_rnacode ${args[@]} ${tmpif} - # >> ${outfile:-/dev/stdout} + run_rnacode ${args[@]} ${tmpif} >> ${outfile:-/dev/stdout} echo -n > ${tmpif} else if [[ -z $ref && "$line" =~ ^s ]]; then @@ -167,8 +166,7 @@ done < ${file:-/dev/stdin} # if there is something left -> process it if [[ "`cat ${tmpif} | wc -l`" -gt "0" ]]; then - run_rnacode ${args[@]} ${tmpif} - # >> ${outfile:-/dev/stdout} + run_rnacode ${args[@]} ${tmpif} >> ${outfile:-/dev/stdout} fi if [[ ! -z "$eps" ]]; then