Multi Blast NCBIWWW Filtering Human Genome and excluding Models and Uncultured sample sequences

Question

[malj]

Hello everyone!

I have been looking at the NCBIWWW documentation but I still don't know how to do this search done in NCBI Blastn from the browser (input explained below) but with Biopython command line.

Input: Fasta file with huge number of sequences to blast. Database Human genomic plus transcript (Human G + T) Exclude Models (XM/XP) and Exclude Uncultured/Environmental sample sequences Optimize for Highly similar sequences (Megablast)

http://biopython.org/DIST/docs/api/Bio.Blast.NCBIWWW-module.html

I would like to do it like this just because I am having problems with download it in XML format from the blast in the browser. And I want to check if through the command line I can skip this error. If anyone has the solution for the problem of download it from the browser it will be really welcome too. I would like 1 single file, anyway I will play around with several xml output files to see if it works.

The file downloaded is corrupted is containing these lines:

SYSTEM CAN'T PROCESS YOUR REQUEST, PLEASE CONTACT blasthelp.RID: X0SCK763015<BR>
<B>INFO: X0SCK763015-ALIGNMENT-XML</B><BR>

Thanks!

[Yi]

same issue. I tried downloading other formats, then back to the format I want, then it worked.