chiaravanni
2/22/2016 - 4:27 PM

clstr_rev_CD-HIT.sh

#!/bin/bash -l
#$ -cwd
#$ -j y
#$ -N clstr_rev
#$ -pe threaded 8
#$ -V

set -x
set -e
set -o pipefail
set -o errexit
set -o errtrace
set -o nounset 

C_REV=/bioinf/software/cd-hit/ch-hit-4.6
PFAM=${REFS}/hmm_RefSeq_Pfam28/database

#explanation: 80.clstr only lists sequences from 90.clstr, script clstr_rev.pl add the original sequences from input file but not in 90.clstr into the output file 80_from90.clstr

${C_REV}/clstr_rev.pl TARA_OSD_GOS.orf.aa.pfam27.nohit.90.clstr TARA_OSD_GOS.orf.aa.pfam28.nohit.90.80.clstr > TARA_OSD_GOS.orf.aa.pfam27.nohit.80_from90.clstr

${C_REV}/clstr_rev.pl TARA_OSD_GOS.orf.aa.pfam27.nohit.80_from90.clstr TARA_OSD_GOS.orf.aa.pfam28.nohit.90.80.60.clstr > TARA_OSD_GOS.orf.aa.pfam27.nohit.60_from90.clstr

${C_REV}/clstr_rev.pl TARA_OSD_GOS.orf.aa.pfam27.nohit.60_from90.clstr TARA_OSD_GOS.orf.aa.pfam28.nohit.90.80.60.30.clstr > TARA_OSD_GOS.orf.aa.pfam27.nohit.30_from90.clstr

echo "DONE"