Cython API: compiling but not working
This commit is contained in:
Celine Mercier
@ -1,5 +1,5 @@
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from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
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from obitools3.obidms._obidms import OBIDMS # TODO cimport doesn't work
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from obitools3.dms.dms import OBIDMS # TODO cimport doesn't work
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from obitools3.utils cimport bytes2str
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import time
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@ -1,5 +1,6 @@
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from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
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from obitools3.obidms._obidms import OBIDMS, OBIView, OBIView_line_selection # TODO cimport doesn't work
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from obitools3.dms.dms import OBIDMS # TODO cimport doesn't work
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#, OBIView, OBIView_line_selection # TODO cimport doesn't work
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from functools import reduce
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import time
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@ -56,34 +57,34 @@ def run(config):
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d = OBIDMS(config['obi']['defaultdms'])
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# Open input view 1
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iview = d.open_view(config['obi']['inputview'])
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# Initialize the progress bar
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pb = ProgressBar(len(iview), config, seconde=5)
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# Apply filter
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selection = OBIView_line_selection(iview)
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for i in range(len(iview)) :
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pb(i)
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line = iview[i]
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loc_env = {'sequence': line, 'line': line} # TODO add taxonomy
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good = (reduce(lambda bint x, bint y: x and y,
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(bool(eval(p, loc_env, line))
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for p in config['grep']['predicates']), True))
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if good :
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selection.append(i)
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# Create output view with the line selection
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oview = d.clone_view_with_line_selection(config['obi']['outputview'], selection, comments="obi grep: "+str(config['grep']['predicates'])+"\n")
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#print("\n")
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#print(repr(oview))
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iview.close()
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oview.close()
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# iview = d.open_view(config['obi']['inputview'])
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#
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# # Initialize the progress bar
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# pb = ProgressBar(len(iview), config, seconde=5)
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#
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# # Apply filter
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# selection = OBIView_line_selection(iview)
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# for i in range(len(iview)) :
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# pb(i)
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# line = iview[i]
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#
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# loc_env = {'sequence': line, 'line': line} # TODO add taxonomy
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#
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# good = (reduce(lambda bint x, bint y: x and y,
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# (bool(eval(p, loc_env, line))
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# for p in config['grep']['predicates']), True))
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#
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# if good :
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# selection.append(i)
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#
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# # Create output view with the line selection
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# oview = d.clone_view_with_line_selection(config['obi']['outputview'], selection, comments="obi grep: "+str(config['grep']['predicates'])+"\n")
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#
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# #print("\n")
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# #print(repr(oview))
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#
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# iview.close()
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# oview.close()
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d.close()
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@ -2,7 +2,7 @@ from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
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from obitools3.files.universalopener cimport uopen
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from obitools3.parsers.fasta import fastaIterator
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from obitools3.parsers.fastq import fastqIterator
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from obitools3.obidms._obidms import OBIDMS
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from obitools3.dms.dms import OBIDMS # TODO cimport doesn't work
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import time
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@ -109,22 +109,22 @@ def run(config):
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d = OBIDMS(config['obi']['defaultdms'])
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# Create view
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view = d.new_view(config['import']['destview'], view_type=view_type, quality_column=get_quality)
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i = 0
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for seq in iseq:
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pb(i)
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view[i].id = seq['id']
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view[i].definition = seq['definition']
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view[i].nuc_seq = seq['sequence']
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if get_quality :
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view[i].quality = seq['quality']
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for tag in seq['tags'] :
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view[i][tag] = seq['tags'][tag]
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i+=1
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#print(view.__repr__())
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view.close()
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# view = d.new_view(config['import']['destview'], view_type=view_type, quality_column=get_quality)
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#
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# i = 0
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# for seq in iseq:
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# pb(i)
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# view[i].id = seq['id']
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# view[i].definition = seq['definition']
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# view[i].nuc_seq = seq['sequence']
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# if get_quality :
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# view[i].quality = seq['quality']
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# for tag in seq['tags'] :
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# view[i][tag] = seq['tags'][tag]
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# i+=1
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#
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# #print(view.__repr__())
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#
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# view.close()
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d.close()
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@ -1,11 +1,11 @@
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#cython: language_level=3
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from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
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from obitools3.obidms._obidms cimport OBIDMS # TODO cimport doesn't work
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from obitools3.dms.dms import OBIDMS # TODO cimport doesn't work
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from obitools3.utils cimport str2bytes
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from obitools3.obidms.capi.obialign cimport obi_lcs_align_one_column, \
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obi_lcs_align_two_columns
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from obitools3.dms.capi.obialign cimport obi_lcs_align_one_column, \
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obi_lcs_align_two_columns
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import time
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@ -155,82 +155,82 @@ def addOptions(parser):
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help="Number of threads to use for the computation. Default: one.")
