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

minor bug in chlorodb

Browse Source 
Former-commit-id: 7017655ac86e7b7837c7b581bf8a1abb86c08b30
Former-commit-id: dcedd4e32e3c7ce302eed94abd2b975a4506df97
This commit is contained in:
alain viari
2015-11-14 15:16:16 +01:00
parent a6ee2f0781
commit d83201fd2f
1 changed files with 5 additions and 5 deletions
Download Patch File Download Diff File Expand all files Collapse all files

10
detectors/cds/tools/chlorodb/go_chlorodb.sh
View File

@ -36,7 +36,7 @@ cd $DB_BASE/info
if (! -e $DB_BASE/parameters.sh) then
Notify "no $DB_BASE/parameters.sh found : creating one for you"
@ n = `find $DB_BASE/download -depth 1 -type f -print | wc -l`
@ n = `find $DB_BASE/download -maxdepth 1 -type f -print | wc -l`
@ cor_cutoff = $n / 2
@ atg_cutoff = $n / 10
@ dbs_cutoff = $n / 4
@ -85,7 +85,7 @@ source $DB_BASE/parameters.sh
# temporarily uncompress
#
set ff = `find $DB_BASE/download -depth 1 -name \*.gz -print`
set ff = `find $DB_BASE/download -maxdepth 1 -name \*.gz -print`
if ($#ff != 0) then
Notify "uncompressing $#ff entries"
@ -98,7 +98,7 @@ endif
# convert gbk/embl to fasta
#
set ff = `find $DB_BASE/download -depth 1 \( -name \*.gbk -or -name \*.embl \) -print`
set ff = `find $DB_BASE/download -maxdepth 1 \( -name \*.gbk -or -name \*.embl \) -print`
Notify "convert $#ff gbk/embl entries to fasta"
@ -241,7 +241,7 @@ endif
# recompress entries
#
set ff = `find $DB_BASE/download -depth 1 -type f -print`
set ff = `find $DB_BASE/download -maxdepth 1 -type f -print`
if ($#ff != 0) then
Notify "recompressing $#ff entries"
@ -252,7 +252,7 @@ endif
# compress fasta
set ff = `find $DB_BASE/fasta -depth 1 -name \*.fst -print`
set ff = `find $DB_BASE/fasta -maxdepth 1 -name \*.fst -print`
if ($#ff != 0) then
Notify "compressing $#ff fasta entries"