Moderator: a.zielezinski
a.zielezinski ♦ 9.2k
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Andrzej Zielezinski
Posts by a.zielezinski
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1
answer
139
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1
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... Glad I could help. I just updated my answer to show all ids at once. ...
written 23 days ago by
a.zielezinski ♦ 9.2k
0
votes
1
answer
139
views
1
answers
... 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 23 days ago by
a.zielezinski ♦ 9.2k
0
votes
0
answers
144
views
0
answers
... 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 5 weeks ago by
a.zielezinski ♦ 9.2k
0
votes
0
answers
112
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0
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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 5 weeks ago by
a.zielezinski ♦ 9.2k
1
vote
1
answer
1.8k
views
1
answers
... 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 3 months ago by
a.zielezinski ♦ 9.2k
0
votes
4
answers
283
views
4
answers
... Are sure the output is correct? I think that only "SpoScf_15890 12 2376" fulfils the criteria (start or end in the file1 should be less than in file2, and the difference shouldn't be greater than 1000) ...
written 4 months ago by
a.zielezinski ♦ 9.2k
0
votes
4
answers
283
views
4
answers
... import sys
d = {}
for argv in [2, 1]:
with open(sys.argv[argv]) as fh:
for line in fh:
sl = line.split()
id = sl[0]
st = int(sl[1])
en = int(sl[2])
if argv == 2:
d ...
written 4 months ago by
a.zielezinski ♦ 9.2k
1
vote
4
answers
283
views
4
answers
... Here's Python script:
import sys
d = {}
for argv in [2, 1]:
with open(sys.argv[argv]) as fh:
for line in fh:
sl = line.split()
id = sl[0]
st = int(sl[1])
en = int(sl[2])
if argv == 2 ...
written 4 months ago by
a.zielezinski ♦ 9.2k
0
votes
1
answer
301
views
1
answers
... Thank you for sharing! ...
written 4 months ago by
a.zielezinski ♦ 9.2k
3
votes
1
answer
301
views
1
answers
... You can modify your script to try downloading the sequence record three times until all fail. If all three attempts fail, skip this record.
from urllib.request import urlopen
from Bio import Entrez
import time
Entrez.email = "xxxx@xxxxx.com"
IDs = ['AY851612', 'hahdshjhdasd ...
written 4 months ago by
a.zielezinski ♦ 9.2k
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