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cpdef align(str dms_n,
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str input_view_1_n, str output_view_n,
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str input_view_2_n="",
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str input_column_1_n="", str input_column_2_n="",
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str input_elt_1_n="", str input_elt_2_n="",
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str id_column_1_n="", str id_column_2_n="",
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double threshold=0.0, bint normalize=True,
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int reference=0, bint similarity_mode=True,
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bint print_seq=False, bint print_count=False,
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comments="",
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int thread_count=1) :
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cdef OBIDMS d
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d = OBIDMS(dms_n)
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if input_view_2_n == "" and input_column_2_n == "" :
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if obi_lcs_align_one_column(d._pointer, \
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str2bytes(input_view_1_n), \
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str2bytes(input_column_1_n), \
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str2bytes(input_elt_1_n), \
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str2bytes(id_column_1_n), \
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str2bytes(output_view_n), \
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str2bytes(comments), \
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print_seq, \
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print_count, \
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threshold, normalize, reference, similarity_mode,
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thread_count) < 0 :
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raise Exception("Error aligning sequences")
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else :
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if obi_lcs_align_two_columns(d._pointer, \
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str2bytes(input_view_1_n), \
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str2bytes(input_view_2_n), \
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str2bytes(input_column_1_n), \
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str2bytes(input_column_2_n), \
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str2bytes(input_elt_1_n), \
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str2bytes(input_elt_2_n), \
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str2bytes(id_column_1_n), \
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str2bytes(id_column_2_n), \
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str2bytes(output_view_n), \
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str2bytes(comments), \
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print_seq, \
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print_count, \
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threshold, normalize, reference, similarity_mode) < 0 :
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raise Exception("Error aligning sequences")
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d.close()
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def run(config):
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# TODO: Build formatted comments with all parameters etc
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comments = "Obi align"
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# Call cython alignment function
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align(config['obi']['defaultdms'], \
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config['obi']['inputview1'], \
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config['obi']['outputview'], \
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input_view_2_n = config['obi']['inputview2'], \
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input_column_1_n = config['obi']['inputcolumn1'], \
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input_column_2_n = config['obi']['inputcolumn2'], \
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input_elt_1_n = config['obi']['inputelement1'], \
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input_elt_2_n = config['obi']['inputelement2'], \
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id_column_1_n = config['obi']['idcolumn1'], \
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id_column_2_n = config['obi']['idcolumn2'], \
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threshold = config['align']['threshold'], \
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normalize = config['align']['normalize'], \
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reference = config['align']['reflength'], \
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similarity_mode = config['align']['similarity'], \
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print_seq = config['align']['printseq'], \
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print_count = config['align']['printcount'], \
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comments = comments, \
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thread_count = config['align']['threadcount'])
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print("Done.")
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# cpdef align(str dms_n,
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# str input_view_1_n, str output_view_n,
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# str input_view_2_n="",
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# str input_column_1_n="", str input_column_2_n="",
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# str input_elt_1_n="", str input_elt_2_n="",
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# str id_column_1_n="", str id_column_2_n="",
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# double threshold=0.0, bint normalize=True,
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# int reference=0, bint similarity_mode=True,
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# bint print_seq=False, bint print_count=False,
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# comments="",
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# int thread_count=1) :
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#
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# cdef OBIDMS d
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# d = OBIDMS(dms_n)
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#
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# if input_view_2_n == "" and input_column_2_n == "" :
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# if obi_lcs_align_one_column(d._pointer, \
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# str2bytes(input_view_1_n), \
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# str2bytes(input_column_1_n), \
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# str2bytes(input_elt_1_n), \
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# str2bytes(id_column_1_n), \
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# str2bytes(output_view_n), \
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# str2bytes(comments), \
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# print_seq, \
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# print_count, \
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# threshold, normalize, reference, similarity_mode,
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# thread_count) < 0 :
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# raise Exception("Error aligning sequences")
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# else :
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# if obi_lcs_align_two_columns(d._pointer, \
