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README_forBrowser
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#### these are teh gffs produced by relocate
cat *mping.all_inserts.gff | grep -v Reference-only > mping.inserts.gff
cat *mping.all_inserts.gff | grep Reference-only > mping.ref_only.inserts.gff
perl -pi -e 's/^(\S+\t(\S+).+ID=)/$1$2./' all.mping.inserts.gff
perl -pi -e 's/^(\S+\t(\S+).+ID=)/$1$2./' all.pings.inserts.gff
####robb@biocluster:~/project/bisulfide/forBrowser$ perl -pi -e 's/ID=ping/ID=mping/' mping.NB.inserts.gff
##cat mping.NB.inserts.gff >> mping.inserts.gff
## mping.relocate.out is the collection of all the RElocate confident_nonref.txt output of all the mping inserts
grep NB mping.relocate.out > NB.relocate.out
perl reformat_relocate_2_gff.pl NB.relocate.out > mping.NB.inserts.gff
perl combine_insert_gffs.pl mping.NB.inserts.gff mping.ref_only.inserts.gff > mping.Ref.gff
cat mping.Ref.gff >> mping.inserts.gff
perl reformat_relocate_2_gff.pl pings.relocate.out > pings.inserts.gff
##manually add in Names
## otherTEs
cat /rhome/robb/rice/TE_success/otherTEs/Rv3/11282013_0.1M_*/*/results/*gff | grep Non-reference > otherTEs.nonRef.gff
cat /rhome/robb/rice/TE_success/otherTEs/Rv3/11282013_0.1M_*/*/results/*gff | grep -v Non-reference > otherTEs.redundantRef.gff
cat /rhome/robb/rice/RILs/otherTEs/12202013_0.1M_RIL*/*/results/*gff | grep Non-reference > RILs.otherTEs.nonRef.gff
cat /rhome/robb/rice/RILs/otherTEs/12202013_0.1M_RIL*/*/results/*gff | grep -v Non-reference > RILs.otherTEs.redundantRef.gff
cat RILs.otherTEs.nonRef.gff otherTEs.nonRef.gff > all.otherTEs.nonRef.gff
cat RILs.otherTEs.redundantRef.gff otherTEs.redundantRef.gff > all.otherTEs.redundantRef.gff
perl combine_insert_gffs.pl all.otherTEs.redundantRef.gff > all.otherTEs.Ref.gff
perl -pi -e 's/^(\S+\t(\S+).+ID=)/$1$2./' all.otherTEs.nonRef.gff
perl -pi -e 's/^(\S+\t(\S+).+ID=)/$1$2./' all.otherTEs.Ref.gff
## otherDANTEs
cat /rhome/robb/rice/TE_success/otherDNATEs/07312013_*/*/results/*gff | grep Non-reference > otherDNATEs.nonRef.gff
cat /rhome/robb/rice/TE_success/otherDNATEs/07312013_*/*/results/*gff | grep -v Non-reference > otherDNATEs.redundantRef.gff
cat /rhome/robb/rice/RILs/otherDNATEs/12202013_0.1M_RIL*/*/results/*gff | grep Non-reference > RILs.otherDNATEs.nonRef.gff
cat /rhome/robb/rice/RILs/otherDNATEs/12202013_0.1M_RIL*/*/results/*gff | grep -v Non-reference > RILs.otherDNATEs.redundantRef.gff
cat RILs.otherDNATEs.nonRef.gff otherDNATEs.nonRef.gff > all.otherDNATEs.nonRef.gff
cat RILs.otherDNATEs.redundantRef.gff otherDNATEs.redundantRef.gff > all.otherDNATEs.redundantRef.gff
perl combine_insert_gffs.pl all.otherDNATEs.redundantRef.gff > all.otherDNATEs.Ref.gff
perl -pi -e 's/^(\S+\t(\S+).+ID=)/$1$2./' all.otherDNATEs.Ref.gff
perl -pi -e 's/^(\S+\t(\S+).+ID=)/$1$2./' all.otherDNATEs.nonRef.gff
#~/project/bisulfide/forBrowser/inserts_near_genes$ bp_seqfeature_load -a DBI::SQLite -d rice.sqlite -f ../final/mping.inserts.gff ../final/otherDNATEs.Ref.gff ../final/otherDNATEs.nonRef.gff ../final/otherTEs.Ref.gff ../final/otherTEs.nonRef.gff ../final/pings.inserts.gff
cp /rhome/robb/rice/database/backup_sqlite_db/MSUr7.all.annotations.sqlite rice.sqlite
bp_seqfeature_load -a DBI::SQLite -d rice.sqlite -f ../final/mping.inserts.gff ../final/all.otherTEs.Ref.gff ../final/all.otherTEs.nonRef.gff ../final/pings.inserts.gff
bp_seqfeature_load -a DBI::SQLite -d rice.sqlite -f ../final/all.otherDNATEs.Ref.gff ../final/all.otherDNATEs.nonRef.gff