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Update klebsiella pneumoniae analysis [thesis][skip CI]
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results/klebsiella/kleb_pneumoniae/assembly/get-max-covg.sh
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,10 @@ | ||
| #!/bin/bash | ||
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| # usage: get-max-covg.sh <genome-size> <in.fa> | ||
| # output: <number_of_contigs> <sum_of_lengths> <longest_len> <shortest_len> | ||
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| genome=$1 | ||
| seqfile=$2 | ||
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| dnacat -L "$seqfile" | cut -f2 | sort -rn | \ | ||
| awk '{if(x+$1>'$genome'){exit;} x+=$1; n+=1; l=$1; if(!f){f=$1}} END{print n,x,f,l}' |
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results/klebsiella/kleb_pneumoniae/assembly/make-dot-plots.sh
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| Original file line number | Diff line number | Diff line change |
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| #!/bin/bash | ||
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| set -ou pipefail | ||
| set -o xtrace | ||
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| # | ||
| # Make MUMMER dot plot | ||
| # Requires: mummer (nucmer, mummerplot), gnuplot, dnacat, ghostscript (ps2pdf) | ||
| # | ||
| # Clean up: | ||
| # rm -rf links plain truthref | ||
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| LINKCONTIGS=k31_links/klebPneu.rmdup.fa | ||
| PLAINCONTIGS=k31_plain/klebPneu.rmdup.fa | ||
| TRUTH=../truth/CAV1016.fa | ||
| REF=../ref/GCF_000016305.1_ASM1630v1_genomic.fa | ||
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| CONTIGSTATS=~/mccortex/libs/bioinf-perl/fastn_scripts/contig_stats.pl | ||
| ASSEM_NCONTIGS=./get-max-covg.sh | ||
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| REFLEN=$(dnacat -P $REF | awk '{x+=length($1)} END{print x}') | ||
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| # Fix issues, re-run gnuplot | ||
| function fix_mummer_gp { | ||
| local prefix=$1 | ||
| sed -i '.tmp' 's/^set mouse clipboardformat/\#set mouse clipboardformat/g' $prefix.gp | ||
| gnuplot $prefix.gp | ||
| } | ||
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| # make plot $prefix'_cov.pdf' | ||
| # make plot $prefix'_dot.pdf' | ||
| function mk_mummer_plots { | ||
| local prefix=$1; shift | ||
| # local otheropts=$2 | ||
| # coverage plot | ||
| mummerplot -t postscript -c -p $prefix"_cov" $prefix.delta | ||
| fix_mummer_gp $prefix"_cov" | ||
| ps2pdf $prefix"_cov.ps" $prefix"_cov.pdf" | ||
| # dot plot | ||
| # removed: --breaklen 10000 | ||
| mummerplot -t postscript -l "$@" -p $prefix"_dot" $prefix.delta | ||
| fix_mummer_gp $prefix"_dot" | ||
| ps2pdf $prefix"_dot.ps" $prefix"_dot.pdf" | ||
| } | ||
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| function get_longest_contigs { | ||
| local seqin=$1 | ||
| local seqout=$2 | ||
| local reflen=$3 | ||
| local ncontigs=$($ASSEM_NCONTIGS $reflen $seqin | awk '{print $1}') | ||
| set +o xtrace | ||
| dnacat -P $seqin | awk '{print length($1),$1}' | sort -k1rn,2 | \ | ||
| awk '{print $2}' | head -$ncontigs | \ | ||
| dnacat -F -M <(i=0; while true; do echo "r$i"; ((i++)); done) > $seqout | ||
| set -o xtrace | ||
| } | ||
| # mkdir -p links | ||
| # get_longest_contigs $LINKCONTIGS links/contigs.fa $REFLEN | ||
| # nucmer -mum -p links/links $TRUTH links/contigs.fa | ||
| # mk_mummer_plots links/links | ||
| # nucmer -mum -p links/linksswap links/contigs.fa $TRUTH | ||
| # mk_mummer_plots links/linksswap | ||
| # mkdir -p plain | ||
| # get_longest_contigs $PLAINCONTIGS plain/contigs.fa $REFLEN | ||
| # nucmer -mum -p plain/plain $TRUTH plain/contigs.fa | ||
| # mk_mummer_plots plain/plain | ||
| # nucmer -mum -p plain/plainswap plain/contigs.fa $TRUTH | ||
| # mk_mummer_plots plain/plainswap | ||
| # # Make plot between ref and truth | ||
| # mkdir -p truthref | ||
| # nucmer -mum -p truthref/truthref $TRUTH $REF | ||
| # mk_mummer_plots truthref/truthref | ||
| # nucmer -mum -p truthref/truthrefswap $REF $TRUTH | ||
| # mk_mummer_plots truthref/truthrefswap | ||
| $CONTIGSTATS links/contigs.fa > links/contig_stats.txt | ||
| $CONTIGSTATS plain/contigs.fa > plain/contig_stats.txt |
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