gauravcodepro / gawk-awk-paf-alignments

gawk and awk combined functions for working with pacbiohifi aligned data.

gawk-awk-paf-alignments

a combination of the gawk and the awk basic compiler to create a function that will estimate the aligned genome fractions from the paf alignment of the genome long reads to the genome. This includes multiple functions which also allow for the filtering of the quality alignments before estimating the genome length coverage. You can find more functions in the awk library but you can use this like: Adding the support for the gnu visualziation libraries.

pafalignments="aligned.paf"
cat aligned.paf | awk '{ print  $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7" \
                                    \t"$8"\t"$9"\t"$10"\t"$11"\t"$12 }' | \
                                    awk '{ print $4-$3 }' | awk '{ print $1 }' | \
                                                      gawk '{ sum += $1 }; END { print sum }'
cat aligned.paf | awk '{ print  $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7" \
                                    \t"$8"\t"$9"\t"$10"\t"$11"\t"$12 }' | \
                                    awk '{ print $9-$8 }' | awk '{ print $1 }' | \
                                                      gawk '{ sum += $1 }; END { print sum }'

# estimating the total of the aligned length based on the computed alignments
pafalignments="aligned.paf"
genomelength=""genomelength
# query aligned genome fractions  percentage as compared to the genome length of the reference genome
cat aligned.paf | awk '{ print  $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7" \
                                    \t"$8"\t"$9"\t"$10"\t"$11"\t"$12 }' | \
                                    awk '{ print $4-$3 }' | awk '{ print $1 }' | \
                                                      gawk '{ sum += $1 }; END { print sum }' | \
                                                                        awk '{ print $1/$genomelength*100 }'
# reference aligned genome fractions percentage as compared to the genome length of the reference genome
cat aligned.paf | awk '{ print  $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7" \
                                    \t"$8"\t"$9"\t"$10"\t"$11"\t"$12 }' | \
                                    awk '{ print $9-$8 }' | awk '{ print $1 }' | \
                                                      gawk '{ sum += $1 }; END { print sum }' | \
                                                                        awk '{ print $1/$genomelength*100 }'

Gaurav
Academic Staff Member
Bioinformatics
Institute for Biochemistry and Biology
University of Potsdam
Potsdam,Germany