c_cpp/fromOthers/PEAR/test/test.py

   1 #! /usr/bin/env python
   2 import sys
   3 import os
   4 import filecmp
   5 import subprocess
   6 import shutil
   7
   8 def unit_test(f, r, o, fcompare):
   9     subprocess.call(["../src/pear", "-f", f, "-r", r, "-o", o, "-c", "0"], stdout=open(os.devnull, "w"), stderr=subprocess.STDOUT)
  10     correct = filecmp.cmp(o+".assembled.fastq", fcompare)
  11     os.remove(o+".assembled.fastq")
  12     os.remove(o+".discarded.fastq")
  13     os.remove(o+".unassembled.forward.fastq")
  14     os.remove(o+".unassembled.reverse.fastq")
  15     if correct:
  16         return "passed"
  17     else:
  18         return "failed"
  19
  20 def gen(f, r, o, fcompare):
  21     subprocess.call(["../src/pear", "-f", f, "-r", r, "-o", o, "-c", "0"], stdout=open(os.devnull, "w"), stderr=subprocess.STDOUT)
  22     shutil.copyfile(o+".assembled.fastq", fcompare)
  23     os.remove(o+".discarded.fastq")
  24     os.remove(o+".unassembled.forward.fastq")
  25     os.remove(o+".unassembled.reverse.fastq")
  26
  27
  28 if __name__ == "__main__":
  29     test_files = [["raw/16S_101bp1.fq", "raw/16S_101bp2.fq", "raw/compare/101bp.assembled.fastq"],
  30                   ["raw/16S_101bp1.fq.through.fastq", "raw/16S_101bp2.fq.through.fastq", "raw/compare/101bp.through.assembled.fastq"],
  31                   ["raw/16S_150bp1.fq", "raw/16S_150bp2.fq", "raw/compare/150bp.assembled.fastq"],
  32                   ["raw/16S_165bp1.fq", "raw/16S_165bp2.fq", "raw/compare/165bp.assembled.fastq"],
  33                   ["raw/16S_180bp1.fq", "raw/16S_180bp2.fq", "raw/compare/180bp.assembled.fastq"],
  34                   ["raw/16S_190bp1.fq", "raw/16S_190bp2.fq", "raw/compare/190bp.assembled.fastq"],
  35                   ["raw/16S_250bp1.fq", "raw/16S_250bp2.fq", "raw/compare/250bp.assembled.fastq"],
  36                   ["nooverlap/equall_1.fq", "nooverlap/equall_2.fq", "nooverlap/compare/equall.assembled.fastq"],
  37                   ["nooverlap/f_long_1.fq", "nooverlap/f_long_2.fq", "nooverlap/compare/f_long.assembled.fastq"],
  38                   ["nooverlap/r_long_1.fq", "nooverlap/r_long_2.fq", "nooverlap/compare/r_long.assembled.fastq"],
  39                   ["normal/equall_1.fq", "normal/equall_2.fq", "normal/compare/equall.assembled.fastq"],
  40                   ["normal/f_long_1.fq", "normal/f_long_2.fq", "normal/compare/f_long.assembled.fastq"],
  41                   ["normal/r_long_1.fq", "normal/r_long_2.fq", "normal/compare/r_long.assembled.fastq"],
  42                   ["runthrough/equall_1.fq", "runthrough/equall_2.fq", "runthrough/compare/equall.assembled.fastq"],
  43                   ["runthrough/f_long_c2_1.fq", "runthrough/f_long_c2_2.fq", "runthrough/compare/f_long_c2.assembled.fastq"],
  44                   ["runthrough/f_long_c3_1.fq", "runthrough/f_long_c3_2.fq", "runthrough/compare/f_long_c3.assembled.fastq"],
  45                   ["runthrough/r_long_c2_1.fq", "runthrough/r_long_c2_2.fq", "runthrough/compare/r_long_c2.assembled.fastq"],
  46                   ["runthrough/r_long_c3_1.fq", "runthrough/r_long_c3_2.fq", "runthrough/compare/r_long_c3.assembled.fastq"],
  47                   ]
  48     i = 1
  49     for test in test_files:
  50         #gen(test[0], test[1], "temp", test[2])
  51         flag = unit_test(test[0], test[1], "temp", test[2])
  52         print("Test " + repr(i) + " " + flag)
  53         i = i + 1