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Extract all fasta sequences except ids !

  • Public
By Rahul Nayak 1030 days ago
awk 'BEGIN{while((getline<"omi_ids_updated.txt")>0)l[">"$1]=1}/^>/{f=!l[$1]}f' genomic.fna > filtered_without_omi.fasta #extract subseq seqtk subseq omi_ids.fa omi_single_id.txt > omi_single_id.fa #cat omi and all the rest cat omi_single_id.fa filtered_without_omi.fasta > omi_single_id_plus_all.fa #Extract unique kmer ./uniquekmer -f omi_single_id_plus_all.fa -k 19 # Extract the kmer of omi seqtk subseq kmercollection.fasta ../omi_single_id.txt > omi_kmer19.fa #reformat to 19mer reformat.sh in=omi_kmer19.fa out=omi_kmer19_formated.fa fastawrap=19 #Extract and number the kmers perl storeKmer.pl omi_kmer19_formated.fa > omi_kmer19_formated_numbered.fa # cat all *.rd file cat *.rd > all_reads_hits #count the lines in each file -- go in folder for FILE in *; do wc -l $FILE; done > all_hits_lines.txt