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# str2bytes(input_view_1_n), \
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# str2bytes(input_view_2_n), \
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# str2bytes(input_column_1_n), \
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# str2bytes(input_column_2_n), \
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# str2bytes(input_elt_1_n), \
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# str2bytes(input_elt_2_n), \
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# str2bytes(id_column_1_n), \
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# str2bytes(id_column_2_n), \
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# str2bytes(output_view_n), \
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# str2bytes(comments), \
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# print_seq, \
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# print_count, \
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# threshold, normalize, reference, similarity_mode) < 0 :
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# raise Exception("Error aligning sequences")
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#
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# d.close()
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#
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#
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# def run(config):
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#
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# # TODO: Build formatted comments with all parameters etc
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# comments = "Obi align"
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#
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# # Call cython alignment function
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# align(config['obi']['defaultdms'], \
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# config['obi']['inputview1'], \
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# config['obi']['outputview'], \
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# input_view_2_n = config['obi']['inputview2'], \
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# input_column_1_n = config['obi']['inputcolumn1'], \
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# input_column_2_n = config['obi']['inputcolumn2'], \
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# input_elt_1_n = config['obi']['inputelement1'], \
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# input_elt_2_n = config['obi']['inputelement2'], \
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# id_column_1_n = config['obi']['idcolumn1'], \
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# id_column_2_n = config['obi']['idcolumn2'], \
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# threshold = config['align']['threshold'], \
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# normalize = config['align']['normalize'], \
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# reference = config['align']['reflength'], \
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# similarity_mode = config['align']['similarity'], \
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# print_seq = config['align']['printseq'], \
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# print_count = config['align']['printcount'], \
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# comments = comments, \
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# thread_count = config['align']['threadcount'])
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#
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# print("Done.")
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#
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#
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#
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#
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#
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@ -1,383 +1,383 @@
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from obitools3.apps.progress cimport ProgressBar # TODO I absolutely don't understand why it doesn't work without that line
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from obitools3.obidms._obidms import OBIDMS # TODO cimport doesn't work
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from obitools3.obidms._obidms import OBIView_line_selection
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from obitools3.utils cimport str2bytes
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import shutil
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import string
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import random
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VIEW_TYPES = ["", "NUC_SEQS_VIEW"]
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COL_TYPES = ["OBI_BOOL", "OBI_CHAR", "OBI_FLOAT", "OBI_INT", "OBI_SEQ", "OBI_STR"]
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NUC_SEQUENCE_COLUMN = "NUC_SEQ"
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ID_COLUMN = "ID"
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DEFINITION_COLUMN = "DEFINITION"
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QUALITY_COLUMN = "QUALITY"
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SPECIAL_COLUMNS = [NUC_SEQUENCE_COLUMN, ID_COLUMN, DEFINITION_COLUMN, QUALITY_COLUMN]
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NAME_MAX_LEN = 200
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COL_COMMENTS_MAX_LEN = 2048
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MAX_INT = 2147483647 # used to generate random float values
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__title__="Tests if the obitools are working properly"
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default_config = {
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}
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def random_length(max_len):
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return random.randint(1, max_len)
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def random_bool(config):
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return random.choice([True, False])
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def random_char(config):
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return random.choice(string.ascii_lowercase)
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def random_float(config):
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return random.randint(0, MAX_INT) + random.random()
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def random_int(config):
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return random.randint(0, config['test']['maxlinenb'])
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def random_seq(config):
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return str2bytes(''.join(random.choice(['a','t','g','c']) for i in range(random_length(config['test']['seqmaxlen']))))
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def random_str(config):
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return random_str_with_max_len(config['test']['strmaxlen'])
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def random_str_with_max_len(max_len):
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return ''.join(random.choice(string.ascii_lowercase) for i in range(random_length(max_len)))
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def random_column(infos):
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return random.choice(sorted(list(infos['view'].columns)))
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def random_unique_name(infos):
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name = ""
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while name == "" or name in infos['unique_names'] :
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name = random_str_with_max_len(NAME_MAX_LEN)
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infos['unique_names'].append(name)
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return name
