Moderator: a.zielezinski
a.zielezinski ♦ 9.4k
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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.zielezinski ♦ 9.4k
1
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1
answer
123
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1
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... Hi mchimich, I just updated my answer. Hope it helps. ...
written 5 weeks ago by
a.zielezinski ♦ 9.4k
3
votes
1
answer
123
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1
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... 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.zielezinski ♦ 9.4k
2
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1
answer
167
views
1
answers
... 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.zielezinski ♦ 9.4k
0
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167
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1
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... 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.zielezinski ♦ 9.4k
0
votes
1
answer
194
views
1
answers
... Glad I could help. I just updated my answer to show all ids at once. ...
written 3 months ago by
a.zielezinski ♦ 9.4k
0
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1
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194
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1
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... 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.zielezinski ♦ 9.4k
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255
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... 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.zielezinski ♦ 9.4k
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... 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.zielezinski ♦ 9.4k
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vote
1
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1
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... 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.zielezinski ♦ 9.4k
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