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Merge pull request #74 from TobyBaril/patch_4.0.2
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Patch 4.0.2
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@TobyBaril
TobyBaril authored Nov 30, 2023
2 parents 2a41691 + a0cba40 commit 759cfed
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Showing 3 changed files with 10 additions and 8 deletions.
4 changes: 2 additions & 2 deletions earlGrey
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Original file line number Diff line number Diff line change
Expand Up @@ -205,14 +205,14 @@ calcDivRL()
mergeRep()
{
mkdir ${OUTDIR}/${species}_mergedRepeats/looseMerge
${SCRIPT_DIR}/rcMergeRepeatsLoose -f $genome -s $species -d ${OUTDIR}/${species}_mergedRepeats/looseMerge -u ${OUTDIR}/${species}_RepeatMasker_Against_Custom_Library/$(basename $genome).out -q ${OUTDIR}/${species}_RepeatMasker_Against_Custom_Library/$(basename $genome).tbl -t $ProcNum -b ${dict}
${SCRIPT_DIR}/rcMergeRepeatsLoose -f $genome -s $species -d ${OUTDIR}/${species}_mergedRepeats/looseMerge -u ${OUTDIR}/${species}_RepeatMasker_Against_Custom_Library/$(basename $genome).out -q ${OUTDIR}/${species}_RepeatMasker_Against_Custom_Library/$(basename $genome).tbl -t $ProcNum -b ${dict} -m $margin
if [ -f "${OUTDIR}/${species}_mergedRepeats/looseMerge/${species}.filteredRepeats.bed" ]; then
awk '{OFS="\t"}{print $1, $2, $3, $4, $5, $6, $7, $8, toupper($9)}' ${OUTDIR}/${species}_mergedRepeats/looseMerge/${species}.filteredRepeats.gff > ${OUTDIR}/${species}_mergedRepeats/looseMerge/${species}.filteredRepeats.gff.1 && mv ${OUTDIR}/${species}_mergedRepeats/looseMerge/${species}.filteredRepeats.gff{.1,}
fi
if [ ! -f "${OUTDIR}/${species}_mergedRepeats/looseMerge/${species}.filteredRepeats.bed" ]; then
echo "ERROR: loose merge defragmentation failed, trying strict merge..."
cd ${OUTDIR}/${species}_mergedRepeats/
${SCRIPT_DIR}/rcMergeRepeats -f $genome -s $species -d ${OUTDIR}/${species}_mergedRepeats/ -u ${OUTDIR}/${species}_RepeatMasker_Against_Custom_Library/$(basename $genome).out -q ${OUTDIR}/${species}_RepeatMasker_Against_Custom_Library/$(basename $genome).tbl -t $ProcNum -b ${dict}
${SCRIPT_DIR}/rcMergeRepeats -f $genome -s $species -d ${OUTDIR}/${species}_mergedRepeats/ -u ${OUTDIR}/${species}_RepeatMasker_Against_Custom_Library/$(basename $genome).out -q ${OUTDIR}/${species}_RepeatMasker_Against_Custom_Library/$(basename $genome).tbl -t $ProcNum -b ${dict} -m $margin
if [ ! -f "${OUTDIR}/${species}_mergedRepeats/${species}.filteredRepeats.bed" ]; then
echo "ERROR: strict merge also failed, check ${OUTDIR}/${species}_RepeatMasker_Against_Custom_Library/$(basename $genome).out looks as expected"
exit 2
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7 changes: 4 additions & 3 deletions scripts/rcMergeRepeats
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Original file line number Diff line number Diff line change
Expand Up @@ -2,11 +2,11 @@

usage()
{
echo "Usage: rcMergeRepeats -f genome.fasta -s species -d output_directory -u RepeatMasker.out -q RepeatMasker.tbl -c repeatcraft.cfg -t ThreadNum -b dictionary | -h"
echo "Usage: rcMergeRepeats -f genome.fasta -s species -d output_directory -u RepeatMasker.out -q RepeatMasker.tbl -c repeatcraft.cfg -t ThreadNum -b dictionary -m yes|no | -h"
}


