decon_notes.txt

GitHub Repositories
=======================
contamination files: https://github.com/epaule/btk_sequences_to_remove
blast scripts: https://github.com/Aquatic-Symbiosis-Genomics-Project/BLAST-scripts

decon blast
===========
bash decon_blastBTK.sh <FASTA-file> <CSV file with ticks> <output directory>

Useful one-liners:
=======================

# create stubs from a BTK CSV file
perl -nE 's/"//g;chomp;@F=split(",");say "REMOVE\t$F[-1] #$F[-3]"' *.csv |sort -k3

# after blasting, grep all Schisto hits and stub them into a remove
head -3 *out |perl -anE 'next if /==>|^\n|No hits/; say "$F[0]\t$F[10]\t$F[13] $F[14]"'|grep Schistosoma |perl -anE 'say "REMOVE\t$F[0]"' |sort -u

# categories from contamination files
cat *.contamination | grep \#  |grep -v query |sort -u |perl -nE 's/\#//;chomp;push @G,"$_";END{say join(", ",@G)}'

# duplicated lines
perl -nE 'next if /^\n|\#/;print if $h{$_};$h{$_}++' daMisOron1.20220213.contamination

# remove duplicated decon lines
perl -i  -ne 'if(/REMOVE\s+(\S+)/){print unless $h{$1};$h{$1}=1}else{print}' icElmAene2.20221111.haplotigs.contamination_

#fire off NCBI-gx
bsub -o fcs_genome.log -M 400000 -n 36 -R'select[mem>400000, tmp>500G] rusage[mem=400000, tmp=600G]' bash /lustre/scratch123/tol/teams/grit/mh6/ncbi-decon/singularity_test/gx_pipeline/gx_map_wrapper.bash -o . -f fasta1.gz -f fasta2.gz -t <taxid>

# run the mito blast outside of the Jira-pipeline (output will be in the local work-driectory and not ):
$PROJECT_DIR/scripts/mito_contamination_screen.sh ./NC_040858.1.fa.gz ./bHalAlb1.20221031.fa.gz

#stubs from FCS
grep EXC drAceCamp1.20221031.fa.66205.fcs_gx_report.txt |perl -F'\t' -ane 'print if $F[6] >= 20' |sort -k6

#create curation.bed lines from the gzipped fasta and the BTK CSV (need to rewrite this in crystal, so it universally works)
ruby -rzlib -rbio -e 's=Hash.new;Bio::FlatFile.auto(Zlib::GzipReader.open(ARGV[0])){|file|file.each{|e|s[e.entry_id]=e.seq.length}};File.open(ARGV[1]){|f|f.each_line{|line|line.chomp!;c=line.split(",");puts "#{c[1]}\t0\t#{s[c[1]]}\tREMOVE" if c[0] == "true"}}' htOpiVive1.20231009.fa.gz blast.me