Strand not working in biopython efetch

Question

[tim.ivanov.92]

I noticed i can't get efetch to retrieve sequence on a reverse strand:

def fasta_from_chords(x): 
    import sys
    sys.path.append('/uge_mnt/home/tim_ivanov/pythonlibs/biopython-1.71')
    from Bio import Entrez, SeqIO
    Entrez.email = "[e-mail]" 
    handle = Entrez.efetch(db="nucleotide",id=x[0],seq_start=x[1],seq_stop=x[2],strand=x[3],rettype="fasta")
    record = SeqIO.read(handle, "fasta")
    handle.close()
    return record

this is the function i've made, where x variable contans an array with: accession number, coordinate 1, coordinate 2, strand When i use it, the sequence returns on the straight strand only. Is there a way to fix it?

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Moderator note: edited to remove authors email address

Answer 1

[Sej Modha]

Can you confirm that you are passing 1 or 2 as strand argument instead of + and -? https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.EFetch

Strand of DNA to retrieve. Available values are "1" for the plus strand and "2" for the minus strand.

[tim.ivanov.92]

No i can't! Thank you - that did it, i was using 1, -1 instead

[finswimmer]

Hello tim.ivanov.92,

Don't forget to follow up on your threads.

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