update plotting scripts and manifest

2018-01-17-within_vs_across/entropy_manifest.tab

@@ -11,9 +11,9 @@ NZ_CP012981.1	NZ_CP012982.1,NZ_CP012983.1	Burkholderia	cepacia	ATCC25416	APZ15_R
 NC_008095.1	NA	Myxococcus	xanthus	DK_1622	MXAN_RS01560	WP_011550462.1	Proteobacteria	Deltaproteobacteria	Myxococcales	Myxococcaceae	SRR4236978	DSM_16526
 NC_020555.1	NA	Helicobacter	cinaedi	18818=ATCC_BAA-847	HCBAA847_RS00680	WP_002956213.1	Proteobacteria	Epsilonproteobacteria	Campylobacterales	Helicobacteraceae	DRR090193	MRY12-0051
 NC_008570.1	NA	Aeromonas	hydrophila	ATCC7966	AHA_0076	YP_854603.1	Proteobacteria	Gammaproteobacteria	Aeromonadales	Aeromonadaceae	GAGE-B	SSU
-NC_000913.3	NA	Escherichia	coli	MG1655	b0200	NP_414742.1	Proteobacteria	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Simulated	
-BA000007.2	NA	Escherichia	coli	Sakai	ECs0202	BAB33625.1	Proteobacteria	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Simulated	
-CP003200.1	NA	Klebsiella	pneumoniae	HS11286	KPHS_00140	AEW58712.1	Proteobacteria	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Simulated	
+NC_000913.3	NA	Escherichia	coli	MG1655	b0200	NP_414742.1	Proteobacteria	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Simulated	NA
+BA000007.2	NA	Escherichia	coli	Sakai	ECs0202	BAB33625.1	Proteobacteria	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Simulated	NA
+CP003200.1	NA	Klebsiella	pneumoniae	HS11286	KPHS_00140	AEW58712.1	Proteobacteria	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Simulated	NA
 CP015377.1	NA	Pseudomonas	aeruginosa	BAMCPA07-48	A6R75_01940	ANA68941.1	Proteobacteria	Gammaproteobacteria	Pseudomonadaceae	Pseudomonadaceae	SRR3500543	BAMCPA07-48-HiSeq
 NZ_CP017149.1	NA	Pseudomonas	aeruginosa	ATCC15692	BGV84_RS03410	WP_003113167.1	Proteobacteria	Gammaproteobacteria	Pseudomonadaceae	Pseudomonadaceae	SRR3500543	BAMCPA07-48-HiSeq
 NC_002505.1	NC_002506.1	Vibrio	cholerae	El_tor_st_N16961	VC0058	NP_229717.1	Proteobacteria	Gammaproteobacteria	Vibrionales	Vibrionaceae	GAGE-B	CO_1032(5)

riboSeed/riboStructure.py

@@ -322,7 +322,7 @@ def plot_rDNAs(
     ax2.xaxis.set_ticks_position('none')
     # ax.tick_params(axis='y', colors='dimgrey')
     ax.tick_params(axis='x', colors='dimgrey')
-
+    ax.xaxis.get_major_formatter().set_scientific(False)
     # set axis labels
     ax.xaxis.label.set_color('black')
 

scripts/recreating_tables_and_figures.md

@@ -293,3 +293,27 @@ Then, we ran riboSeed:
 /home/nw42839/miniconda3/bin/ribo select ./scan/scannedScaffolds.gb -o select
 /home/nw42839/miniconda3/bin/ribo seed ./select/riboSelect_grouped_loci.txt -r ./scan/scannedScaffolds.gb -F ./SRR2064286_1_sub.fastq -R ./SRR2064286_2_sub.fastq --ref_as_contig trusted --cores 4 --memory 24 -z -o seed_trusted
 ```
+
+
+## More entropy the suppl figures:
+for generating the entropy figures within and across genomes, we updated things to use a script: runEntropyComparisons.sh.  Its a clunky one, but it works.  It reads the entropy_manifest.tab file, and requires a combined archaeal/bacterial assemblies_summary.txt file from NCBI.  The beginning of the script has comments about how to regenerate that file.  In short, I manually inspected each genome and picked a gene close the the first rDNA operon.  The script picks up to 25 randome genomes of the same genus and species, and runs the analysis outlined above (extract those regions + 10bk up and down, find the rDNAs, extract the rDNAs, allign with mafft, plot).  It also plots the within-genome rDNA entropy for that genome.  We got the sense that the supplementary material was too short, and figured this would lengthen things substantially.  (Just kidding, a reviewer asked).
+
+## The ribo structure analysis
+We found several genomes with strange  rDNA structures, and downloaded them manually from ncbi.  Then, after putting them in a folder called "./2018-01-26-odd_rDNAs/", we ran riboStrcuture:
+
+```
+ribo structure ./2018-01-26-odd_rDNAs/ -o oddballs
+```
+
+as a comparison, because we had the genomes already for the entropy experiment, we copied those all to a new dir:
+
+```
+cp 2018-01-17-within_vs_across/*/ref/*.fasta ./2018-01-27-normal/
+```
+
+and ran ribostructure
+
+
+```
+rm normal/ -r; ribo structure ./2018-01-27-normal/ -o normal
+```

scripts/runEntropyComparisons.sh

@@ -97,7 +97,24 @@ do
     title="$ ${genus} $ $ ${species} $ ${strain}"
     echo "$title"
     ribo snag ./scan_${refacc}/scannedScaffolds.gb ./select_${refacc}/riboSelect_grouped_loci.txt -o ./snag_${refacc}/ --msa_tool mafft -v 3 --title "rDNAs within ${title}" --skip_kmers --skip_blast
+    cd ../
+done < ./entropy_manifest.tab
 
 
-    cd ../
+# copy and rename results:
+mkdir results_figs
+counter=1
+while read refacc refother genus species strain gene geneacc phylum order class family sra compstrain
+do
+    echo "Processing $genus $species $strain $geneacc ..."
+    thisdir="${genus}_${species}_${strain}"
+    if [ -d "${thisdir}/snag_${gene}" ]
+    then
+
+	cp ${thisdir}/snag_${refacc}/entropy_plot.png results_figs/${counter}_genome.png
+	cp ${thisdir}/snag_${gene}/entropy_plot.png results_figs/${counter}_gene.png
+	counter=$((counter + 1))
+    else
+	echo "no results found"
+    fi
 done < ./entropy_manifest.tab