!fastaFromBed -s -name -fi /Volumes/web/cnidarian/oyster.v9.fa -bed /Volumes/web/bivalvia/wholegenomefiles_MBDbsSeq_gill/qDOD_RepeatProteinMask_v9_gffformat.gff -fo /Volumes/web/cnidarian/TJGR_RepProMask_TE.fa

!head /Volumes/web/cnidarian/TJGR_RepProMask_TE.fa

!head /Volumes/web/bivalvia/wholegenomefiles_MBDbsSeq_gill/oyster_v9_pearlTE.fa
python methratio.py -d /Volumes/web/cnidarian/TJGR_RepProMask_TE.fa -z -g -o  /Volumes/web/cnidarian/BiGill_methratio_TEonly_A.txt -s /Volumes/Bay3/Software/BSMAP/bsmap-2.73/samtools /Volumes/web/cnidarian/BiGill_BSMAP_TEonly_v2.sam