Header Leaderboard Ad

Collapse

automated remote blasting issue

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • automated remote blasting issue

    Hi everyone,

    I'm trying to remotely blast about 70 200-nt sequences using Biopython.
    I've been trying for hours to figure out why the following Python script won't work.
    I can get it to work for a read file that contains just one fasta using SeqIO.read, but when I try to switch to SeqIO.parse, I don't get anything in the .xml save file that I create.
    Any ideas?

    As a side note, if anyone knows the option syntax for excluding organisms from the results (as is possible when using the ncbi website, please let me know).

    Thanks very much for any help.

    Matt

    from Bio.Blast import NCBIWWW
    from Bio import SeqIO
    import tkinter.filedialog as tkfd
    in_file=tkfd.askopenfilename()
    record = SeqIO.parse(in_file, format="fasta")
    out_file = tkfd.asksaveasfilename()
    save_file = open(out_file, "w")
    for rec in record:
    ....print(rec)
    ....result_handle = NCBIWWW.qblast("blastn", "nt", rec.format("fasta"))
    ....save_file.write(result_handle.read())
    ....result_handle.close()
    else:
    ....save_file.close()

    This is the content of the in_file that I'm using as a test file (the line formatting of my file is set at 80 char, which might have been lost below):
    >165613
    TAACTGCAGTGTTTTGTGTCGAGCCTTTTTTGTGCCTTTTTTATAAAGGCATAACGTTATATTTAATTGAAGAGTTTGAT
    TCTGGCTCAGATTGAACGCTAGCGGCATGCTTAACACATGCAAGTCGAACGGCAGCGCGGGGAGCTTGCTCCCTGGCGGC
    GAGTGGCGGACGGGTGAGTAATGCGTAGGAATCTACCTTG
    >165875
    GGGATCTTCGGACCTCGTGCTATAAGATGAGCCTACGTCGGATTAGCTTGTTGGTGGGGTAATGGCCTACCAAGGCGACG
    ATCCGTAGCTGGTCTGAGAGGACGATCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGG
    GAATATTGGACAATGGGGGAAACCCTGATCCAGCAATGCC
    Last edited by queueing; 04-29-2015, 06:12 AM. Reason: fixed indentation

  • #2
    Species restriction can be down with qblast setting entrez_query (or BLAST+ using -remote) and an Entrez [orgn] query, e.g. http://news.open-bio.org/news/2009/0...nfo-biopython/

    As to your script, try adding a bit more debugging, e.g.

    Code:
        data = result_handle.read()
        print("Got back: %r" % data)
        save_file.write(data)

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Improved Targeted Sequencing: A Comprehensive Guide to Amplicon Sequencing
      by seqadmin



      Amplicon sequencing is a targeted approach that allows researchers to investigate specific regions of the genome. This technique is routinely used in applications such as variant identification, clinical research, and infectious disease surveillance. The amplicon sequencing process begins by designing primers that flank the regions of interest. The DNA sequences are then amplified through PCR (typically multiplex PCR) to produce amplicons complementary to the targets. RNA targets...
      03-21-2023, 01:49 PM
    • seqadmin
      Targeted Sequencing: Choosing Between Hybridization Capture and Amplicon Sequencing
      by seqadmin




      Targeted sequencing is an effective way to sequence and analyze specific genomic regions of interest. This method enables researchers to focus their efforts on their desired targets, as opposed to other methods like whole genome sequencing that involve the sequencing of total DNA. Utilizing targeted sequencing is an attractive option for many researchers because it is often faster, more cost-effective, and only generates applicable data. While there are many approaches...
      03-10-2023, 05:31 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, Today, 02:45 PM
    0 responses
    8 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-22-2023, 12:26 PM
    0 responses
    12 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-17-2023, 12:32 PM
    0 responses
    15 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-15-2023, 12:42 PM
    0 responses
    21 views
    0 likes
    Last Post seqadmin  
    Working...
    X