retrieving <Hit_def> information from XML output

[tonybert]

Greetings, I am trying to retrieve information regarding the putative taxonomic identifications of 16S/18S rRNA genes retrieved from a HiSeq Illumina run using BLASTN (from the blast+ package). Thus far i have been relying on biopython to parse the data. I'm able to retrieve information regarding the e-values to each query, alignment lengths and such for all of the hits using commands like the ones below.

###############################################
>>>from Bio.Blast import NCBIXML
>>>blast = NCBIXML.parse(open('16SxmlResults', 'rU'))
>>>for record in blast:
>>> print record.alignments[0].hsps[0].score
###############################################

The above prints all the high-scoring pair bit scores to standard output.
However, the piece of information i can't seem to access is located in the <Hit_def>. Looks like this;

<Hit_def>JR951091.270.2233 Bacteria;Proteobacteria;Alphaproteobacteria;Rickettsiales;mitochondria;Pisum sativum (pea)

I have looked into the biopython Bio.Blast.Record documention, as well as the tutorial, and can't seem to find any mixes/matches of how to retrieve this information. As well, I have also tried using elementtree to parse the data. This works, but i'm having a hard time "looping" through the whole file (there are ~4000 entries.

If anyone has any suggestions, or can provide some guidance i would sincerely appreciate it. Thanks,

-Tony

[maubp]

You want the alignment's hit_def attribute, e.g.

from Bio.Blast import NCBIXML
blast = NCBIXML.parse(open('16SxmlResults', 'rU'))
for record in blast:
    for align in record.alignments:
        for hsp in align.hsps:
            print hsp.score, align.hit_def

Tip: Explore dir(x) and help(x) at the Python prompt where x is an unfamiliar class.

[a0909]

I am very new to python, as the codes above are just printing, could you please tell me how to save this in a file(.csv or .txt).

Thanks

[maubp]

Easy way: When you run BLAST+ rather than asking for XML output with

-outfmt 5

ask for tabular output with

-outfmt 6

(or ask for CSV if you prefer).

Hard way: Convert the BLAST XML into tabular format using a script like https://github.com/peterjc/galaxy_bl..._to_tabular.py

[bernardo_bello]

You want the alignment's hit_def attribute, e.g.

from Bio.Blast import NCBIXML
blast = NCBIXML.parse(open('16SxmlResults', 'rU'))
for record in blast:
    for align in record.alignments:
        for hsp in align.hsps:
            print hsp.score, align.hit_def

Tip: Explore dir(x) and help(x) at the Python prompt where x is an unfamiliar class.

What does 'rU' refers to? a second input file?

[GenoMax]

What does 'rU' refers to? a second input file?

r is open for reading. As for "U"

Python is usually built with universal newlines support; supplying 'U' opens the file as a text file, but lines may be terminated by any of the following: the Unix end-of-line convention '\n', the Macintosh convention '\r', or the Windows convention '\r\n'. All of these external representations are seen as '\n' by the Python program.