Code Monkey home page Code Monkey logo

Comments (1)

franciscozorrilla avatar franciscozorrilla commented on July 29, 2024

Temporary workaround to deal with megahit, shovil, and metaGEM outputs

# Check if bins are original (megahit-assembled) or strict/permissive (metaspades-assembled)
            if [[ $bin == *.strict.fa ]] || [[ $bin == *.permissive.fa ]] || [[ $bin == *.s.fa ]] || [[ $bin == *.p.fa ]];then
                less $bin |grep ">"|cut -d '_' -f4|awk '{{sum+=$1}}END{{print sum}}' >> $(echo "$bin"|sed "s/.fa/.map/")
            elif [[ $bin == *.shovill.fa ]];then
                less $bin |grep ">"|cut -d ' ' -f2|sed 's/len=//g'|awk '{{sum+=$1}}END{{print sum}}' >> $(echo "$bin"|sed "s/.fa/.map/")
            elif [[ $bin == *megahit.fa ]];then
                less $bin |grep ">"|cut -d '-' -f4|sed 's/len=//g'|awk '{{sum+=$1}}END{{print sum}}' >> $(echo "$bin"|sed "s/.fa/.map/")
            else
                less $bin |grep ">"|cut -d '-' -f4|sed 's/len_//g'|awk '{{sum+=$1}}END{{print sum}}' >> $(echo "$bin"|sed "s/.fa/.map/")
            fi

Rather than keep extending this for each possible case, just use wc to count bp after removing newlines

genome.fa|grep -v '>'|tr -d '\n'|wc -m

from metagem.

Related Issues (20)

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.