format uniref90.xml to database for BLAST

[maubp]

OK then... first this is how I just extracted the uniref90.xml file from the FTP site (multiple levels of bundling!):

$ wget ftp://ftp.uniprot.org/pub/databases/uniprot/previous_releases/release10.0/uniref/uniref10.0.tar.gz
...
$ tar -zxvf uniref10.0.tar.gz 
uniref100.tar
uniref50.tar
$ tar -xvf uniref90.tar 
README
uniref90.dtd
uniref90.xml.gz
$ gunzip uniref90.xml.gz

And here is what the start of the file looks like for me too (same as emanlee reported):

$ head -n 25 uniref90.xml 
<?xml version="1.0" encoding="ISO-8859-1" ?>
<UniRef90 xmlns="http://uniprot.org/uniref" 
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" 
xsi:schemaLocation="http://uniprot.org/uniref http://www.uniprot.org/support/docs/uniref.xsd" 
 releaseDate="2007-03-06" version="10.0"> 
<entry id="UniRef90_Q3ASY8" updated="2007-03-06">
<name>Cluster: Parallel beta-helix repeat</name>
<property type="member count" value="1"/>
<property type="common taxon" value="Chlorobium chlorochromatii CaD3"/>
<property type="common taxon ID" value="340177"/>
<representativeMember>
<dbReference type="UniProtKB ID" id="Q3ASY8_CHLCH">
<property type="UniProtKB accession" value="Q3ASY8"/>
<property type="UniParc ID" value="UPI00005D5563"/>
<property type="UniRef100 ID" value="UniRef100_Q3ASY8"/>
<property type="UniRef50 ID" value="UniRef50_Q3ASY8"/>
<property type="protein name" value="Parallel beta-helix repeat"/>
<property type="source organism" value="Chlorobium chlorochromatii (strain CaD3)"/>
<property type="NCBI taxonomy" value="340177"/>
<property type="length" value="36805"/>
<property type="isSeed" value="true"/>
</dbReference>
<sequence length="36805" checksum="A7A8EA21B9345FF9">
MKPRFYIEQLEPRILLSGDILSELVPLLSSREASQMQSDYLLEHPEARRVAPLSAVEAAR
ACMVVVQSEAPSLLTEDGLMYPFEVGVGEERSSEANAEPTLAADFSADYTFSKSEWDALE

And here's how many records there seem to be according to grep:

$ grep -c "^<entry id" uniref90.xml 
2781437

Biopython 1.61 and 1.62 do appear to have a problem parsing this - I suspect the XML is different in some way to what we expect.

Update: Raised here: http://lists.open-bio.org/pipermail/...er/010909.html

[GenoMax]

The file linked by kmcarr does not refer to a "version 10.0" that emanlee was asking for. Perhaps that is not important.

[maubp]

Wouldn't it just be much easier to download the UniRef90 FASTA file directly?

Indeed, I should have doubled checked that really didn't exist.

As to the Biopython conversion failing, that is probably a bug - I'd have replied earlier but missed the thread reply alert - sorry.

[kmcarr]

Could you help us, thanks.

Wouldn't it just be much easier to download the UniRef90 FASTA file directly?

[emanlee]

>>> from Bio import SeqIO
>>> count = SeqIO.convert("uniref90.xml", "uniprot-xml", "uniref90converted.fasta", "fasta")
>>> print("Converted %i records" % count)

Converted 0 records

We checked uniref90.xml:
more uniref90.xml

<?xml version="1.0" encoding="ISO-8859-1" ?>
<UniRef90 xmlns="http://uniprot.org/uniref" 
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" 
xsi:schemaLocation="http://uniprot.org/uniref http://www.uniprot.org/support/docs/uniref.xsd" 
 releaseDate="2007-03-06" version="10.0"> 
<entry id="UniRef90_Q3ASY8" updated="2007-03-06">
<name>Cluster: Parallel beta-helix repeat</name>
<property type="member count" value="1"/>
<property type="common taxon" value="Chlorobium chlorochromatii CaD3"/>
<property type="common taxon ID" value="340177"/>
<representativeMember>
<dbReference type="UniProtKB ID" id="Q3ASY8_CHLCH">
<property type="UniProtKB accession" value="Q3ASY8"/>
<property type="UniParc ID" value="UPI00005D5563"/>
<property type="UniRef100 ID" value="UniRef100_Q3ASY8"/>
<property type="UniRef50 ID" value="UniRef50_Q3ASY8"/>
<property type="protein name" value="Parallel beta-helix repeat"/>
<property type="source organism" value="Chlorobium chlorochromatii (strain CaD3)"/>
<property type="NCBI taxonomy" value="340177"/>
<property type="length" value="36805"/>
<property type="isSeed" value="true"/>
</dbReference>
<sequence length="36805" checksum="A7A8EA21B9345FF9">
MKPRFYIEQLEPRILLSGDILSELVPLLSSREASQMQSDYLLEHPEARRVAPLSAVEAAR
....

Could you help us, thanks.

[emanlee]

Thank you for your quick reply. I'll try it out.

[maubp]

You should be able to convert the UniProt XML to FASTA using Biopython,

from Bio import SeqIO
count = SeqIO.convert("uniref90.xml", "uniprot-xml", "converted.fasta", "fasta")
print("Converted %i records" % count)

[emanlee]

we want to get a formated database for BLAST from Uniref90.
we referred an article which used an early release Uniref90, say version 10.0
ftp.uniprot.org only provide the XML format of this version.

How can we convert XML uniref90.xml to uniref90.fasta ? or, can formatdb take XML file as input file?
Thanks!

XML file:
ftp://ftp.uniprot.org/pub/databases/...ref10.0.tar.gz