@hackage xml2x0.4.2

SYNOPSIS

xml2x - convert blast output in XML format, either to a (csv)
    table suitable for e.g. importing into Excel or OOCalc, or
    to HTML.  Optionally annotating the output with GO terms
    and KEGG KOs.

INSTALLATION

The usual cabal routine, should also be possible to compile via
the Makefile.

USAGE

xml2x [options] xmlfile1 xmlfile2...

Use -v if you are on an interactive terminal to keep track of
progress.

Output format is specified with -C (CSV) or -H (HTML), with -C
being the default.  Note that only one output format can be used
at a time.

CSV OUTPUT

For CSV output, the following modes are supported

  --all    - output all blast matches (HSPs), one per line
  --top    - output only the top hit for each input sequence
  --region - output top hit for regions that overlap <50%

Use -o to specify an output file, the default is to output to
standard out.

HTML OUTPUT

For HTML output, a directory called "blast.d" is created (or
re-used if already present), and an index is constructed in a file
named "index.html" in the current directory.  The index lists some
information about the highest scoring blast hit, and links to the
file displaying the alignment.

The directory contains one HTML file per input
sequence, and uses a HTML table to rendering the alignments.
Color codes indicate level of identity (not total match score or
E-value!), so short, brightly red matches may have lower score than long gray
ones.  Frame (for BLASTX) or strand (for BLASTN) is indicated as
text for each match.

The files are named consistently, so if you run BLAST in both
directions (i.e.  swapping -i and -d), you should be able to go
back and forth by clicking on the sequence names.

ANNOTATIONS

Options include --annotations to specify the mapping between
UniProt accessions and GO terms.  This file is usually called
"gene_association.goa_uniprot", and is available from the GO
consortium [1].  The file is several GB, you may want to consider
trimming it down a bit by filtering out the automatic (IEA)
annotations - however, xml2x will first scan the blast output to
extract only relevant GO annotations, so keeping it all in memory
is not necessary.

Additionally, you can use --ontology to specify the description of
the GO terms, and the output will then be somewhat more
meaningful.  The file is usually called "gene_ontology.obo",
similarly available [2].

You can also add KEGG annotations with the -k (or --kegg-organism)
option. This option takes a file prefix as a parameter, and
for a prefix $P, expects to find files $P_uniprot.list and
$P_ko.list.  These files are read, and used to mapp KEGG KOs to
each UniProt hit.  Available from [3].

BUGS

XML parsing is slow, but ndm said he'd look into it.

Must be compiled with -smp to avoid huge memory requirements, but
the plus side is that with -smp, we use a lot less RAM than
AutoFact.

REFERENCES

[1] http://www.geneontology.org/ontology/gene_ontology.obo
[2] ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/
[3] ftp://ftp.genome.jp/pub/kegg/genes/organisms/