User: peterlageweg603

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Posts by peterlageweg603

<prev • 12 results • page 1 of 2 • next >
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Comment: C: convert GCF code to outer leaf Organism name
... I'm sorry! GCF_001598035 ...
written 12 weeks ago by peterlageweg60310
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convert GCF code to outer leaf Organism name
... Hi all! I have a phylogenetic tree with GCF numbers as outer leaves. I would like to convert these numbers into species names. I already tried to solve this with ete3 within Python or Archaeopteryx to download this information from NCBI. This did not work out. Would be great if someone knows the so ...
phylogeny ete3 figtree archaeopteryx written 12 weeks ago by peterlageweg60310
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Comment: C: Remove part of headers in FASTA file
... Thanks for the quick respond! It almost works perfectly. >lcl|NC_002712.2_cds_NP_268424.1_10 [gene=dnaZA] When the "_numerical" goes up to 10 or 100 it is not substituted. ...
written 3 months ago by peterlageweg60310
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Comment: C: Remove part of headers in FASTA file
... Thanks for the heads up! I downloaded this from GenBank. I will include tr " " "_" in my unix command. ...
written 3 months ago by peterlageweg60310
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Remove part of headers in FASTA file
... I want to delete the part starting after ">" until "cds_". And the characters after the accession. In the example "_1" and "_2". In the original file this counts up to 784, so "_784". Can someone help me with a solution? Would be great. From this >lcl|NC_002712.2_cds_NP_268424.1_1 [gene= ...
fasta header counter unix written 3 months ago by peterlageweg60310 • updated 3 months ago by Macspider3.0k
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Installing AntiSMASH for Mac
... I want to install Antismash through conda with the mac terminal. But I got a permission error when performing the command below: conda install -c bioconda antismash Error: ERROR conda.core.link:_execute(568): An error occurred while uninstalling package 'defaults::qt-5.9.7-h468cd18_1'. ...
antismash secondary metabolites written 7 months ago by peterlageweg60310
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Comment: C: Extract Tree Topology From Ncbi Taxonomy Database
... Ah thank you for the fast responding and help!! This is exactly what I needed :) ...
written 8 months ago by peterlageweg60310
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Comment: C: Extract Tree Topology From Ncbi Taxonomy Database
... Thanks SMK. I tried this but it does not work. tree.write(features=["sci_name", "rank"], outfile="tree.nw") t_file = Tree("tree.nw") for node in t_file.traverse(): node.name = node.sci_name tree.write(features=["node.name"], outfile="labeled_tree.nw") AttributeErr ...
written 8 months ago by peterlageweg60310
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Comment: C: Extract Tree Topology From Ncbi Taxonomy Database
... Thanks! This works as well. Is there a way to replace the TaxIDs with the scientific names? ...
written 8 months ago by peterlageweg60310
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Comment: C: Extract Tree Topology From Ncbi Taxonomy Database
... Is there a way to replace the TaxIDs with the scientific names? ...
written 8 months ago by peterlageweg60310

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