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annotation_submission.sh~
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#!/bin/bash
datadir=/pym/Data/Nanopore/projects/prolificans
if [ $1 == sqn ] ; then
~/software/table2asn \
-M n -Z -J -c w \
-euk \
-locus-tag-prefix jhhlp \
-augustus-fix \
-gaps-min 5 \
-gaps-unknown 100 \
-l paired-ends \
-j "[organism=Lomentospora prolificans] [isolate=JHH-5317]" \
-t $datadir/nina_annot/st5317.sbt \
-i $datadir/nina_names/st5317.final2-new_names.fasta \
-f $datadir/nina_annot/st5317.final2.fasta.functional_note.pseudo_label.gff \
-o $datadir/nina_annot/st5317.sqn
fi
if [ $1 == st31 ] ; then
~/software/table2asn \
-M n -Z -J -c w \
-euk \
-locus-tag-prefix SC321 \
-augustus-fix \
-gaps-min 5 \
-gaps-unknown 100 \
-l paired-ends \
-j "[organism=Lomentospora prolificans] [isolate=3.1]" \
-t $datadir/nina_annot/st31.sbt \
-i $datadir/nina_names/st31.final2-new_names.fasta \
-f $datadir/nina_annot/st31.final2.fasta.functional_note.pseudo_label.gff \
-o $datadir/nina_annot/st31.sqn
fi
if [ $1 == st90853 ] ; then
~/software/table2asn \
-M n -Z -J -c w \
-euk \
-locus-tag-prefix SC322 \
-augustus-fix \
-gaps-min 5 \
-gaps-unknown 100 \
-l paired-ends \
-j "[organism=Lomentospora prolificans] [isolate=90853]" \
-t $datadir/nina_annot/st90853.sbt \
-i $datadir/nina_names/st90853.final2-new_names.fasta \
-f $datadir/nina_annot/st90853.final2.fasta.functional_note.pseudo_label.gff \
-o $datadir/nina_annot/st90853.sqn
fi
if [ $1 == add_pseudo ] ; then
for i in st90853 st31 st5317 ;
do
python ./add_pseudo.py \
-g $datadir/nina_annot/$i.final2.fasta.functional_note.pseudo_label.gff \
-v $datadir/nina_annot/$i.val \
-o $datadir/nina_annot/$i.final2.fasta.functional_note.pseudo_label.yfan.gff
done
fi