Question: can not get the alignment result from needle alignment
0
Medhat ♦ 7.6k 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?
