Moderator: 5heikki
5heikki ♦ 6.5k
- Reputation:
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- Finland
- Last seen:
- 15 hours ago
- Joined:
- 3 years, 7 months ago
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Posts by 5heikki
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... Blast is bad algorithm for this stuff. Try the RDP classifier from their github. You can get species level classification with it as long as you have a species level map file.. ...
written 13 days ago by
5heikki ♦ 6.5k
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... Oftentimes even full 16S doesn't offer enough resolution for species level classification.. ...
written 13 days ago by
5heikki ♦ 6.5k
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237
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... Field separator is space, if line doesn't begin with ">" output uppercase, else output first field as is.
awk 'BEGIN{FS=" "}{if(!/>/){print toupper($0)}else{print $1}}' in.fna > out.fna
...
written 15 days ago by
5heikki ♦ 6.5k
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Comment:
C: grep chromosome on blast result
... How about:
man grep
...
written 15 days ago by
5heikki ♦ 6.5k
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... All this stuff is well documented, [seq][1] & [itertools][2].
[1]: http://biopython.org/DIST/docs/api/Bio.Seq.Seq-class.html
[2]: https://docs.python.org/2/library/itertools.html ...
written 15 days ago by
5heikki ♦ 6.5k
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... This is super easy with Python, see e.g. [here][1].
Copy pasted one option below:
from Bio import Seq
from itertools import product
def extend_ambiguous_dna(seq):
"""return list of all possible sequences given an ambiguous DNA input"""
d = Seq.IUPAC.IUPACData.ambiguo ...
written 17 days ago by
5heikki ♦ 6.5k
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... *I assumed that this means that only the TOP ten alignment result would be stored into the resulted testing file.*
-max_target_seqs =1>
Maximum number of aligned sequences to keep
Not applicable for outfmt <= 4
Note, maximum number of aligned sequences, not maximum number ...
written 17 days ago by
5heikki ♦ 6.5k
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224
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... cut -f1 -d ":" in.fa > out.fa
edit. nevermind, thought you wanted the first "field".. ...
written 22 days ago by
5heikki ♦ 6.5k
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229
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Comment:
C: Retrieve genbank viral genomes
... viral.1.1 & viral.2.1 contain entries such as:
>ref|NC_021094.1| White clover cryptic virus 2 isolate IPP_Lirepa segment RNA 1, complete sequence
>ref|NC_021095.1| White clover cryptic virus 2 isolate IPP_Lirepa segment RNA 2, complete sequence
>ref|NC_021096.1| Red clover ...
written 23 days ago by
5heikki ♦ 6.5k
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... Replying to a very old post.. dual socket setups are Xeon only. Anyway, we're living interesting times and it sure seems like AMD's threadripper CPU's are the obvious choice right now.. ...
written 24 days ago by
5heikki ♦ 6.5k
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