1.1 --- a/Makefile	Thu Jul 21 18:29:42 2011 +0400
     1.2 +++ b/Makefile	Thu Jul 21 18:34:27 2011 +0400
     1.3 @@ -1,7 +1,8 @@
     1.4  all: tests doc codes blocks3d-wt blocks3d-www pair-cores-www
     1.5  
     1.6  tests:
     1.7 -	PYTHONPATH=$(PWD) nosetests --with-coverage
     1.8 +	PYTHONPATH=$(PWD) nosetests --with-doctest \
     1.9 +		--with-coverage --cover-package=allpy
    1.10  
    1.11  doc:
    1.12  	sphinx-autopackage --suffix=rst --dest-dir=docs/source/allpy/ allpy

     2.1 --- a/test/test_usecases.py	Thu Jul 21 18:29:42 2011 +0400
     2.2 +++ b/test/test_usecases.py	Thu Jul 21 18:34:27 2011 +0400
     2.3 @@ -1,16 +1,19 @@
     2.4 -def capture_stdout(module_name, stdin=None):
     2.5 +import os
     2.6 +from subprocess import Popen, PIPE
     2.7 +
     2.8 +def capture_stdout(module_name, stdin=None, argv=()):
     2.9      """Helper: import module by name, return it's stdout ouput as string."""
    2.10 -    import sys
    2.11 -    from StringIO import StringIO
    2.12 -    stdout_bak = sys.stdout
    2.13 -    sys.stdout = result = StringIO()
    2.14 -    sys.stdout.name = 'stdout'
    2.15 -    if stdin is not None:
    2.16 -        sys.stdin = StringIO(stdin)
    2.17 -        sys.stdin.name = 'stdin'
    2.18 -    __import__(module_name)
    2.19 -    sys.stdout = stdout_bak
    2.20 -    return result.getvalue()
    2.21 +    file = os.path.join(os.path.dirname(__file__), module_name + '.py')
    2.22 +    command = [file] + list(argv)
    2.23 +    print command, stdin
    2.24 +    if stdin:
    2.25 +        p = Popen(command, stdin=PIPE, stdout=PIPE)
    2.26 +        p.stdin.write(str(stdin))
    2.27 +        p.stdin.close()
    2.28 +    else:
    2.29 +        p = Popen(command, stdout=PIPE)
    2.30 +    assert p.wait() == 0
    2.31 +    return p.stdout.read()
    2.32  
    2.33  def test_usecase1():
    2.34      """Run usecase1, assert it produced the expected results."""
    2.35 @@ -56,7 +59,7 @@
    2.36          'AATI---KPD-VK--D--SKEYFKN----------------------------\n'
    2.37          ''
    2.38      )
    2.39 -    output = capture_stdout("usecase3", input)
    2.40 +    output = capture_stdout("usecase3", input, ['0:5,7:12', '-', '-'])
    2.41      assert output == expect, "Usecase1:\nexpect\t%r\noutput\t%r" % (expect, output)
    2.42  
    2.43  # vim: set et ts=4 sts=4 sw=4:

     3.1 --- a/test/usecase1.py	Thu Jul 21 18:29:42 2011 +0400
     3.2 +++ b/test/usecase1.py	Thu Jul 21 18:34:27 2011 +0400
     3.3 @@ -1,3 +1,4 @@
     3.4 +#!/usr/bin/python
     3.5  import sys
     3.6  from allpy import protein
     3.7  from allpy import processors

     4.1 --- a/test/usecase2.py	Thu Jul 21 18:29:42 2011 +0400
     4.2 +++ b/test/usecase2.py	Thu Jul 21 18:34:27 2011 +0400
     4.3 @@ -1,11 +1,16 @@
     4.4 +#!/usr/bin/python
     4.5  import sys
     4.6 +from collections import deque
     4.7  from allpy import dna
     4.8  from allpy.processors import Needle, Left
     4.9  from allpy.fileio import FastaFile
    4.10 -from collections import deque
    4.11 +from allpy.util import open
    4.12  
    4.13  width = 15
    4.14  threshold = 10
    4.15 +if __name__ == "__main__":
    4.16 +    infile = open(sys.argv[1])
    4.17 +    outfile = open(sys.argv[2])
    4.18  
    4.19  def has_identity(column):
    4.20      as_list = column.values()
    4.21 @@ -38,7 +43,7 @@
    4.22      return "".join(column.in_block for column in alignment.columns)
    4.23  
    4.24  def main():
    4.25 -    alignment = dna.Alignment().append_file(sys.stdin)
    4.26 +    alignment = dna.Alignment().append_file(infile)
    4.27      assert len(alignment.sequences) == 2, "Input must have TWO sequences!"
    4.28      alignment.realign(Left())
    4.29      alignment.realign(Needle())
    4.30 @@ -47,8 +52,8 @@
    4.31      for n, block in enumerate(blocks, 1):
    4.32          block.to_file(open("block_%02d.fasta" % n, "w"))
    4.33  
    4.34 -    alignment.to_file(sys.stdout)
    4.35 -    FastaFile(sys.stdout).write_string(
    4.36 +    alignment.to_file(outfile)
    4.37 +    FastaFile(outfile).write_string(
    4.38        blocks_markup(alignment, blocks),
    4.39        "markup",
    4.40        "In run with window %s and threshold %s" % (width, threshold)

     5.1 --- a/test/usecase3.py	Thu Jul 21 18:29:42 2011 +0400
     5.2 +++ b/test/usecase3.py	Thu Jul 21 18:34:27 2011 +0400
     5.3 @@ -1,14 +1,22 @@
     5.4 +#!/usr/bin/python
     5.5  from allpy import protein
     5.6  from allpy.processors import Left
     5.7 +from allpy.util import open
     5.8  import sys
     5.9  
    5.10 -ranges = [(0,5), (7,12)]
    5.11 +if __name__ == "__main__":
    5.12 +    ranges = sys.argv[1]
    5.13 +    infile = open(sys.argv[2])
    5.14 +    outfile = open(sys.argv[3])
    5.15  
    5.16 -alignment = protein.Alignment().append_file(sys.stdin)
    5.17 -for begin, end in ranges:
    5.18 -    columns = alignment.columns[begin:end]
    5.19 -    protein.Block.from_alignment(alignment, columns=columns).realign(Left())
    5.20 -alignment.remove_gap_columns()
    5.21 -alignment.to_file(sys.stdout)
    5.22 +    # This accepts ranges in form "0:5,7:12,1:-1"
    5.23 +    ranges = [map(int, range.split(':')) for range in ranges.split(',')]
    5.24 +
    5.25 +    alignment = protein.Alignment().append_file(sys.stdin)
    5.26 +    for begin, end in ranges:
    5.27 +        columns = alignment.columns[begin:end]
    5.28 +        protein.Block.from_alignment(alignment, columns=columns).realign(Left())
    5.29 +    alignment.remove_gap_columns()
    5.30 +    alignment.to_file(sys.stdout)
    5.31  
    5.32  # vim: set et ts=4 sts=4 sw=4: