User: Buffo
Buffo • 460
- Reputation:
- 460
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Posts by Buffo
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2
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... You are a very funny person WouterDeCoster :). I'm glad you're learning to program but, in addition to online courses I recommend using common sense, sometimes it is very useful!
Best. ...
written 21 days ago by
Buffo • 460
2
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1
answer
181
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... > Also, it allows specifying both the output name and output directory.
prefix = sys.argv[1].split('.')[0]
output = open(prefix + '_output.txt', 'w') #you will never have to specify output name or directory
> you should use the 'with' statement for opening files
??? Why? ...
written 21 days ago by
Buffo • 460
2
votes
1
answer
181
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... More profesional use .write:
import sys
output = open('output.txt', 'w')
with open(sys.argv[1]) as input:
while True:
line1 = [item for item in input.readline().split()]
if len(line1) == 0:
break
line2 = [item for item in input.readline().split( ...
written 21 days ago by
Buffo • 460
0
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0
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78
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... Hi everybody,
Somebody has worked with UTR-DB? I`m working with miRNA target prediction, so I need 3' UTRs, this is available on UTRdb, but each sequence name corresponds to accession number and locus which is absolute useless, I need the name of the protein that corresponds to that UTR for each se ...
written 23 days ago by
Buffo • 460
0
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2
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132
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2
answers
Comment:
C: Blastx versus nr?
... Thanks, I had heard about that, but I was looking for a suitable solution with blast, I will try diamond. ...
written 23 days ago by
Buffo • 460
3
votes
2
answers
132
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... Hi everybody,
I want to perform a blastx versus nr locally for 2200 sequences, it is normal to take long long time? expected time to make it is about 800 hours!!
Somebody has had the same problem?
Any suggestions? ...
written 23 days ago by
Buffo • 460
• updated
22 days ago by
Jacob Warner • 310
1
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0
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129
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Comment:
C: miRanda output meaning?
... In order to parse the output try:
grep -A 1 "Scores for this hit:" miranda_out.txt | sort | grep '>'
you will get:
>mirna_name transcript_target 143.00 -22.87 2 18 339 357 16 75.00% 87.50%
And this is the header:
mirna Target Score Energy-Kcal/Mol Quer ...
written 29 days ago by
Buffo • 460
0
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0
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79
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... I would call them "conserved" more than orthologues, I THINK it is more appropriate. ...
written 4 weeks ago by
Buffo • 460
0
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2
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120
views
2
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... For a very close related species SPADES works even better and faster than IDBA_hybrid. ...
written 4 weeks ago by
Buffo • 460
0
votes
2
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120
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2
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... spades.py --only-assembler --trusted-contigs trusted_contigs.fa -1 file_r1.fastq -2 file_r2.fastq -o spades_hybrid_assembly ...
written 4 weeks ago by
Buffo • 460
Latest awards to Buffo
Scholar
7 weeks ago,
created an answer that has been accepted.
For A: How can I get FASTA if i have Names of proteins ?
Centurion
8 weeks ago,
created 100 posts.
Scholar
5 months ago,
created an answer that has been accepted.
For A: How can I get FASTA if i have Names of proteins ?
Teacher
5 months ago,
created an answer with at least 3 up-votes.
For A: How can I get FASTA if i have Names of proteins ?
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