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

cds/tools/chlorodb added

Browse Source 
Former-commit-id: 0579e878a69b7c285ca71870e9ca5730649a2fda
Former-commit-id: 7cced5b488441d87bf070a9a444317db0e048880
This commit is contained in:
alain viari
2015-11-13 17:41:18 +01:00
parent 0d5f0c1f20
commit e4d6a8484d
585 changed files with 4750 additions and 50 deletions
Download Patch File Download Diff File Expand all files Collapse all files

20
detectors/cds/bin/go_cds.sh
View File

@ -13,7 +13,7 @@
# Results are printed to the standard output
#
#========================================================================================
# usage: go_cds.sh fasta
# usage: go_cds.sh fasta [db_core]
#
unsetenv ORG_SOURCED
@ -22,13 +22,19 @@ source $ORG_HOME/scripts/csh_init.sh
NeedArg 1
set Fasta = $Argv[1]
set Fasta = $Argv[1]; Shift
NeedFile $Fasta
set Genome = `basename $Fasta:r`
NeedFile $CDS_DATA_DIR/chlorodb/core
set DbCore = $CDS_DATA_DIR/chlorodb/core
if ($#Argv > 0) then
set DbCore = $Argv[1]; Shift
endif
NeedFile $DbCore/Annot.lst
#
# run everything into temporary place
@ -44,15 +50,15 @@ endif
# pass1: run exonerate
#
set fams = `ls $CDS_DATA_DIR/chlorodb/core/*.fst`
set fams = `ls $DbCore/*.fst`
Notify "running pass1: exonerate of $Genome"
Notify "running pass1: exonerate of $Genome on $DbCore"
foreach f ($fams)
set prot = `basename $f:r`
$PROG_DIR/go_pass1.sh $Fasta $prot $temp
$PROG_DIR/do_exonerate.sh $Fasta $f $temp
end
#
# pass2: transsplicing
#