profiles with jarvis

profiles/JARVIS_profiles.sh

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+#!/bin/bash
+#
+# ==============================================================================
+# |                                                                            |
+# |           THIS PROGRAM COMPUTES COMPLEXITY PROFILES WITH JARVIS            |
+# |           =====================================================            |
+# |                                                                            |
+# |                    ./JARVIS_profiles.sh sequence.fa                        |
+# |                                                                            |
+# |                     FILE NEEDED TO THE COMPUTATION:                        |
+# |                                                                            |
+# |                     $1  >  FILE WITH THE GENOMES ID                        |
+# |                                                                            |
+# ==============================================================================
+#
+# ==============================================================================
+# ================================ DEFINITIONS =================================
+#
+GET_GTO=0;
+GET_JARVIS=1;
+RUN_COMPARISON=1;
+#
+# ==============================================================================
+# ================================== GET GTO ===================================
+if [[ "$GET_GTO" -eq "1" ]];
+  then
+  conda install -c cobilab gto --yes
+  fi
+#
+# ==============================================================================
+# ============================= === GET JARVIS =================================
+if [[ "$GET_JARVIS" -eq "1" ]];
+  then
+  git clone https://github.com/cobilab/jarvis
+  cd jarvis/src/
+  make
+  cp JARVIS ../../
+  cd ../../
+  fi
+#
+# ==============================================================================
+# =============================== RUN COMPARISON ===============================
+if [[ "$RUN_COMPARISON" -eq "1" ]];
+  then
+  gto_fasta_rand_extra_chars < $1 | gto_fasta_to_seq > SEQ;
+  gto_reverse < SEQ > SEQ_R;
+  #
+  # GET WINDOW SIZE BY SEQUENCE SIZE
+  LENGTH=`gto_info < SEQ | grep "Number of sym" | awk '{ print $5}'`;
+  WINDOW_SIZE=`echo "$LENGTH / 285" | bc`;
+  echo "WINDOW SIZE: $WINDOW_SIZE";
+  #
+  ./JARVIS -v -l 5 -e SEQ
+  ./JARVIS -v -l 5 -e SEQ_R
+  #
+  gto_upper_bound -u 2 < SEQ.iae   > SEQ_UB
+  gto_upper_bound -u 2 < SEQ_R.iae > SEQ_R_UB
+  #
+  gto_filter -d 2 -w $WINDOW_SIZE -c < SEQ_UB   > FIL_UB.x
+  gto_filter -d 2 -w $WINDOW_SIZE -c < SEQ_R_UB > FIL_UB_R.x
+  #
+  tac FIL_UB_R.x > FIL_UB_N.x
+  awk '{print $1;}' FIL_UB.x   > IDXES
+  awk '{print $2;}' FIL_UB.x   > A_D
+  awk '{print $2;}' FIL_UB_R.x > A_R
+  #
+  gto_min -f A_D -s A_R > A_min
+  #
+  paste -d '\t' IDXES A_min > PROFILE_N
+  #
+  gnuplot << EOF
+    reset
+    set terminal pdfcairo enhanced color font 'Verdana,12'
+    set output "profile.pdf"
+    set style line 101 lc rgb '#000000' lt 1 lw 4
+    set border 3 front ls 101
+    set tics nomirror out scale 0.75
+    set format '%g'
+    set size ratio 0.1
+    unset key
+    set yrange [:2] 
+    set xrange [:]
+    set xtics auto
+    set ytics 0.5
+    set grid 
+    set ylabel "Bps"
+    set xlabel "Length"
+    set border linewidth 1.5
+    set style line 1 lc rgb '#0060ad' lt 1 lw 2 pt 5 ps 0.4 # --- blue
+    set style line 2 lc rgb '#0060ad' lt 1 lw 4 pt 6 ps 0.4 # --- green
+    plot "PROFILE_N" using 1:2 with lines ls 1
+EOF
+  fi
+#
+#
+# ==============================================================================
+# ==============================================================================
+