Results for "python"

Bio-Scripts

  • Install grabseqs with conda !

    (JitMetaENV) ➜ JitMeta conda install grabseqs -c louiejtaylor -c bioconda -c conda-forge Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists.

    1180 days ago

  • Python script to download covid genome !

    #!/usr/bin/env python3 # these are the publicly available "complete" sequences # https://www.gisaid.org/ has more (1200?), but they require you to sign up import reques...

    1099 days ago

  • Estimate Genome Size

    # Count k-mer occurrence using Jellyfish 2.2.6 jellyfish count -t 8 -C -m 19 -s 5G -o 19mer_out --min-qual-char=? sread_1.fastq sread_2.fastq # points for a histogram jellyfish histo -o 19mer_out.histo 19mer_out #Plot results using R ##load the data into dataframe19 dataframe19

    2227 days ago

  • Mapping with BWA-mem or BWA-sampe in one go with python script !

    ..._to_ctg_map.py) for obtaining sorted and indexed BAM files with BWA-mem or BWA-sampe in one go. An example call for mapping with this script is python reads_to_ctg_map.py /path/to/...

    2087 days ago

  • Bash script to run Busco2 !

    ...USTUS_CONFIG_PATH=/home/urbe/Tools/augustus-3.2.3/config #run BUSCO python BUSCO.py -i /media/urbe/MyDDr...30 -l metazoa_odb9 -o GRAALHaploid_BUSCO -m genome -f #Plot BUSCO python BUSCO_plot.py -wd GRAALHaploi...

    2100 days ago

  • Install Python locally on shared Linux server !

    #Install python to local directory #Firstly,...home directory, download the python source and extract it mkdir ~/python cd ~/python wget http...p. By the default, if we type python command, it will use the defa...k, run this command: which python #it should show you the path...

    2061 days ago

  • Installing pb-assembly on Linux !

    ...016a BLAST+/2.3.0-foss-2016a-Python-2.7.11...numpy/1.6.2-goolf-1.4.10-Python-2.7.3 fftw3/gcc/64/3.1.2...Python/2.7.3-goolf-1.4.10 goalf/1.1...a237_0 bioconda python-sortedcontainers: 2.0.4-py_0...

    1997 days ago

  • Installing Platypus on Ubuntu !

    ...Preparing to unpack .../0-libpython3.6_3.6.6-1~18.04_amd64.deb .....Downloading https://files.pythonhosted.org/packages/85/29/ccdb...e/anaconda3/envs/py27/include/python2.7 -c cython/cerrormodel.c -o...rbe/anaconda3/envs/py27/lib -lpython2.7 -o build/lib.linux-x86_64-...

    1982 days ago

  • Setting up falconUnzip conda environments for genome assembly !

    ...622 KB conda-forge avro-python2-1.8.2 |...964 KB conda-forge python-edlib-1.2.3.post1 | py27h...conda-forge avro-python2: 1.8.2-py_1...bioconda python-edlib: 1.2.3.post1...

    1953 days ago

  • Backward Elimination with Python

    #Backward Elimination with p-values only: import statsmodels.formula.api as sm def backwardElimination(x, sl): numVars = len(x[0]) for i in range(0, numVa...

    1918 days ago