Update 1.4.2_gene_finding_II.md

Author: vmkhot

_episodes/1.4.2_gene_finding_II.md

@@ -244,9 +244,9 @@ You no longer need the pharokka database and we recommend modifying the followin
 > mkdir -p $outdir
 > 
 > # get the contig.gff and contig.fasta
-> grep $contig_name 10_pharokka/results/pharokka.gff > $outdir/$contig_name.gff
+> grep $contig_name 10_pharokka/results/pharokka.gff > $outdir/${contig_name}.gff
 > 
-> sed -n '/$contig_name/,/>/p' $assembly | head -n -1  > $outdir/$contig_name.fasta
+> sed -n '/$contig_name/,/>/p' $assembly | head -n -1  > $outdir/${contig_name}.fasta
 > 
 > # next, we get the contig.gbk using a python script
 > # change the names accordingly
@@ -257,7 +257,7 @@ You no longer need the pharokka database and we recommend modifying the followin
 > # the inputs for the following python script should be
 > # python3 script.py input.gbk output.gbk $contig_name
 > input_gbk='10_pharokka/results/pharokka.gbk'
-> output_gbk='20_selected_contig/$contig_name.gbk'
+> output_gbk='20_selected_contig/${contig_name}.gbk'
 > 
 > python3 ../python_scripts/1.4_extract_contig.py $input_gbk $output_gbk $contig_name
 > 
@@ -270,9 +270,9 @@ You no longer need the pharokka database and we recommend modifying the followin
 > # define all your file paths for readability
 > outdir='20_selected_contig/'
 > 
-> fasta='20_selected_contig/$contig_name.fasta'
-> gff='20_selected_contig/$contig_name.gff'
-> gbk='20_selected_contig/$contig_name.gbk'
+> fasta='20_selected_contig/${contig_name}.fasta'
+> gff='20_selected_contig/${contig_name}.gff'
+> gbk='20_selected_contig/${contig_name}.gbk'
 > 
 > pharokka_plotter.py -i $fasta -n $outdir/pharokka_plot --gff $gff --genbank $gbk
 >