No i can't! Thank you - that did it, i was using 1, -1 instead
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 = "user@email.com"
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?
Moderator note: edited to remove authors email address
1 answer
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.
Hello tim.ivanov.92,
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