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Question: can not get the alignment result from needle alignment
0
gravatar for Medhat
5.3 years ago by
Medhat ♦ 8.8k
Texas
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?
alignment sequence • 1.1k views
ADD COMMENT • link •
modified 5.3 years ago by Kamil • 2.0k • written 5.3 years ago by Medhat ♦ 8.8k
0
gravatar for Kamil
5.3 years ago by
Kamil • 2.0k
Baltimore
Kamil • 2.0k wrote:

Consider checking the examples in the documentation for the MultipleSeqAlignment class returned by AlignIO.

I guess this might do what you want:

print alignments[:,:]
ADD COMMENT • link modified 14 months ago by _r_am ♦ 32k • written 5.3 years ago by Kamil • 2.0k
1

I figured it I need to add another loop to get the sequence

for alignment in AlignIO.parse(filename, format):
    for sequence in alignment:
        print(sequence.seq)
ADD REPLY • link modified 14 months ago by _r_am ♦ 32k • written 5.2 years ago by Medhat ♦ 8.8k

I changed the method from parse to read like this

alignments = AlignIO.read(filename, format)
print alignments[:,:]

but, the result is the same

SingleLetterAlphabet() alignment with 2 rows and 2258 columns
TTGATGAGTGGGCACCATGATTGCCCGACTGTTATTACCGTCAA...TCT ref
TGGATGAGTGGGCACCATGATTGCCCGACTGTTATTACCGTCAA...T-- corr

any Idea?

ADD REPLY • link modified 14 months ago by _r_am ♦ 32k • written 5.2 years ago by Medhat ♦ 8.8k
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