merge changes

Merge branch 'master' of github.com:ISUgenomics/common_analyses

generate_i-AdHore_ini-file.sh

@@ -0,0 +1,47 @@
+#!/bin/bash
+gff="$1"
+base="$2"
+#table="$3"
+mkdir -p $base
+awk '$3=="mRNA" {print $1"\t"$7"\t"$9}' $gff |\
+     sed 's/;/\t/1' | sed 's/ID=//g' |\
+     awk -v x="$base" '{print x"_"$1"\t"$3""$2}' |\
+     sed 's/Sobic./'$base'_/g' >  $base/${base}_full.lst
+awk '$3=="mRNA" {print $9}' $gff |\
+     sed -e 's/;/\t/1' -e 's/ID=//g' |\
+     cut -f 1  |\
+     awk '{print $1"\tfamily."$1}' |\
+     sed -e 's/family.Sobic./OG_/g' -e 's/.mrna.\{1,3\}$//g' |\
+     sed 's/^Sobic./'$base'_/1'  >>  blast_table.txt
+
+awk '{print>$1"_chr.list"}'  ${base}/${base}_full.lst
+#echo "blast_table=$(realpath ${base}_blast.pairs)"
+echo "genome=${base}"
+i=1
+for list in ${base}*_chr.list; do
+cut -f 2 $list > $list.temp;
+mv $list.temp $base/$list;
+echo "CO$i ${base}/${list}"
+rm $list
+((i++))
+done
+cat <<EOF
+blast_table=blast_table.txt
+table_type=family
+cluster_type=colinear
+tandem_gap=10
+prob_cutoff=0.1
+write_stats=true
+multiple_hypothesis_correction=FDR
+gap_size=15
+cluster_gap=20
+q_value=0.7
+anchor_points=5
+alignment_method=gg2
+max_gaps_in_alignment=20
+output_path=$(pwd)/iadhore_output2
+number_of_threads=16
+visualizeGHM=true
+visualizeAlignment=true
+verbose_output=true
+EOF

runGMAP.sh

@@ -0,0 +1,14 @@
+#!/bin/bash
+module load gmap-gsnap
+db="$1"
+fasta="$2"
+threads=36
+out="${db%.*}_${fasta%.*}"
+for type in match_est match_cdna gene; do
+if [ ! -f "${out}_${type}.gff3.done" ]; then
+gmap -D /work/LAS/mhufford-lab/arnstrm/NAM/genomes -d ${db} -B 4 -t $threads -f gff3_${type} ${fasta} > ${out}_${type}.gff3 2> ${out}_${type}.err
+if [ $? -eq 0 ]; then
+    touch "${out}_${type}.gff3.done"
+fi
+fi
+done