https://github.com/applicativesystem/lastz-awk

analyzing lastz alignments using awk
https://github.com/applicativesystem/lastz-awk

awk awk-programming-language awk-script bioinformatics bioinformatics-genome genome-alignments-bioinfromatics genome-genome-alignment genome-protein-alignment lastz

Last synced: 7 days ago
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analyzing lastz alignments using awk

• Host: GitHub
• URL: https://github.com/applicativesystem/lastz-awk
• Owner: applicativesystem
• License: mit
• Created: 2024-08-17T19:50:55.000Z (4 months ago)
• Default Branch: main
• Last Pushed: 2024-08-17T19:52:18.000Z (4 months ago)
• Last Synced: 2024-11-10T20:18:12.241Z (about 1 month ago)
• Topics: awk, awk-programming-language, awk-script, bioinformatics, bioinformatics-genome, genome-alignments-bioinfromatics, genome-genome-alignment, genome-protein-alignment, lastz
• Language: Awk
• Homepage:
• Size: 20.5 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# lastz-alignment-awk

genome sorting and plotting the length alignment from the lastz alignment for the node calculations before you import them for the calculations. 

```

gem install youplot

cat lastzalignment.txt | awk '{ print $10 }' | cut -f 1 -d "-" > length1.txt \ 

              && cat lastzalignment.txt | awk '{ print $10 }' | cut -f 2 -d "-" > \

                                          length2.txt && paste length1.txt length2.txt \ 

                                                    | awk '{ print $2-$1 }' | youplot barplot

cat lastzalignment.txt | awk '{ print $12 }' | cut -f 1 -d "-" > length1.txt \ 

              && cat lastzalignment.txt | awk '{ print $12 }' | cut -f 2 -d "-" > \

                                          length2.txt && paste length1.txt length2.txt \ 

                                                    | awk '{ print $2-$1 }' | youplot barplot

```

Gaurav Sablok \

University of Potsdam \

Potsdam,Germany