update scripts

analysis_scripts/run_diamond.sh

@@ -0,0 +1,18 @@
+#!/bin/bash
+
+basedir=${PWD}
+species=$1
+faa=$2
+
+echo ${basedir}
+echo $species
+echo ${faa}
+./../diamond makedb --in ${faa} -d ${basedir}/${species}/diamond_refseq
+
+mkdir -p ${basedir}/${species}/Comparison/GFs/diamond
+for x in $(ls ${basedir}/${species}/Comparison/GFs/fasta) 
+do 
+echo $x 
+./../diamond  blastx -d ${basedir}/${species}/diamond_refseq -q ${basedir}/${species}/Comparison/GFs/fasta/$x -o ${basedir}/${species}/Comparison/GFs/diamond/$x.tsv;
+done
+

analysis_scripts/run_ete3.sh

@@ -0,0 +1,14 @@
+#!/bin/bash
+basedir=${PWD}
+for sp in synth_myco synth_ecoli synth_paeru; do
+	for frag in 0.5 0.8 1; do 
+		species=${sp}/${frag}
+		echo ${species}
+		#conda activate ete3
+		ete3 compare -t ${basedir}/${species}/Comparison/GFs/CG/msa_delos/concat.tree \
+		${basedir}/${species}/Roary/output/core_gene_alignment_renamed.tree \
+		${basedir}/${species}/Comparison/GFs/CG/msa_genapi/concat.tree \
+		${basedir}/${species}/Comparison/GFs/CG/msa_panaroo/concat.tree  \
+		-r ${basedir}/${sp}/1/Comparison/GFs/CG/msa_prova/${sp}.tree --unrooted > ${basedir}/${species}/Comparison/ete3.log
+	done
+done

analysis_scripts/run_fasttree.sh

@@ -0,0 +1,9 @@
+#!/bin/bash
+
+basedir=${PWD}
+species=$1
+faa=$2
+out=$3 
+
+./../FastTree  -gtr -nt ${faa} > ${out}
+

analysis_scripts/run_mafft.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+basedir=${PWD}
+species=$1
+faa=$2
+out=$3
+
+echo ${basedir}
+echo $species
+echo ${faa}
+
+mafft ${faa} > ${out}
+

process_metagenomes.ipynb

@@ -1412,7 +1412,7 @@
    "source": [
     "import subprocess\n",
     "faa_reference = prokkadir+'/prokka_'+ref_genome+'/*.faa'\n",
-    "ret=subprocess.call(['bash',basedir+\"/run_diamond.sh\",species,faa_reference],stdout=subprocess.DEVNULL)"
+    "ret=subprocess.call(['bash',basedir+\"/analysis_scripts/run_diamond.sh\",species,faa_reference],stdout=subprocess.DEVNULL)"
    ]
   },
   {