User: horsedog

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horsedog30
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Posts by horsedog

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Comment: C: To get the name of the strains by searching assembly genome number GCF_
... Hi , thanks , but it says `"SyntaxError: invalid syntax"` at `Sub_value` do you mean by replacing ID = open("assembly_ID").read() handle = Entrez.efetch(db="assembly", id= ID, rettype="gb") by your code? but here the `-query` is not just one ID, there are thousands of ...
written 4 months ago by horsedog30
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To get the name of the strains by searching assembly genome number GCF_
... I have a bunch of refseq assembly genome number like`GCF_002514765.1,GCF_002485085.1,GCF_002201835.1,GCF_000593305.2,GCF_001887655.1,GCF_000194215.1,GCF_002098145.1,GCF_002807875.1` Now I want to use these to search which genome it is , for example, the first one is `Escherichia coli strain MOD1- ...
ncbi python efetch written 4 months ago by horsedog30 • updated 4 months ago by Joseph Hughes2.6k
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Comment: C: Technical question about python "to find the strings"
... hello, do you mean by this? with open("file") as ID, open("file2") as data: for line1.strip() in ID: for line2.strip() in data: if line1.strip() in line2.strip(): print(line1.strip()) ? ...
written 4 months ago by horsedog30
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Comment: C: Technical question about python "to find the strings"
... Hi, thanks for correction, but I tried , still blank, here is my new code: with open("file") as ID, open("file2") as data: for line1 in ID: for line2 in data: if line1 in line2: print(line1) ...
written 4 months ago by horsedog30
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Technical question about python "to find the strings"
... Hi there, I have two files, file 1 looks like this : NP_208181.1 NP_220259.1 NP_224629.1 WP_232131 WP_3432434 WP_2441241221 File 2 looks like this: NP_208181.1,GCF_000008525.1 NP_212206.1,GCF_000008685.2 NP_213866.1,GCF_000008625.1 NP_219784.1,GCF_000008725. ...
python written 4 months ago by horsedog30 • updated 3 months ago by shoujun.gu330
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Any good models and softwares to analyse the phylogeny of Prokaryotes' amino acid ?
... Hi, I'm studying molecular evolution of a protein complex in prokaryotes, I have a tremendous fasta file that contains thousands of aa sequences of this protein from NCBI ref-seq protein database.Now I'd like to do the multiple alignment first and analyse the phylogeny. I used MUSCLE and FastTree ...
phylogeny written 4 months ago by horsedog30
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Comment: C: How to remove duplicate sequences in fasta file using python?
... Well thank you very much! I'll take a look into CDHIT! no reason just I'm practising python recently so I would like to see how people solve problem by python. ...
written 4 months ago by horsedog30
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Comment: C: How to remove duplicate sequences in fasta file using python?
... Hi again, well you're right it works now, but it's so weird cuz in the "answer.fa" it contains even more lines than file1 plus file2, which means that seems it didn't 'remove' but 'add'? (I used wc -l to count lines) ...
written 4 months ago by horsedog30
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Comment: C: How to remove duplicate sequences in fasta file using python?
... hi , it said "invalid -v" ...
written 4 months ago by horsedog30
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How to remove duplicate sequences in fasta file using python?
... I have a two fasta files, file 1 and file 2 ,they have a lot of overlapped sequences but not all of them, here I want to merge these two files into one file file 3 and remove the duplicate part, just keeping the unique one, is there code example for python use? Well the duplicate here means the exac ...
python written 4 months ago by horsedog30 • updated 5 weeks ago by pauley-p10

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