Moderator: a.zielezinski
a.zielezinski ♦ 9.6k
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Andrzej Zielezinski
2
votes
1
answer
8.1k
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 8 months ago by
a.zielezinski ♦ 9.6k
0
votes
4
answers
467
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 9 months ago by
a.zielezinski ♦ 9.6k
0
votes
4
answers
467
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 9 months ago by
a.zielezinski ♦ 9.6k
2
votes
4
answers
467
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 9 months ago by
a.zielezinski ♦ 9.6k
0
votes
1
answer
490
views
1
answers
... Thank you for sharing! ...
written 9 months ago by
a.zielezinski ♦ 9.6k
4
votes
1
answer
490
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 9 months ago by
a.zielezinski ♦ 9.6k
3
votes
3
answers
418
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 months ago by
a.zielezinski ♦ 9.6k
1
vote
1
answer
292
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 9 months ago by
a.zielezinski ♦ 9.6k
1
vote
1
answer
517
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 10 months ago by
a.zielezinski ♦ 9.6k
5
votes
3
answers
651
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 10 months ago by
a.zielezinski ♦ 9.6k
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