New feature: advanced queries with SQL

PHLAWD now has the ability to accept raw SQL query strings to use when searching the source database for potential sequences of interest. This provides a great deal more power than the default search functionality that simply matches against a set of terms. Now one can use exclusion, be explicit about the treatment of flanking whitespace, use all available SQL wildcards, and use boolean operators such as AND and OR, among other things.

Of course, with great power comes great responsibility…

For more information, see the manual page for SQL queries.

03. August 2012

outlier detection

PHLAWD now has some procedures for outlier detection. The information can be found here. As always, git pull, make, sudo make install.

25. April 2012

New division codes

It can be helpful to combine divisions for the database creation. I have added  two codes to do this

met for all metazoan with divisions 1-5

1. pri – primate sequences
2. rod – rodent sequences
3. mam – other mammalian sequences
4. vrt – other vertebrate sequences
5. inv – invertebrate sequences

all for all divisions from 1 – 7 including (be careful, this is more than 30GB)

1. pri – primate sequences
2. rod – rodent sequences
3. mam – other mammalian sequences
4. vrt – other vertebrate sequences
5. inv – invertebrate sequences
6. pln – plant, fungal, and algal sequences
7. bct – bacterial sequences

To use this functionality you need to git pull the latest version.

04. April 2012

Uploaded the link to the inv database

I loaded the inv database to the most recent release. Find it here.

02. April 2012

Updated the link to the pln database

I updated the pln database to the most recent release. Find it here.

23. March 2012

Building Genbank database

I just committed to git the ability to create the GenBank database with the PHLAWD program instead of the python scripts. This is much much faster due to a homemade flat Genbank file parser. To use this, just pull the most recent source (you can see how to install from source here). Then, after compilation and installation, create a file with simple information, lets call it db.setup and it will have

db = pln.db
division = pln
download

Here, db = pln.db is just the outfile. division = pln is the division as defined by Genbank that you want to build (see all the divisions below). download just means that you want to download the files and you haven’t already done it. Then just run

PHLAWD setupdb db.setup

It will download the necessary files and put them into the database with the name that was specified in db.setup. The only planned additional functionality is more general than division downloads.

The divisions are

1. pri – primate sequences
2. rod – rodent sequences
3. mam – other mammalian sequences
4. vrt – other vertebrate sequences
5. inv – invertebrate sequences
6. pln – plant, fungal, and algal sequences
7. bct – bacterial sequences
8. vrl – viral sequences
9. phg – bacteriophage sequences
10. syn – synthetic sequences
11. una – unannotated sequences
12. est – EST sequences (expressed sequence tags)
13. pat – patent sequences
14. sts – STS sequences (sequence tagged sites)
15. gss – GSS sequences (genome survey sequences)
16. htg – HTG sequences (high-throughput genomic sequences)
17. htc – unfinished high-throughput cDNA sequencing
18. env – environmental sampling sequences

23. March 2012