User: oseias.rf.junior

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Posts by oseias.rf.junior

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Comment: A: How to retrieve all GO terms at level 2 from a list input
... Hi all, Thank you, Jean-Karim Heriche and Pierre Lindenbaum, for all the answers... I have tried the solutions you guys told me to. But unfortunatelly I haven't been able to figure it out those solutions (I'm a beginner in programming). On the other hand I have found the API page in quickGO websi ...
written 9 months ago by oseias.rf.junior0
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How to retrieve all GO terms at level 2 from a list input
... Hi everybody, I have a list of GO terms (not the GO ID, but the GO terms, like, "pathogenesis" or "intracellular organelle part") that I want to get the ancestral GO term at the level 2 ("biological process", "cellular component", respectvelly). Is there any easy script to do that? ...
go written 9 months ago by oseias.rf.junior0 • updated 4 months ago by miles.thorburn90
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Virsorter Output Incomplete
... Does anyone already had an error such like mine? VirSorter are generating outputs like this for some of my draft genomes: >VIRSorter_AWYH01000028_1-cat_1 CTGTCGGAATATCTTCGCCCCGTCCAGAATGCCGCTTGCCGCGTCCGGAATAGTCATACATTTGATAGGTCAC... With no information regarding the contig coordinate ...
virsorter written 15 months ago by oseias.rf.junior0
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Comment: C: Multifasta to Singlefasta (replace headers for 'NNNNNNNNNN', then join the multi
... It didn't need to be an arbitrary number of Ns. But anyway, thank you both very much genomax, jrj.healey and Ram for give me some clues and advices in a so fast way. I'll follow what you guys indicated/wrote. ...
written 16 months ago by oseias.rf.junior0
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Comment: C: Multifasta to Singlefasta (replace headers for 'NNNNNNNNNN', then join the multi
... It's not my script (the one who finds IS in complete genomes). Someone designed it like I described. I'm just trying to figure something to have a first look on my data (the ones there are not complete genomes). ...
written 16 months ago by oseias.rf.junior0
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Comment: C: Multifasta to Singlefasta (replace headers for 'NNNNNNNNNN', then join the multi
... Because some genomes have something like 300 contigs. It doesn't seem to me an idea with practicality (split them all). I would probably loose the track of each contig of a single file. The script for IS gives me the coordinates so I can track the IS local later. ...
written 16 months ago by oseias.rf.junior0
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Comment: A: Multifasta to Singlefasta (replace headers for 'NNNNNNNNNN', then join the multi
... BTW, An example of what I want the python script might do: ~BEFORE_MULTIFASTA_FILE~ >some header ATCGATCGATCGATCG >another header ATCGATCGATCGATCG ~AFTER_SINGLEFASTA_FILE~ >some header ATCGATCGATCGATCGNNNNNNNNNNATCGATCGATCGATCGATCG ...
written 16 months ago by oseias.rf.junior0 • updated 16 months ago by genomax75k
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Multifasta to Singlefasta (replace headers for 'NNNNNNNNNN', then join the multiple contigs)
... Hi to all, I'm trying to use a script to find IS on my genomes. But the script will run only on singlefasta files (i.e., complete genomes). Some of the genome files I have are multifasta files. I wonder if there is any python (or perl) script to remove all the contig headers of a file (e.g. ">co ...
perl python singlefasta multifasta written 16 months ago by oseias.rf.junior0

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