Question: can not get the alignment result from needle alignment
0
Medhat ♦ 8.8k wrote:
I am using this script to compare to sequence and parse the result:
from Bio.Emboss.Applications import NeedleCommandline from Bio import AlignIO needle_cline = NeedleCommandline(asequence="a.fa", bsequence="b.fa", gapopen=10, gapextend=0.5, outfile="needle.txt") filename= "needle.txt" format = "emboss" alignments = list(AlignIO.parse(filename, format))
when i try to print the results in the alignments list it gives me only part of the last line
like that
SingleLetterAlphabet() alignment with 2 rows and 2258 columns TTGATGAGTGGGCACCATGATTGCCCGACTGTTATTACCGTCAA...TCT ref TGGATGAGTGGGCACCATGATTGCCCGACTGTTATTACCGTCAA...T-- corr
any Idea?