Moderator: a.zielezinski
a.zielezinski ♦ 7.3k
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Andrzej Zielezinski
Posts by a.zielezinski
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0
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4
answers
249
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4
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... Or even simpler:
import sys
for c, l in enumerate(sys.stdin, start=1):
sys.stdout.write(">%d\n%s\n" % (c, l)) ...
written 11 days ago by
a.zielezinski ♦ 7.3k
0
votes
1
answer
142
views
1
answers
... Sure! If I answered your question, please mark my post as accepted by clicking on the thick (check sign) icon. ...
written 19 days ago by
a.zielezinski ♦ 7.3k
0
votes
2
answers
168
views
2
answers
... As genomax said, this task is too simple for Python. However, if you still insist on solving this with Python, here's the solution:
import os
DIR = 'fasta_files/'
oh = open('one_fasta_file.fasta', 'w')
for f in os.listdir(DIR):
fh = open(os.path.join(DIR, f))
...
written 22 days ago by
a.zielezinski ♦ 7.3k
1
vote
0
answers
124
views
0
answers
Comment:
C: Batch PFam search
... Download PfamScan from [ftp://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/][1] and use it from the command-line.
[1]: ftp://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/ ...
written 23 days ago by
a.zielezinski ♦ 7.3k
3
votes
1
answer
142
views
1
answers
... 1. Go to UniProt website
2. Search for: `taxonomy:viridiplantae`
3. Click on the `Download` button:
- Check `Download all`
- Select **Format:** `FASTA`
- Check `Compressed`
- Click **GO**.
...
written 23 days ago by
a.zielezinski ♦ 7.3k
2
votes
1
answer
166
views
1
answers
... The method `reverse_complement()` executed on mutable sequence, reverse the sequence in place and returns `None` value, so you shouldn't assign it to a variable.
For example:
from Bio.Seq import Seq
seq = Seq("ACGTTGCAC")
mutseq = seq.tomutable()
mutseq.reverse_complement()
...
written 4 weeks ago by
a.zielezinski ♦ 7.3k
4
votes
1
answer
242
views
1
answers
... This should do the work:
from Bio import SeqIO
infile = "seq.fa"
...
written 4 weeks ago by
a.zielezinski ♦ 7.3k
2
votes
1
answer
187
views
1
answers
... Files mapping HORVU* identifiers to UniProt/RefSeq accession numbers:
[ftp://ftp.ensemblgenomes.org/pub/release-36/plants/tsv/hordeum_vulgare/][1]
or alternatively, you can use [BioMart tool in Ensembl Plants][2] to translate identifiers.
[1]: ftp://ftp.ensemblgenomes.org/pub/release-36/plants ...
written 5 weeks ago by
a.zielezinski ♦ 7.3k
2
votes
6
answers
364
views
6
answers
Answer:
A: Intall local BLAST in Ubuntu
... sudo apt-get install ncbi-blast+ ...
written 6 weeks ago by
a.zielezinski ♦ 7.3k
0
votes
2
answers
366
views
2
answers
... Thanks for posting this info. Good to know that. ...
written 7 weeks ago by
a.zielezinski ♦ 7.3k
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