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I would strongly recommend to use Bioconda instead of compiling. It is one of the channels ("distributors of packages") in Anaconda Cloud which is basically a package source for conda. In short - conda allows you to create virtual environments isolated from system and to install various precompiled software packages with one command (so, by the way, you can ...


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The manual says fields in a tabular output file are space-delimited. It should be fairly straightforward to load a space-delimited file in pandas. From the manual: --tblout <f> Save a simple tabular (space-delimited) file summarizing the per-target output, with one data line per homologous target model found.


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Most likely your Augustus installation is not functioning properly. Did you install Augustus from source or using conda? I believe the conda version of Augustus is known to have some issues. Something worth trying: Running a complete busco install in a VM. This image has all dependencies installed and properly configured.


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I don't have time to give you a polished fully functional version but this will get you started. The next step will be a bit harder as you will need to capture the start of the first CDS in the chunk and end of the last CDS instead of just hardcoding as I have here. fout = open('/path/first3.gbk','w') for record in SeqIO.parse('/path/NC_000962.3.final.gbk','...


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You can use NCBI EntrezDirect to download data in GenBank format for a specific region of the sequence as follows: efetch -db nuccore -id NC_000962.3 -format gb -seq_start 1 -seq_stop 99000 > seq.gb


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This time conda uninstall hmmer in the root environment did the job. The sequence of commands that led me there is shown below. Thanks Devon Ryan. conda list | grep hmmer hmmer 3.1b2 3 bioconda conda uninstall hmmer Solving environment: done ## Package Plan ## environment location: /Users/user/anaconda ...


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