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def random_unique_element_name(config, infos):
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name = ""
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while name == "" or name in infos['unique_names'] :
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name = random_str_with_max_len(config['test']['elt_name_max_len'])
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infos['unique_names'].append(name)
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return name
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def print_test(config, sentence):
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if config['test']['verbose'] :
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print(sentence)
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def test_set_and_get(config, infos):
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print_test(config, ">>> Set and get test")
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col_name = random_column(infos)
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col = infos['view'][col_name]
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element_names = col.elements_names
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data_type = col.data_type
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if data_type == "OBI_QUAL" :
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print_test(config, "-")
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return
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idx = random_int(config)
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value = infos['random_generator'][data_type](config)
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if col.nb_elements_per_line > 1 :
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elt = random.choice(element_names)
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col[idx][elt] = value
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assert col[idx][elt] == value, "Set value != gotten value "+str(col[idx][elt])+" != "+str(value)
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else:
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col[idx] = value
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assert col[idx] == value, "Set value != gotten value "+str(col[idx])+" != "+str(value)
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print_test(config, ">>> Set and get test OK")
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def test_add_col(config, infos):
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print_test(config, ">>> Add column test")
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#existing_col = random_bool(config) # TODO doesn't work because of line count problem. See obiview.c line 1737
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#if existing_col and infos["view_names"] != [] :
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# random_view = infos['dms'].open_view(random.choice(infos["view_names"]))
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# random_column = random_view[random.choice(sorted(list(random_view.columns))]
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# random_column_refs = random_column.refs
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# if random_column_refs['name'] in infos['view'] :
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# alias = random_unique_name(infos)
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# else :
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# alias = ''
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# infos['view'].add_column(random_column_refs['name'], version_number=random_column_refs['version'], alias=alias, create=False)
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# random_view.close()
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#else :
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create_random_column(config, infos)
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print_test(config, ">>> Add column test OK")
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def test_delete_col(config, infos):
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print_test(config, ">>> Delete column test")
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if len(list(infos['view'].columns)) <= 1 :
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print_test(config, "-")
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return
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col_name = random_column(infos)
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if col_name in SPECIAL_COLUMNS :
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print_test(config, "-")
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return
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infos['view'].delete_column(col_name)
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print_test(config, ">>> Delete column test OK")
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def test_col_alias(config, infos):
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print_test(config, ">>> Changing column alias test")
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col_name = random_column(infos)
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if col_name in SPECIAL_COLUMNS :
|
||||
print_test(config, "-")
|
||||
return
|
||||
infos['view'][col_name].alias = random_unique_name(infos)
|
||||
print_test(config, ">>> Changing column alias test OK")
|
||||
|
||||
|
||||
def test_new_view(config, infos):
|
||||
print_test(config, ">>> New view test")
|
||||
random_new_view(config, infos)
|
||||
print_test(config, ">>> New view test OK")
|
||||
|
||||
|
||||
def random_test(config, infos):
|
||||
return random.choice(infos['tests'])(config, infos)
|
||||
|
||||
|
||||
def random_view_type():
|
||||
return random.choice(VIEW_TYPES)
|
||||
|
||||
|
||||
def random_col_type():
|
||||
return random.choice(COL_TYPES)
|
||||
|
||||
|
||||
def fill_column(config, infos, col) :
|
||||
data_type = col.data_type
|
||||
element_names = col.elements_names
|
||||
|
||||
if len(element_names) > 1 :
|
||||
for i in range(random_int(config)) :
|
||||
for j in range(len(element_names)) :
|
||||
col[i][element_names[j]] = infos['random_generator'][data_type](config)
|
||||
else :
|
||||
for i in range(random_int(config)) :
|
||||
col[i] = infos['random_generator'][data_type](config)
|
||||
|
||||
|
||||
def create_random_column(config, infos) :
|
||||
alias = random.choice(['', random_unique_name(infos)])
|
||||
nb_elements_per_line=random.randint(1, config['test']['maxelts'])
|
||||
elements_names = []
|
||||
for i in range(nb_elements_per_line) :
|
||||
elements_names.append(random_unique_element_name(config, infos))
|
||||
elements_names = random.choice([None, elements_names])
|
||||
name = random_unique_name(infos)
|
||||
infos['view'].add_column(name,
|
||||
alias=alias,
|
||||
type=random_col_type(),
|
||||
nb_elements_per_line=nb_elements_per_line,
|
||||
elements_names=elements_names,
|
||||
indexer_name=random.choice(['', random_unique_name(infos)]),
|
||||
comments=random_str_with_max_len(COL_COMMENTS_MAX_LEN),
|
||||
create=True
|
||||
)
|
||||
if alias != '' :
|
||||
return infos['view'][alias]
|
||||
else :
|
||||
return infos['view'][name]
|
||||
|
||||
|
||||
def fill_view(config, infos):
|
||||
for i in range(random.randint(1, config['test']['maxinicolcount'])) :
|
||||
col = create_random_column(config, infos)
|
||||
fill_column(config, infos, col)
|
||||
|
||||
|
||||
def random_new_view(config, infos, first=False):
|
||||
v_to_clone = None
|
||||
line_selection = None
|
||||
quality_col = False # TODO
|
||||
if not first:
|
||||
infos['view_names'].append(infos['view'].name)
|
||||
infos['view'].close()
|
||||
v_to_clone = infos['dms'].open_view(random.choice(infos["view_names"]))
|
||||
v_type = ""
|
||||
print_test(config, "View to clone: ")
|
||||
print_test(config, repr(v_to_clone))
|
||||
create_line_selection = random_bool(config)
|
||||
if create_line_selection and v_to_clone.line_count > 0:
|
||||
print_test(config, "New view with new line selection.")
