diff tests/run.sh @ 18:e4d75f9efb90 draft

planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tests/run.sh	Thu Feb 02 18:44:31 2017 -0500
@@ -0,0 +1,133 @@
+#!/usr/bin/env bash
+if [ x$BASH = x ] || [ ! $BASH_VERSINFO ] || [ $BASH_VERSINFO -lt 4 ]; then
+  echo "Error: Must use bash version 4+." >&2
+  exit 1
+fi
+# get the name of the test directory
+dirname=$(dirname $0)
+
+USAGE="Usage: \$ $(basename $0) [options] [test1 [test2]]"
+
+
+function main {
+
+  do_all=true
+  verbose=true
+  # Run the requested tests
+  for arg in "$@"; do
+    # Check for options
+    #TODO: option to keep test data at end instead of removing it.
+    if [[ ${arg:0:1} == '-' ]]; then
+      case "$arg" in
+        -h)
+          echo "$USAGE" >&2
+          echo "Currently valid tests:" >&2
+          list_tests >&2
+          exit 1;;
+        -q)
+          verbose='';;
+        -v)
+          verbose=true;;
+        *)
+          echo "Unrecognized option \"$arg\"." >&2;;
+      esac
+      continue
+    fi
+    # Execute valid tests (if they're existing functions).
+    if [[ $(type -t $arg) == function ]]; then
+      do_all=''
+      if [[ $verbose ]]; then
+        $arg
+      else
+        $arg 2>/dev/null
+      fi
+    else
+      echo "Unrecognized test \"$arg\"." >&2
+      do_all=''
+    fi
+  done
+
+  # If no tests were specified in arguments, do all tests.
+  if [[ $do_all ]]; then
+    if [[ $verbose ]]; then
+      all
+    else
+      all 2>/dev/null
+    fi
+  fi
+}
+
+function fail {
+  echo "$@" >&2
+  exit 1
+}
+
+function list_tests {
+  while read declare f test; do
+    # Filter out functions that aren't tests.
+    if echo "$initial_declarations" | grep -qF 'declare -f '"$test"; then
+      continue
+    else
+      echo "$test"
+    fi
+  done < <(declare -F)
+}
+
+# Capture a list of all functions defined before the tests, to tell which are actual functions
+# and which are tests.
+initial_declarations=$(declare -F)
+
+########## Functional tests ##########
+
+# Do all tests.
+function all {
+  align
+  align_p3
+  duplex
+  duplex_qual
+  stats_diffs
+}
+
+function barcodes {
+  echo -e "\tmake-barcodes.awk ::: families.raw_[12].fq"
+  paste "$dirname/families.raw_1.fq" "$dirname/families.raw_2.fq" | paste - - - - \
+    | awk -f "$dirname/../make-barcodes.awk" -v TAG_LEN=12 -v INVARIANT=5 | sort \
+    | diff -s - "$dirname/families.sort.tsv"
+}
+
+# align_families.py
+function align {
+  echo -e "\talign_families.py ::: families.sort.tsv:"
+  python "$dirname/../align_families.py" "$dirname/families.sort.tsv" | diff -s - "$dirname/families.msa.tsv"
+}
+
+# align_families.py with 3 processes
+function align_p3 {
+  echo -e "\talign_families.py ::: families.sort.tsv:"
+  python "$dirname/../align_families.py" -p 3 "$dirname/families.sort.tsv" | diff -s - "$dirname/families.msa.tsv"
+}
+
+# dunovo.py defaults on toy data
+function duplex {
+  echo -e "\tdunovo.py ::: families.msa.tsv:"
+  python "$dirname/../dunovo.py" "$dirname/families.msa.tsv" | diff -s - "$dirname/families.cons.fa"
+  python "$dirname/../dunovo.py" --incl-sscs "$dirname/families.msa.tsv" | diff -s - "$dirname/families.cons.incl-sscs.fa"
+}
+
+# dunovo.py quality score consideration
+function duplex_qual {
+  echo -e "\tdunovo.py ::: qual.msa.tsv:"
+  python "$dirname/../dunovo.py" --incl-sscs -q 20 "$dirname/qual.msa.tsv" | diff -s - "$dirname/qual.cons.fa"
+}
+
+function duplex_gapqual {
+  echo -e "\tdunovo.py ::: gapqual.msa.tsv:"
+  python "$dirname/../dunovo.py" --incl-sscs -q 25 "$dirname/gapqual.msa.tsv" | diff -s - "$dirname/gapqual.cons.fa"
+}
+
+function stats_diffs {
+  echo -e "\tstats.py diffs ::: gaps.msa.tsv:"
+  python "$dirname/../stats.py" diffs "$dirname/gaps.msa.tsv" | diff -s - "$dirname/gaps-diffs.out.tsv"
+}
+
+main "$@"