Moderator: a.zielezinski

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a.zielezinski9.4k
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Andrzej Zielezinski

Posts by a.zielezinski

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Comment: C: Problem with Bio.SeqIO
... Looks okay to me. Is `output_fq` an output filename or output file handle? Are you sure the `SeqIO.write(..)` is called only once on a single file (`output_fq`) in your code (it should)? ...
written 15 days ago by a.zielezinski9.4k
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Comment: C: Get closest taxa of a target species in a phylogeny
... Hi mchimich, I just updated my answer. Hope it helps. ...
written 5 weeks ago by a.zielezinski9.4k
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Answer: A: Get closest taxa of a target species in a phylogeny
... In Python you can use [ete3][1] package. **UPDATED:** The following code finds a sister group to your query taxon and prints all leaves of that sister group (if bootstrap value is equal or greater than threshold) import ete3 YOUR_TREE = '((raccoon:19.19959,bear:6.80041)50:0.84600,((s ...
written 5 weeks ago by a.zielezinski9.4k
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Answer: A: Need help with Pairwise Alignment module in iterating over the alignment
... Here's my suggestion: from Bio import SeqIO from Bio import Align ref_seq_1 = SeqIO.read('seq1.fasta','fasta') seq1 = SeqIO.read('seq2.fasta','fasta') aligner = Align.PairwiseAligner() aligner.mode = 'global' aligner.match_score = 1 aligner.mismatch_sc ...
written 10 weeks ago by a.zielezinski9.4k
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Comment: C: Need help with Pairwise Alignment module in iterating over the alignment
... Replace `alignments = aligner.score(ref_seq_1.seq, seq1.seq)` with `alignments = aligner.align(ref_seq_1.seq, seq1.seq)`. ...
written 10 weeks ago by a.zielezinski9.4k
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Comment: C: Printing for each specific sequence and its residue in msa , every msa position
... Glad I could help. I just updated my answer to show all ids at once. ...
written 3 months ago by a.zielezinski9.4k
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Answer: A: Printing for each specific sequence and its residue in msa , every msa position
... Maybe this will help. from Bio.Align import MultipleSeqAlignment from Bio.Alphabet import generic_dna from Bio.Seq import Seq from Bio.SeqRecord import SeqRecord def map_positions(aln, id): rec = next((r for r in aln if r.id==id), None) seq_pos = 0 f ...
written 3 months ago by a.zielezinski9.4k
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Comment: C: How to combine p-values of differentially expressed genes from different timepoi
... Can't you just take the maximum p-value (max_p) from these few genes and report it as p <= max_p. You can do the same with the foldchange. ...
written 4 months ago by a.zielezinski9.4k
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Comment: C: Calculate Ka/Ks using examples of two sequences.
... Do you want to calculate Ka/Ks ratio by hand or just use a tool? There are at least six different methods to calculate Ka/Ks ratio. ...
written 4 months ago by a.zielezinski9.4k
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Answer: A: python 3.8 'No module named pip'
... Download `get-pip.py` script to install pip: curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py Install pip: python3 get-pip.py Install biopython: python3 -m pip install biopython or pip3 install biopython ...
written 6 months ago by a.zielezinski9.4k

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Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: biopython pairwise2 result to a file
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Teacher 4 months ago, created an answer with at least 3 up-votes. For A: biopython pairwise2 result to a file
Great Question 4 months ago, created a question with more than 5,000 views. For Hmmsearch (Hmmer) Tblout Format
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: How To Separate A List Of Genomics Regions Into Several Disjoint Subsets
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Scholar 7 months ago, created an answer that has been accepted. For A: biopython pairwise2 result to a file
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Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: How To Separate A List Of Genomics Regions Into Several Disjoint Subsets
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