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<div dir="ltr" data-setdir="false">Daer Andrew,</div><div dir="ltr" data-setdir="false"><br></div><div dir="ltr" data-setdir="false">Where did you find the example you are following?</div><div dir="ltr" data-setdir="false">See section 6.5.2 in the Biopython documentation for examples how to print the alignment.</div><div dir="ltr" data-setdir="false"><br></div><div dir="ltr" data-setdir="false">Best,</div><div dir="ltr" data-setdir="false">-Michiel<br></div><div><br></div>
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On Tuesday, June 16, 2020, 12:23:26 PM GMT+9, ANDREW LEICHT <asleicht@wisc.edu> wrote:
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Biopython developers;<br>
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I am having some issues after following examples from all over the web to write Pairwise Alignment to files. I am using the exact same syntax, but not sure what I am doing wrong as I am getting errors.</div>
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<span>File "/HOME/venv/lib/python3.7/site-packages/Bio/AlignIO/__init__.py", line 233, in write<br>
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<div> "objects, got: %r" % alignment<br>
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<span>TypeError: Expect a list or iterator of MultipleSeqAlignment objects, got: <Bio.Align.PairwiseAlignment object at HEX_ADDRESS></span></div>
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<span>It will write out empty files, named appropriately, but not with the pairwise alignment in each file as desired.</span><br>
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My code takes genpept files (genbank standard) each with a single protein record inside each ~1500AAs, and input reads them as sequence objects. Then it does a sequence pairwise comparison between a reference file and all other .gp files in a folder, and should
output them as individual multi-fasta alignment files.</div>
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I have tired many iterations of code tweaking: AlignIO.write --> SeqIO.write, set pairwise --> pairwise[0], tried .parse instead of .read, tried using Bio.pairwise2 instead. All these created other errors which did not get me any closer to the desired outcome.<br>
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Using BioPython v1.76</div>
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Python 3.7.7</div>
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MacOS 10.14.6</div>
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Example code below:</div>
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<span>import os<br>
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<div>import sys<br>
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<div>import glob<br>
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<div>from Bio import SeqIO<br>
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<div>from Bio import Align<br>
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<div>from Bio.Align import substitution_matrices<br>
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<span>from Bio import AlignIO</span></div>
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<span>base_path = "SOME_PATH/test/"<br>
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<div>index_ref = "123456.gp"<br>
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<div>seq1 = SeqIO.read(os.path.join(base_path, index_ref), "genbank")</div>
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<div>for gp_file in glob.glob(os.path.join(base_path, "*.gp")):<br>
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<div> seq2 = SeqIO.read(open(gp_file, "r"), "genbank")<br>
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<div> aligner = Align.PairwiseAligner()<br>
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<div> aligner.open_gap_score = -10<br>
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<div> aligner.extend_gap_score = -1<br>
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<div> aligner.substitution_matrix = substitution_matrices.load("BLOSUM62")<br>
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<div> pairwise = aligner.align(seq1.seq, seq2.seq)<br>
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<div> file_out = (seq1.id + "_" + seq2.id + "_" + aligner.algorithm + "_" + aligner.mode)<br>
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<div> pair_out = open(file_out + ".mfa", "w")<br>
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<div> AlignIO.write(pairwise, pair_out, "fasta")<br>
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<span> pair_out.close()</span><br>
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I did some more digging and not sure if it is related to <a rel="nofollow" target="_blank" href="https://github.com/biopython/biopython/issues/2632">
https://github.com/biopython/biopython/issues/2632</a></div>
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Any assistance to get this working or alternative methods would be greatly appreciated.<br>
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<p style="margin-top:0px;margin-bottom:0px;"><span style="font-family:Arial, Helvetica, sans-serif;">Best Regards,</span></p>
<span style="font-family:Arial, Helvetica, sans-serif;"></span><span style="font-family:Arial, Helvetica, sans-serif;">asleicht@wisc.edu</span></div>
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