|
||||
line_selection = OBIView_line_selection(v_to_clone)
|
||||
for i in range(random.randint(1, v_to_clone.line_count)) :
|
||||
line_selection.append(random.randint(0, v_to_clone.line_count-1))
|
||||
#print_test(config, "New line selection: "+str(line_selection))
|
||||
else :
|
||||
v_type = random_view_type()
|
||||
|
||||
if line_selection is not None :
|
||||
infos['view'] = infos['dms'].clone_view_with_line_selection(random_unique_name(infos), line_selection, comments=random_str_with_max_len(config['test']['commentsmaxlen']))
|
||||
elif v_to_clone is not None :
|
||||
infos['view'] = infos['dms'].clone_view(random_unique_name(infos), v_to_clone, comments=random_str_with_max_len(config['test']['commentsmaxlen']))
|
||||
else :
|
||||
infos['view'] = infos['dms'].new_view(random_unique_name(infos), view_type=v_type, comments=random_str_with_max_len(config['test']['commentsmaxlen']), quality_column=quality_col)
|
||||
|
||||
print_test(config, repr(infos['view']))
|
||||
if v_to_clone is not None :
|
||||
if line_selection is None:
|
||||
assert v_to_clone.line_count == infos['view'].line_count, "New view and cloned view don't have the same line count"
|
||||
else :
|
||||
assert len(line_selection) == infos['view'].line_count, "New view with new line selection does not have the right line count"
|
||||
v_to_clone.close()
|
||||
if first :
|
||||
fill_view(config, infos)
|
||||
|
||||
|
||||
def create_test_obidms(config, infos):
|
||||
infos['dms'] = OBIDMS(config['obi']['defaultdms'])
|
||||
|
||||
|
||||
def ini_dms_and_first_view(config, infos):
|
||||
create_test_obidms(config, infos)
|
||||
random_new_view(config, infos, first=True)
|
||||
infos['view_names'] = []
|
||||
|
||||
|
||||
def addOptions(parser):
|
||||
|
||||
# TODO put this common group somewhere else but I don't know where
|
||||
group=parser.add_argument_group('DMS and view options')
|
||||
|
||||
group.add_argument('--default-dms','-d',
|
||||
action="store", dest="obi:defaultdms",
|
||||
metavar='<DMS NAME>',
|
||||
default="/tmp/test_dms",
|
||||
type=str,
|
||||
help="Name of the default DMS for reading and writing data. "
|
||||
"Default: /tmp/test_dms")
|
||||
|
||||
group=parser.add_argument_group('obi test specific options')
|
||||
|
||||
group.add_argument('--nb_tests','-n',
|
||||
action="store", dest="test:nbtests",
|
||||
metavar='<NB_TESTS>',
|
||||
default=1000,
|
||||
type=int,
|
||||
help="Number of tests to carry out. "
|
||||
"Default: 1000")
|
||||
|
||||
group.add_argument('--seq_max_len','-s',
|
||||
action="store", dest="test:seqmaxlen",
|
||||
metavar='<SEQ_MAX_LEN>',
|
||||
default=200,
|
||||
type=int,
|
||||
help="Maximum length of DNA sequences. "
|
||||
"Default: 200")
|
||||
|
||||
group.add_argument('--str_max_len','-t',
|
||||
action="store", dest="test:strmaxlen",
|
||||
metavar='<STR_MAX_LEN>',
|
||||
default=200,
|
||||
type=int,
|
||||
help="Maximum length of character strings. "
|
||||
"Default: 200")
|
||||
|
||||
group.add_argument('--comments_max_len','-c',
|
||||
action="store", dest="test:commentsmaxlen",
|
||||
metavar='<COMMENTS_MAX_LEN>',
|
||||
default=10000,
|
||||
type=int,
|
||||
help="Maximum length of view comments. "
|
||||
"Default: 10000")
|
||||
|
||||
group.add_argument('--max_ini_col_count','-o',
|
||||
action="store", dest="test:maxinicolcount",
|
||||
metavar='<MAX_INI_COL_COUNT>',
|
||||
default=10,
|
||||
type=int,
|
||||
help="Maximum number of columns in the initial view. "
|
||||
"Default: 10")
|
||||
|
||||
group.add_argument('--max_line_nb','-l',
|
||||
action="store", dest="test:maxlinenb",
|
||||
metavar='<MAX_LINE_NB>',
|
||||
