Mercurial > repos > pjbriggs > pal_finder
comparison pal_finder_wrapper.sh @ 7:5e133b7b79a6 draft
Uploaded version 0.02.04.6 (uses conda dependency resolution).
author | pjbriggs |
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date | Mon, 19 Mar 2018 06:33:32 -0400 |
parents | a73c48890bde |
children | 4e625d3672ba |
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6:a73c48890bde | 7:5e133b7b79a6 |
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331 if [ -z "$(tail -n 1 pal_finder.log | grep Done!!)" ] ; then | 331 if [ -z "$(tail -n 1 pal_finder.log | grep Done!!)" ] ; then |
332 echo ERROR pal_finder failed to complete successfully >&2 | 332 echo ERROR pal_finder failed to complete successfully >&2 |
333 exit 1 | 333 exit 1 |
334 fi | 334 fi |
335 # | 335 # |
336 # Sort outputs into a consistent order regardless of Perl version | 336 # Sort microsat_summary output |
337 echo "### Sorting outputs ###" | 337 echo "### Sorting microsat summary output ###" |
338 head -n 7 Output/microsat_summary.txt | sort >microsat_summary.sorted | |
339 grep "^$" Output/microsat_summary.txt>>microsat_summary.sorted | |
340 grep "^Microsat Type" Output/microsat_summary.txt >>microsat_summary.sorted | |
341 tail -n +11 Output/microsat_summary.txt >>microsat_summary.sorted | |
342 mv microsat_summary.sorted Output/microsat_summary.txt | |
343 # | |
344 # Sort PAL_summary output | |
345 echo "### Sorting PAL summary output ###" | |
338 head -1 Output/PAL_summary.txt > Output/PAL_summary.sorted.txt | 346 head -1 Output/PAL_summary.txt > Output/PAL_summary.sorted.txt |
339 if [ "$PLATFORM" == "Illumina" ] ; then | 347 if [ "$PLATFORM" == "Illumina" ] ; then |
340 grep -v "^readPairID" Output/PAL_summary.txt | sort -k 1 >> Output/PAL_summary.sorted.txt | 348 grep -v "^readPairID" Output/PAL_summary.txt | sort -k 1 >> Output/PAL_summary.sorted.txt |
341 else | 349 else |
342 grep -v "^SequenceID" Output/PAL_summary.txt | sort -k 1 >> Output/PAL_summary.sorted.txt | 350 grep -v "^SequenceID" Output/PAL_summary.txt | sort -k 1 >> Output/PAL_summary.sorted.txt |