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Small reduction in temporals for `:ogs`

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lmrodriguezr committed Jun 12, 2019
1 parent c11d279 commit 2a9bfb74152023fe1ad4238686e3c8c8fd36f15a
Showing with 4 additions and 3 deletions.
  1. +3 −2 scripts/ogs.bash
  2. +1 −1 scripts/trimmed_fasta.bash
@@ -23,6 +23,7 @@ if [[ -n $DS ]] ; then
[[ -s "$file" ]] && continue
echo "SELECT seq1,id1,seq2,id2,bitscore from rbm where id >= $MIN_ID;" \
| sqlite3 "../../09.distances/02.aai/$i.db" | tr "\\|" " " \
| perl -pe 's/ gene_/ /g' \
| awk '{ print $1">"$2"'"\\t"'"$3">"$4"'"\\t"'"$5 }' \
> "$file.tmp"
mv "$file.tmp" "$file"
@@ -34,9 +35,9 @@ if [[ -n $DS ]] ; then
# Estimate OGs and Clean RBMs
ogs.mcl.rb -o miga-project.ogs --abc miga-project.abc -t "$CORES"
if [[ $(miga about -P "$PROJECT" -m clean_ogs) == "false" ]] ; then
rm miga-project.abc
else
gzip -9 miga-project.abc
else
rm miga-project.abc
fi
fi

@@ -31,7 +31,7 @@ if [[ -e "../02.trimmed_reads/$b.2.clipped.fastq" ]] ; then
> "$b.SingleReads.fa"
gzip -9 -f "$b.SingleReads.fa"
else
mv "$b.1.fasta" "$b.SingleReads.fa"
mv "$b.1.fasta" "$b.SingleReads.fa"
fi

# Compress input at 01.raw_reads and 02.trimmed_reads

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