Results for "Python Classes"

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...

    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 !

    BAM files and mapping BESST requires sorted and indexed BAM files as input. Any read aligner + samtools can be use...mem or BWA-sampe in one go. An example call for mapping with this script is python...

    2087 days ago

  • Biological Sequence handling with Perl !

    package Sequence::Generic; # File: Sequence/Generic.pm use strict; use Carp; us...te', 'fallback' => 'TRUE'; # These methods should be overriden by child classes # class constructor sub new...

    2144 days ago

  • Bash script to run Busco2 !

    #!/bin/bash #set the path export PATH=$PATH:/home/urbe/Tools/augustus-3.2.3/bin ex...me/urbe/Tools/augustus-3.2.3/config #run BUSCO python BUSCO.py -i /media/urbe/MyDDr...GRAALHaploid_BUSCO -m genome -f #Plot BUSCO python...

    2100 days ago

  • Install Python locally on shared Linux server !

    ...home directory, download the python source and extract it mkdir ~/python cd ~/python wget http...xfv Python-2.7.11.tgz find ~/python -type d | xargs chmod 0755 c...p. By the default, if we type python command, it will use the defa...k, run this command: which python...

    2061 days ago

  • Downloading GATK !

    jitendra@jitendra-UNLOCK-INSTALL[SNP] wget https://github.com/broadinstitute/gatk/rel...y metrics. CollectMultipleMetrics (Picard) Collect multiple classes of metrics. CollectMul...

    2038 days ago

  • Installing pb-assembly on Linux !

    [jnarayan@hmem00 ~]$ module avail ----------------------------...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...

    1997 days ago

  • Installing Platypus on Ubuntu !

    ...bionic-updates/main amd64 libpython3.6 amd64 3.6.6-1~18.04 [1.420...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...

    1982 days ago