Moderator: a.zielezinski
a.zielezinski ♦ 9.2k
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Andrzej Zielezinski
Posts by a.zielezinski
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1
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1
answer
214
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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 4 weeks ago by
a.zielezinski ♦ 9.2k
0
votes
4
answers
207
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 8 weeks ago by
a.zielezinski ♦ 9.2k
0
votes
4
answers
207
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 8 weeks ago by
a.zielezinski ♦ 9.2k
1
vote
4
answers
207
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 8 weeks ago by
a.zielezinski ♦ 9.2k
0
votes
1
answer
147
views
1
answers
... Thank you for sharing! ...
written 8 weeks ago by
a.zielezinski ♦ 9.2k
2
votes
1
answer
147
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 8 weeks ago by
a.zielezinski ♦ 9.2k
2
votes
3
answers
225
views
3
answers
... You can use XML as query for Ensembl. The following example is for two human gene symbols (**MT-TF** and **TNRC6A**).
Format the above XML to one line and download the protein sequences using `wget`.
wget -O re ...
written 9 weeks ago by
a.zielezinski ♦ 9.2k
0
votes
1
answer
108
views
1
answers
... You can find all viral protein sequences (RefSeq) here: [https://ftp.ncbi.nlm.nih.gov/refseq/release/viral/][1]
[1]: https://ftp.ncbi.nlm.nih.gov/refseq/release/viral/ ...
written 11 weeks ago by
a.zielezinski ♦ 9.2k
1
vote
1
answer
188
views
1
answers
... Hi,
I highly recommend on-line service [Phylogeny.fr][1]. It performs:
- Multiple sequence alignment (Clustal / MUSCLE / T-Coffee / ProbCons)
- MSA curation (Gblock / remove positions with gaps)
- Tree construction with bootstrap (NJ / Parsimony / Maximum Likelihood / Bayes)
- Tree visualizati ...
written 3 months ago by
a.zielezinski ♦ 9.2k
4
votes
3
answers
204
views
3
answers
... Interesting question - I never thought of it that way. I ended up with something like this:
import itertools
d = {
'A': ['GCA', 'GCC', 'GCG', 'GCT'],
'C': ['TGC', 'TGT'],
'D': ['GAC', 'GAT'],
'E': ['GAA', 'GAG'],
'F': ['TTC', 'TTT'],
'G': ...
written 3 months ago by
a.zielezinski ♦ 9.2k
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