Thread Rating:
  • 1 Vote(s) - 5 Average
  • 1
  • 2
  • 3
  • 4
  • 5
How to build a reference database - commands
#1
Raw command history from the practicals with Eric on how to setup a reference database from genbank or embl database

```
  168  obiconvert --skip-on-error --ecopcrdb-output=embl-vrt -d ncbi-2015-06-04 rel_std_vrt_01_r123.dat.gz
  169  ls -l
  170  ecoPCR -d embl-vrt -l 80 -L 120 -e 4 TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG > embl-vrt.e4.ecopcr
  171  less embl-vrt.e4.ecopcr
  172  obiconvert embl-vrt.e4.ecopcr | less
  173  obigrep -h  embl-vrt.e4.ecopcr
  174  obigrep --require-rank=species --require-rank=genus --require-rank=family -d embl-vrt  embl-vrt.e4.ecopcr > embl-vrt.goodtaxid.fasta
  175  obicount  embl-vrt.e4.ecopcr
  176  obicount  embl-vrt.goodtaxid.fasta
  177  obigrep --require-rank=species --require-rank=genus --require-rank=family -d embl-vrt  -v embl-vrt.e4.ecopcr | less
  178  obigrep -h
  179  obigrep -s '^[acgt]+$' embl-vrt.goodtaxid.fasta > embl-vrt.acgt.fasta
  180  obicount embl-vrt.acgt.fasta
  181  obicount  embl-vrt.goodtaxid.fasta
  182  obiannotate -k taxid embl-vrt.acgt.fasta > embl-vrt.taxid.fasta
  183  less embl-vrt.taxid.fasta
  184  obiannotate -h
  185  obiannotate --with-taxon-at-rank=species embl-vrt.taxid.fasta # embl-vrt.species.fasta
  186  obiannotate --with-taxon-at-rank=species embl-vrt.taxid.fasta > embl-vrt.species.fasta
  187  less embl-vrt.species.fasta
  188  obiannotate -d embl-vrt --with-taxon-at-rank=species embl-vrt.taxid.fasta > embl-vrt.species.fasta
  189  less embl-vrt.species.fasta
  190  obigrep -p 'species!=taxid' embl-vrt.species.fasta
  191  obigrep -p 'species!=taxid' embl-vrt.species.fasta | less
  192  obigrep -p 'species!=taxid' embl-vrt.species.fasta | obicount
  193  obiuniq -c species embl-vrt.species.fasta > embl-vrt.uniq.fasta
  194  obicount embl-vrt.uniq.fasta
  195  obistat -c count embl-vrt.uniq.fasta
  196  obistat -c count embl-vrt.uniq.fasta | sort -nk 1
  197  obigrep -p 'count==161' embl-vrt.uniq.fasta
  198  obiannotate -h
  199  obiannotate -A taxid -v  -S taxid:species embl-vrt.uniq.fasta # embl-vrt.ref.fasta
  200  obiannotate -A taxid -v  -S taxid:species embl-vrt.uniq.fasta > embl-vrt.ref.fasta
  201  gedit embl-vrt.ref.fasta
```
Reply


Forum Jump:


Users browsing this thread: 1 Guest(s)