clean up files

cenote-taker2.1.1.sh

@@ -1825,11 +1825,11 @@ echo "removing ancillary files"
 
 if [ -d DTR_contigs_with_viral_domain ] ; then
 	cd DTR_contigs_with_viral_domain
-	rm -f *.all_start_stop.txt *.bad_starts.txt *.comb.tbl *.comb2.tbl *.good_start_orfs.txt *.hypo_start_stop.txt *.nucl_orfs.fa *.remove_hypo.txt *.log *.promer.contigs_with_ends.fa *.promer.promer *.out.hhr *.starting_orf.txt *.out.hhr *.nucl_orfs.txt *.called_hmmscan.txt *.hmmscan_replicate.out *.hmmscan.out *.rotate.no_hmmscan.fasta *.starting_orf.1.fa *.phan.*fasta *used_positions.txt *.prodigal.for_prodigal.fa *.prodigal.gff *.trnascan-se2.txt *.for_blastp.txt *.for_hhpred.txt circular_contigs_spades_names.txt SPLIT_CIRCULAR_AA*fasta all_circular_contigs_${run_title}.fna SPLIT_DTR_* circular_contigs_spades_names.txt *called_hmmscan*txt *HH.tbl
+	rm -f *.all_start_stop.txt *.bad_starts.txt *.comb.tbl *.comb2.tbl *.good_start_orfs.txt *.hypo_start_stop.txt *.nucl_orfs.fa *.remove_hypo.txt *.log *.promer.contigs_with_ends.fa *.promer.promer *.out.hhr *.starting_orf.txt *.out.hhr *.nucl_orfs.txt *.called_hmmscan.txt *.hmmscan_replicate.out *.hmmscan.out *.rotate.no_hmmscan.fasta *.starting_orf.1.fa *.phan.*fasta *used_positions.txt *.prodigal.for_prodigal.fa *.prodigal.gff *.trnascan-se2.txt *.for_blastp.txt *.for_hhpred.txt circular_contigs_spades_names.txt SPLIT_CIRCULAR_AA*fasta all_circular_contigs_${run_title}.fna SPLIT_DTR_* *called_hmmscan*txt *HH.tbl 
 	cd ..
 fi
 rm -rf bt2_indices/
-rm -f other_contigs/*.AA.fasta other_contigs/*.AA.sorted.fasta other_contigs/*.out other_contigs/*.dat other_contigs/*called_hmmscan.txt other_contigs/SPLIT_LARGE_GENOME_AA_*fasta ITR_containing_contigs/SPLIT_ITR_AA*fasta SPLIT_CIRCULAR_AA* *called_hmmscan.txt
+rm -f other_contigs/*.AA.fasta other_contigs/*.AA.sorted.fasta other_contigs/*.out other_contigs/*.dat other_contigs/*called_hmmscan.txt other_contigs/SPLIT_LARGE_GENOME_AA_*fasta ITR_containing_contigs/SPLIT_ITR_AA*fasta SPLIT_CIRCULAR_AA* *called_hmmscan.txt circular_contigs_spades_names.txt
 rm -f no_end_contigs_with_viral_domain/*.called_hmmscan2.txt no_end_contigs_with_viral_domain/*.hmmscan2.out no_end_contigs_with_viral_domain/*all_hhpred_queries.AA.fasta no_end_contigs_with_viral_domain/*.all_start_stop.txt no_end_contigs_with_viral_domain/*.trnascan-se2.txt no_end_contigs_with_viral_domain/*.for_hhpred.txt no_end_contigs_with_viral_domain/*.for_blastp.txt no_end_contigs_with_viral_domain/*.HH.tbl no_end_contigs_with_viral_domain/*.hypo_start_stop.txt  no_end_contigs_with_viral_domain/*.remove_hypo.txt no_end_contigs_with_viral_domain/*.rps_nohits.fasta no_end_contigs_with_viral_domain/*.tax_guide.blastx.tab no_end_contigs_with_viral_domain/*.tax_orf.fasta no_end_contigs_with_viral_domain/*.trans.fasta no_end_contigs_with_viral_domain/*.called_hmmscan*.txt no_end_contigs_with_viral_domain/*.no_hmmscan*.fasta no_end_contigs_with_viral_domain/*.comb*.tbl no_end_contigs_with_viral_domain/SPLIT_DTR_HMM2_GENOME_AA*fasta no_end_contigs_with_viral_domain/SPLIT_DTR_sort_GENOME_AA* no_end_contigs_with_viral_domain/SPLIT_DTR_RPS_AA* no_end_contigs_with_viral_domain/*used_positions.txt no_end_contigs_with_viral_domain/*seq_chunk_coordinates.csv
 
 echo " "

old_scripts/rpsblastreport2tbl_mt_sketch_contigs1.pl

@@ -25,7 +25,7 @@ sub Wanted{
 	open(OUTPUT, ">$Tbl");
 	print OUTPUT ">Feature $Label Table1";
 	while(defined(my$line = <MYFILE>)){
-		if($line =~ m/Query= (\w+) \[(\d+) - (\d+)\]/){
+		if($line =~ m/Query= ([^\s]+) \[(\d+) - (\d+)\]/){
 			print OUTPUT "\n$2\t$3\tCDS";
 			print OUTPUT "\n\t\t\tprotein_id\tlcl|$1";