default=10000,
|
||||
type=int,
|
||||
help="Maximum number of lines in a column. "
|
||||
"Default: 10000")
|
||||
|
||||
group.add_argument('--max_elts_per_line','-e',
|
||||
action="store", dest="test:maxelts",
|
||||
metavar='<MAX_ELTS_PER_LINE>',
|
||||
default=20,
|
||||
type=int,
|
||||
help="Maximum number of elements per line in a column. "
|
||||
"Default: 20")
|
||||
|
||||
group.add_argument('--verbose','-v',
|
||||
action="store_true", dest="test:verbose",
|
||||
default=False,
|
||||
help="Print the tests. "
|
||||
"Default: Don't print the tests")
|
||||
|
||||
group.add_argument('--seed','-g',
|
||||
action="store", dest="test:seed",
|
||||
metavar='<SEED>',
|
||||
default=None,
|
||||
help="Seed (use for reproducible tests). "
|
||||
"Default: Seed is determined by Python")
|
||||
|
||||
def run(config):
|
||||
|
||||
if 'seed' in config['test'] :
|
||||
random.seed(config['test']['seed'])
|
||||
|
||||
infos = {'dms': None,
|
||||
'view': None,
|
||||
'view_names': None,
|
||||
'unique_names': [],
|
||||
'random_generator': {"OBI_BOOL": random_bool, "OBI_CHAR": random_char, "OBI_FLOAT": random_float, "OBI_INT": random_int, "OBI_SEQ": random_seq, "OBI_STR": random_str},
|
||||
'tests': [test_set_and_get, test_add_col, test_delete_col, test_col_alias, test_new_view]
|
||||
}
|
||||
|
||||
config['test']['elt_name_max_len'] = int((COL_COMMENTS_MAX_LEN - config['test']['maxelts']) / config['test']['maxelts'])
|
||||
|
||||
print("Initializing the DMS and the first view...")
|
||||
|
||||
shutil.rmtree(config['obi']['defaultdms']+'.obidms', ignore_errors=True)
|
||||
|
||||
ini_dms_and_first_view(config, infos)
|
||||
print_test(config, repr(infos['view']))
|
||||
|
||||
i = 0
|
||||
for t in range(config['test']['nbtests']):
|
||||
random_test(config, infos)
|
||||
print_test(config, repr(infos['view']))
|
||||
i+=1
|
||||
if (i%(config['test']['nbtests']/10)) == 0 :
|
||||
print("Testing......"+str(i*100/config['test']['nbtests'])+"%")
|
||||
|
||||
#print(infos)
|
||||
|
||||
infos['view'].close()
|
||||
infos['dms'].close()
|
||||
shutil.rmtree(config['obi']['defaultdms']+'.obidms', ignore_errors=True)
|
||||
|
||||
print("Done.")
|
||||
from obitools3.dms.dms import OBIDMS # TODO cimport doesn't work
|
||||
# from obitools3.obidms._obidms import OBIView_line_selection
|
||||
# from obitools3.utils cimport str2bytes
|
||||
#
|
||||
# import shutil
|
||||
# import string
|
||||
# import random
|
||||
#
|
||||
#
|
||||
# VIEW_TYPES = ["", "NUC_SEQS_VIEW"]
|
||||
# COL_TYPES = ["OBI_BOOL", "OBI_CHAR", "OBI_FLOAT", "OBI_INT", "OBI_SEQ", "OBI_STR"]
|
||||
# NUC_SEQUENCE_COLUMN = "NUC_SEQ"
|
||||
# ID_COLUMN = "ID"
|
||||
# DEFINITION_COLUMN = "DEFINITION"
|
||||
# QUALITY_COLUMN = "QUALITY"
|
||||
# SPECIAL_COLUMNS = [NUC_SEQUENCE_COLUMN, ID_COLUMN, DEFINITION_COLUMN, QUALITY_COLUMN]
|
||||
#
|
||||
#
|
||||
# NAME_MAX_LEN = 200
|
||||
# COL_COMMENTS_MAX_LEN = 2048
|
||||
# MAX_INT = 2147483647 # used to generate random float values
|
||||
#
|
||||
#
|
||||
# __title__="Tests if the obitools are working properly"
|
||||
#
|
||||
#
|
||||
# default_config = {
|
||||
# }
|
||||
#
|
||||
#
|
||||
# def random_length(max_len):
|
||||
# return random.randint(1, max_len)
|
||||
#
|
||||
#
|
||||
# def random_bool(config):
|
||||
# return random.choice([True, False])
|
||||
#
|
||||
#
|
||||
# def random_char(config):
|
||||
# return random.choice(string.ascii_lowercase)
|
||||
#
|
||||
#
|
||||
# def random_float(config):
|
||||
# return random.randint(0, MAX_INT) + random.random()
|
||||
#
|
||||
#
|
||||
# def random_int(config):
|
||||
# return random.randint(0, config['test']['maxlinenb'])
|
