Moderator: a.zielezinski
a.zielezinski ♦ 7.0k
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Andrzej Zielezinski
Posts by a.zielezinski
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Comment:
C: basic problem on loop python
... But what if `cdna` directory is empty or it has only `*.cdna.abinitio.fa.gz` file (not `cdna.all.fa` as @elisheva requested) :P ...
written 6 weeks ago by
a.zielezinski ♦ 7.0k
4
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152
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2
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Answer:
A: basic problem on loop python
... Code:
fh = open('Content.txt')
oh = open('ftp.txt', 'w')
for line in fh:
if line.startswith('./'):
organism = line.split('/')[1].rstrip(':')
if 'cdna.all.fa' in line:
oh.write(organism + '\n')
fh.close()
oh.close()
ftp.txt:
ano ...
written 6 weeks ago by
a.zielezinski ♦ 7.0k
2
votes
1
answer
104
views
1
answers
... Code:
from Bio import Entrez
from Bio import SeqIO
Entrez.email = 'yourmail@mail.com'
qid = "NM_001135"
handle = Entrez.efetch(db="nucleotide", rettype="gb", retmode="text", id=qid)
seq_record = SeqIO.read(handle, "gb")
for feat in seq_record.features:
if fe ...
written 6 weeks ago by
a.zielezinski ♦ 7.0k
6
votes
1
answer
172
views
1
answers
... Sorry, I couldn't resist.
![enter image description here][1]
[1]: http://i65.tinypic.com/s27i29.png ...
written 7 weeks ago by
a.zielezinski ♦ 7.0k
2
votes
2
answers
204
views
2
answers
... Uniprot has built a database of reference proteomes for most organisms sequences today: http://www.uniprot.org/proteomes/ ...
written 7 weeks ago by
a.zielezinski ♦ 7.0k
4
votes
1
answer
140
views
1
answers
... Hexamers (6 nt long words) are accepted as the most accurate *k*-mer frequency based measure of coding potential. In 1992, a systematic study of more than twenty compositional properties indicated that hexamer composition gave the best discrimination between coding and non-coding regions ([Fickett & ...
written 7 weeks ago by
a.zielezinski ♦ 7.0k
0
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2
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135
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2
answers
... If Philipp and lu.ne correctly answered your question, please accept their answers by clicking on the check mark beside their posts. Accepting an answer is important as it both rewards posters for solving your problem and informs others that your issue is resolved. If an answer has helped you solve ...
written 8 weeks ago by
a.zielezinski ♦ 7.0k
0
votes
3
answers
136
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3
answers
... [NCBI Taxonomy database][1] provides a feature named [Common Tree][2], where you can provide a list of taxonomy identifiers to create a tree of species you are interested in. The tree will be displayed in your browser and you can save it to a file (in text or Newick format).
For example, here is a ...
written 8 weeks ago by
a.zielezinski ♦ 7.0k
5
votes
1
answer
163
views
1
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... A long time ago I wrote a module for handling tabular BLAST output (`-outfmt 6` / `-m8`). Maybe you will find it useful.
\gist https://gist.github.com/aziele/e060d1c0d1ef2acb4bd67e2fc0f165a6
**SAMPLE USAGE:**
Filename: `test.outfmt6`
cgl|CAGL0A00187g ecy|Ecym_8168 31.11 90 49 3 597 676 95 18 ...
written 8 weeks ago by
a.zielezinski ♦ 7.0k
2
votes
2
answers
346
views
2
answers
Comment:
C: genomics overlap python error
... Sorry for that, I made a mistake. It should be: `st, en = [cst, cen] if cstr == '+' else [cen, cst]`. I also corrected the answer. If you want start always less than end (regardless of the strand), just change this line to `st, en = cst, cen`. ...
written 9 weeks ago by
a.zielezinski ♦ 7.0k
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