User: hugo.avila
hugo.avila • 10
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Posts by hugo.avila
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... Ok i will do it
Thanks for all the help ! ...
written 3 months ago by
hugo.avila • 10
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... This works:
#!/usr/bin/env python
from Bio import SeqIO
import sys
def check_feature(feature):
try:
if feature.location.operator == "join":
return True
except:
return False
#save only the first record
rec ...
written 3 months ago by
hugo.avila • 10
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... Thank you for the help.
Replace pop() for remove() works, but only for genes, CDS still present on the output file.
Before:
FEATURES Location/Qualifiers
source 1..5355459
/organism="Klebsiella pneumoniae subsp. pneumoniae"
...
written 3 months ago by
hugo.avila • 10
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... Hi, sorry i forgot to mention, here is the acc of the file NZ_CP012744.1. ...
written 3 months ago by
hugo.avila • 10
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... I need to remove features from a gbk file that have split coordinates:
join{[5355286:5355459](+), [0:17](+)}
join{[5355286:5355459](+), [0:17](+)}
So far i was able to test features to check if they are CompaundLocation types, but i culd not remove all off then from the record object:
...
written 3 months ago by
hugo.avila • 10
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... Hi, I'm trying to run Islandpath-DIMOB (conda version=1.0.4) on refseq genomes and I get this error massage on some files (.gbff):
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: start [5340971] is greater than end [1335].
If you want to truncated and reverse complemen ...
written 4 months ago by
hugo.avila • 10
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... I don't know if I really understand what you want to do, but try this:
(for ID in $(cat file1); do echo -e $ID"\t"$(grep $ID gff1); done;) > output.txt ...
written 4 months ago by
hugo.avila • 10
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... Hi, please post a sample gbk file and define the headers that you want to see in your output file (Ex: seqID, locusTag, sequence ... ). ...
written 5 months ago by
hugo.avila • 10
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... That's very cool ! I'll be wating ;) ...
written 5 months ago by
hugo.avila • 10
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... (Sorry, i replied to the wrong person.)
Hey man, the internet gods send me here. Did you do it ? ...
written 5 months ago by
hugo.avila • 10
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