User: nmkn

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nmkn0
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Posts by nmkn

<prev • 17 results • page 1 of 2 • next >
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Comment: C: BioPython write combined nexus files
... I stated above - don't get a file to write using the sample data either. I do have permissions to write to my directory. Thanks anyway. ...
written 4 days ago by nmkn0
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Answer: A: BioPython write combined nexus files
... I couldn't figure out how to get this to work so I used another program for the same task instead: [Sequence Matrix][1] . [1]: http://www.ggvaidya.com/taxondna/ ...
written 4 days ago by nmkn0
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Comment: C: BioPython write combined nexus files
... Okay, thanks. I'm using Python 3.8.3 (called by python3 since I also have a legacy version) and Biopython 1.77. I don't get a file to write using the sample data either. Do I need to use `<_io.TextIOWrapper name='btCOMBINED.nex' mode='w' encoding='UTF-8'>`? It errors when I try to add that. ...
written 5 days ago by nmkn0
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Comment: C: BioPython write combined nexus files
... Okay, I tried also using `write_nexus_data(filename=open('btCOMBINED.nex', 'w'))` but then got that error which I am unsure how I am using the command wrong. ...
written 6 days ago by nmkn0
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Comment: C: BioPython write combined nexus files
... No file created in the working directory and no error thrown. ...
written 6 days ago by nmkn0
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BioPython write combined nexus files
... I'm trying to concatenate nexus files using BioPython as [documented in this page here][1]. It seems to create the objects just fine but fails to write the actual file - without any error. from Bio.Nexus import Nexus file_list = ['T591_1.nex','T591_2.nex'] nexi = [(fname, Nexu ...
nexus biopython written 6 days ago by nmkn0
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Comment: C: Remove Fasta Sequences with Duplicate IDs (but with different Descriptions) & Ap
... Any suggestions to work this as a loop for hundreds of files? ...
written 20 months ago by nmkn0
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Comment: C: Remove extra sequences without unique names from fasta
... This seqkit worked and was easy! If you add it as an answer I can marked as "accept" ...
written 2.0 years ago by nmkn0
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Comment: C: Remove extra sequences without unique names from fasta
... Thanks for the explanation. I can get the awk step to work using only one fasta file, but when I concat two files and use as input it doesn't work: awk '/^>/ {printf("%s%s\t",(N>0?"\n":""),$0);N++;next;} {printf("%s",$0);} END {printf("\n");}' |\ < sample_file > sample_linear.out ...
written 2.0 years ago by nmkn0
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Comment: C: Remove extra sequences without unique names from fasta
... Just to clarify the steps: 1. (cat) I concatenate all hundreds of my fasta files into ONE fasta file? 2. (awk) this is the linearize step How are the next two steps working? I tried providing the input file but it errors: sort -t $'\t' -k1,1 -u |\ < fasta.file_linearize.out ...
written 2.0 years ago by nmkn0

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Popular Question 19 months ago, created a question with more than 1,000 views. For randomly sample sequences of fasta file per sample name

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