while getopts f:s:d:u:q:t:b:h option
while getopts f:s:d:u:q:t:b:m:h option
do
case "${option}"
in
Expand All @@ -17,6 +17,7 @@ while getopts f:s:d:u:q:t:b:h option
q) table=${OPTARG};;
t) threads=${OPTARG};;
b) dict=${OPTARG};;
m) cutoff=${OPTARG};;
h) usage; exit;;
esac
done
Expand Down Expand Up @@ -57,7 +58,7 @@ mergeRepeats()
sort -s -k1,1 ${dir}/${spe}.rmerge.gff > ${dir}/${spe}.rmerge.gff.sorted
#filter-gff overlap -v --progress -s 1 -d -t -c length -a length ${dir}/${spe}.rmerge.gff.sorted ${dir}/${spe}.rmerge.gff.filtered
Rscript ${SCRIPT_DIR}/filteringOverlappingRepeats.R ${dir}/${spe}.rmerge.gff.sorted ${dir}/${spe}.rmerge.gff.filtered
Rscript ${SCRIPT_DIR}/mergeRepeats.R ${dir}/${spe}.rmerge.gff.filtered ${dir}/${spe}.mergedRepeats.bed $genSize ${dir}/${spe}.mergedRepeats.revisedTable ${dir}/${spe}.filteredRepeats.bed ${dir}/${spe}.filteredRepeats.summary $margin
Rscript ${SCRIPT_DIR}/mergeRepeats.R ${dir}/${spe}.rmerge.gff.filtered ${dir}/${spe}.mergedRepeats.bed $genSize ${dir}/${spe}.mergedRepeats.revisedTable ${dir}/${spe}.filteredRepeats.bed ${dir}/${spe}.filteredRepeats.summary $cutoff
}


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7 changes: 4 additions & 3 deletions scripts/rcMergeRepeatsLoose
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Original file line number Diff line number Diff line change
Expand Up @@ -2,11 +2,11 @@

usage()
{
echo "Usage: rcMergeRepeats -f genome.fasta -s species -d output_directory -u RepeatMasker.out -q RepeatMasker.tbl -c repeatcraft.cfg -t ThreadNum -b dictionary | -h"
echo "Usage: rcMergeRepeats -f genome.fasta -s species -d output_directory -u RepeatMasker.out -q RepeatMasker.tbl -c repeatcraft.cfg -t ThreadNum -b dictionary -m yes|no | -h"
}


while getopts f:s:d:u:q:t:b:h option
while getopts f:s:d:u:q:t:b:m:h option
do
case "${option}"
in
Expand All @@ -17,6 +17,7 @@ while getopts f:s:d:u:q:t:b:h option
q) table=${OPTARG};;
t) threads=${OPTARG};;
b) dict=${OPTARG};;
m) cutoff=${OPTARG};;
h) usage; exit;;
esac
done
Expand Down Expand Up @@ -56,7 +57,7 @@ mergeRepeats()
{
sort -s -k1,1 ${dir}/${spe}.rmerge.gff > ${dir}/${spe}.rmerge.gff.sorted
Rscript ${SCRIPT_DIR}/filteringOverlappingRepeats.R ${dir}/${spe}.rmerge.gff.sorted ${dir}/${spe}.rmerge.gff.filtered
Rscript ${SCRIPT_DIR}/mergeRepeats.R ${dir}/${spe}.rmerge.gff.filtered ${dir}/${spe}.mergedRepeats.bed $genSize ${dir}/${spe}.mergedRepeats.revisedTable ${dir}/${spe}.filteredRepeats.bed ${dir}/${spe}.filteredRepeats.summary $margin
Rscript ${SCRIPT_DIR}/mergeRepeats.R ${dir}/${spe}.rmerge.gff.filtered ${dir}/${spe}.mergedRepeats.bed $genSize ${dir}/${spe}.mergedRepeats.revisedTable ${dir}/${spe}.filteredRepeats.bed ${dir}/${spe}.filteredRepeats.summary $cutoff
}


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