PhyloSkims/annotate
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Patch a bug to launch exonerate on complexe filename

Browse Source 
Former-commit-id: e8357a639a22cb123985a0ed487dfd4018c9bb0a
Former-commit-id: a2e1c2ce75c0eac9574b7a68506f6f209e54ea89
This commit is contained in:
Eric Coissac
2018-01-24 14:30:00 +01:00
parent 4c7ba137d9
commit 8d2ec19fe8
2 changed files with 21 additions and 3 deletions
Download Patch File Download Diff File Expand all files Collapse all files

20
detectors/cds/bin/do_exonerate.csh
View File

@ -110,8 +110,21 @@ set base = $OutDir/$GenoName.$ProtName
#
# Alias the genome filename to a short name
# to circumvent a bug in exonerate
set ShortLink = $OutDir/genome.fasta
ln -s $GenoFile $ShortLink
echo $GenoFile | grep '^/' > /dev/null
if ( $status == 1 ) then
set AbsGenoFile = `pwd`/$GenoFile
set DirGenoFile = `dirname $AbsGenoFile`
set DirGenoFile = `(cd $DirGenoFile;pwd)`
set AbsGenoFile = $DirGenoFile/`basename $AbsGenoFile`
else
set AbsGenoFile = $GenoFile
endif
set ShortDir = `mktemp -d`
set ShortLink = $ShortDir/genome.fasta
ln -s $AbsGenoFile $ShortLink
Notify " Building input shortcut $AbsGenoFile --> $ShortLink"
#
# skip exonerate calculations if already done
@ -232,7 +245,8 @@ $AwkCmd -f $LIB_DIR/toEmbl.awk $base.iff |\
# end
#
rm -f $ShortLink
rm -rf $ShortDir
Notify " output file: $base.res"
(\rm -f ?_$$) >> /dev/null

4
detectors/cds/bin/go_cds.csh
View File

@ -63,6 +63,8 @@ foreach dir ("core" "shell" "dust")
endif
end
cp $temp/ $Genome.cds.fasta $Genome.cds.fasta
#
# pass2: transsplicing
#
@ -71,6 +73,8 @@ end
# pass3: prokov
#
$PROG_DIR/do_prokov.sh $Fasta $Genome.cds.fasta $temp
#
# end : output on stdout
#