User: hugo.avila

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hugo.avila10
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7 months, 4 weeks ago
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Posts by hugo.avila

<prev • 14 results • page 1 of 2 • next >
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Comment: C: How to remove features from GBK files with biopython ?
... Ok i will do it Thanks for all the help ! ...
written 3 months ago by hugo.avila10
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Comment: C: How to remove features from GBK files with biopython ?
... 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.avila10
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Comment: C: How to remove features from GBK files with biopython ?
... 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.avila10
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Comment: C: How to remove features from GBK files with biopython ?
... Hi, sorry i forgot to mention, here is the acc of the file NZ_CP012744.1. ...
written 3 months ago by hugo.avila10
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How to remove features from GBK files with biopython ?
... 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: ...
biopython written 3 months ago by hugo.avila10
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Problems with refseq annotation when running Islandpath-DIMOB
... 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 ...
software error islandpath-dimob bacteria prokka written 4 months ago by hugo.avila10
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Comment: C: grep extract command will remove replicates automatically
... 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.avila10
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Comment: C: How to extract 3', 5' UTR sequences from genbank records using python, PERL and
... 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.avila10
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Comment: C: Program to find genes up/down-regulated by a given gene
... That's very cool ! I'll be wating ;) ...
written 5 months ago by hugo.avila10
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Comment: C: Program to find genes up/down-regulated by a given gene
... (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.avila10

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