||||
#
|
||||
#
|
||||
# def random_seq(config):
|
||||
# return str2bytes(''.join(random.choice(['a','t','g','c']) for i in range(random_length(config['test']['seqmaxlen']))))
|
||||
#
|
||||
#
|
||||
# def random_str(config):
|
||||
# return random_str_with_max_len(config['test']['strmaxlen'])
|
||||
#
|
||||
#
|
||||
# def random_str_with_max_len(max_len):
|
||||
# return ''.join(random.choice(string.ascii_lowercase) for i in range(random_length(max_len)))
|
||||
#
|
||||
#
|
||||
# def random_column(infos):
|
||||
# return random.choice(sorted(list(infos['view'].columns)))
|
||||
#
|
||||
#
|
||||
# def random_unique_name(infos):
|
||||
# name = ""
|
||||
# while name == "" or name in infos['unique_names'] :
|
||||
# name = random_str_with_max_len(NAME_MAX_LEN)
|
||||
# infos['unique_names'].append(name)
|
||||
# return name
|
||||
#
|
||||
#
|
||||
# def random_unique_element_name(config, infos):
|
||||
# name = ""
|
||||
# while name == "" or name in infos['unique_names'] :
|
||||
# name = random_str_with_max_len(config['test']['elt_name_max_len'])
|
||||
# infos['unique_names'].append(name)
|
||||
# return name
|
||||
#
|
||||
#
|
||||
# def print_test(config, sentence):
|
||||
# if config['test']['verbose'] :
|
||||
# print(sentence)
|
||||
#
|
||||
#
|
||||
# def test_set_and_get(config, infos):
|
||||
# print_test(config, ">>> Set and get test")
|
||||
# col_name = random_column(infos)
|
||||
# col = infos['view'][col_name]
|
||||
# element_names = col.elements_names
|
||||
# data_type = col.data_type
|
||||
# if data_type == "OBI_QUAL" :
|
||||
# print_test(config, "-")
|
||||
# return
|
||||
# idx = random_int(config)
|
||||
# value = infos['random_generator'][data_type](config)
|
||||
# if col.nb_elements_per_line > 1 :
|
||||
# elt = random.choice(element_names)
|
||||
# col[idx][elt] = value
|
||||
# assert col[idx][elt] == value, "Set value != gotten value "+str(col[idx][elt])+" != "+str(value)
|
||||
# else:
|
||||
# col[idx] = value
|
||||
# assert col[idx] == value, "Set value != gotten value "+str(col[idx])+" != "+str(value)
|
||||
#
|
||||
# print_test(config, ">>> Set and get test OK")
|
||||
#
|
||||
#
|
||||
# def test_add_col(config, infos):
|
||||
# print_test(config, ">>> Add column test")
|
||||
# #existing_col = random_bool(config) # TODO doesn't work because of line count problem. See obiview.c line 1737
|
||||
# #if existing_col and infos["view_names"] != [] :
|
||||
# # random_view = infos['dms'].open_view(random.choice(infos["view_names"]))
|
||||
# # random_column = random_view[random.choice(sorted(list(random_view.columns))]
|
||||
# # random_column_refs = random_column.refs
|
||||
# # if random_column_refs['name'] in infos['view'] :
|
||||
# # alias = random_unique_name(infos)
|
||||
# # else :
|
||||
# # alias = ''
|
||||
# # infos['view'].add_column(random_column_refs['name'], version_number=random_column_refs['version'], alias=alias, create=False)
|
||||
# # random_view.close()
|
||||
# #else :
|
||||
# create_random_column(config, infos)
|
||||
# print_test(config, ">>> Add column test OK")
|
||||
#
|
||||
#
|
||||
# def test_delete_col(config, infos):
|
||||
# print_test(config, ">>> Delete column test")
|
||||
# if len(list(infos['view'].columns)) <= 1 :
|
||||
# print_test(config, "-")
|
||||
# return
|
||||
# col_name = random_column(infos)
|
||||
# if col_name in SPECIAL_COLUMNS :
|
||||
# print_test(config, "-")
|
||||
# return
|
||||
# infos['view'].delete_column(col_name)
|
||||
# print_test(config, ">>> Delete column test OK")
|
||||
#
|
||||
#
|
||||
# def test_col_alias(config, infos):
|
||||
