Mercurial > repos > pjbriggs > pal_finder
diff pal_finder_wrapper.sh @ 7:5e133b7b79a6 draft
Uploaded version 0.02.04.6 (uses conda dependency resolution).
| author | pjbriggs |
|---|---|
| date | Mon, 19 Mar 2018 06:33:32 -0400 |
| parents | a73c48890bde |
| children | 4e625d3672ba |
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--- a/pal_finder_wrapper.sh Tue Jun 06 08:54:49 2017 -0400 +++ b/pal_finder_wrapper.sh Mon Mar 19 06:33:32 2018 -0400 @@ -333,8 +333,16 @@ exit 1 fi # -# Sort outputs into a consistent order regardless of Perl version -echo "### Sorting outputs ###" +# Sort microsat_summary output +echo "### Sorting microsat summary output ###" +head -n 7 Output/microsat_summary.txt | sort >microsat_summary.sorted +grep "^$" Output/microsat_summary.txt>>microsat_summary.sorted +grep "^Microsat Type" Output/microsat_summary.txt >>microsat_summary.sorted +tail -n +11 Output/microsat_summary.txt >>microsat_summary.sorted +mv microsat_summary.sorted Output/microsat_summary.txt +# +# Sort PAL_summary output +echo "### Sorting PAL summary output ###" head -1 Output/PAL_summary.txt > Output/PAL_summary.sorted.txt if [ "$PLATFORM" == "Illumina" ] ; then grep -v "^readPairID" Output/PAL_summary.txt | sort -k 1 >> Output/PAL_summary.sorted.txt