# print_test(config, ">>> Changing column alias test")
|
||||
# col_name = random_column(infos)
|
||||
# if col_name in SPECIAL_COLUMNS :
|
||||
# print_test(config, "-")
|
||||
# return
|
||||
# infos['view'][col_name].alias = random_unique_name(infos)
|
||||
# print_test(config, ">>> Changing column alias test OK")
|
||||
#
|
||||
#
|
||||
# def test_new_view(config, infos):
|
||||
# print_test(config, ">>> New view test")
|
||||
# random_new_view(config, infos)
|
||||
# print_test(config, ">>> New view test OK")
|
||||
#
|
||||
#
|
||||
# def random_test(config, infos):
|
||||
# return random.choice(infos['tests'])(config, infos)
|
||||
#
|
||||
#
|
||||
# def random_view_type():
|
||||
# return random.choice(VIEW_TYPES)
|
||||
#
|
||||
#
|
||||
# def random_col_type():
|
||||
# return random.choice(COL_TYPES)
|
||||
#
|
||||
#
|
||||
# def fill_column(config, infos, col) :
|
||||
# data_type = col.data_type
|
||||
# element_names = col.elements_names
|
||||
#
|
||||
# if len(element_names) > 1 :
|
||||
# for i in range(random_int(config)) :
|
||||
# for j in range(len(element_names)) :
|
||||
# col[i][element_names[j]] = infos['random_generator'][data_type](config)
|
||||
# else :
|
||||
# for i in range(random_int(config)) :
|
||||
# col[i] = infos['random_generator'][data_type](config)
|
||||
#
|
||||
#
|
||||
# def create_random_column(config, infos) :
|
||||
# alias = random.choice(['', random_unique_name(infos)])
|
||||
# nb_elements_per_line=random.randint(1, config['test']['maxelts'])
|
||||
# elements_names = []
|
||||
# for i in range(nb_elements_per_line) :
|
||||
# elements_names.append(random_unique_element_name(config, infos))
|
||||
# elements_names = random.choice([None, elements_names])
|
||||
# name = random_unique_name(infos)
|
||||
# infos['view'].add_column(name,
|
||||
# alias=alias,
|
||||
# type=random_col_type(),
|
||||
# nb_elements_per_line=nb_elements_per_line,
|
||||
# elements_names=elements_names,
|
||||
# indexer_name=random.choice(['', random_unique_name(infos)]),
|
||||
# comments=random_str_with_max_len(COL_COMMENTS_MAX_LEN),
|
||||
# create=True
|
||||
# )
|
||||
# if alias != '' :
|
||||
# return infos['view'][alias]
|
||||
# else :
|
||||
# return infos['view'][name]
|
||||
#
|
||||
#
|
||||
# def fill_view(config, infos):
|
||||
# for i in range(random.randint(1, config['test']['maxinicolcount'])) :
|
||||
# col = create_random_column(config, infos)
|
||||
# fill_column(config, infos, col)
|
||||
#
|
||||
#
|
||||
# def random_new_view(config, infos, first=False):
|
||||
# v_to_clone = None
|
||||
# line_selection = None
|
||||
# quality_col = False # TODO
|
||||
# if not first:
|
||||
# infos['view_names'].append(infos['view'].name)
|
||||
# infos['view'].close()
|
||||
# v_to_clone = infos['dms'].open_view(random.choice(infos["view_names"]))
|
||||
# v_type = ""
|
||||
# print_test(config, "View to clone: ")
|
||||
# print_test(config, repr(v_to_clone))
|
||||
# create_line_selection = random_bool(config)
|
||||
# if create_line_selection and v_to_clone.line_count > 0:
|
||||
# print_test(config, "New view with new line selection.")
|
||||
# line_selection = OBIView_line_selection(v_to_clone)
|
||||
# for i in range(random.randint(1, v_to_clone.line_count)) :
|
||||
# line_selection.append(random.randint(0, v_to_clone.line_count-1))
|
||||
# #print_test(config, "New line selection: "+str(line_selection))
|
||||
# else :
|
||||
# v_type = random_view_type()
|
||||
#
|
||||
# if line_selection is not None :
|
||||
# infos['view'] = infos['dms'].clone_view_with_line_selection(random_unique_name(infos), line_selection, comments=random_str_with_max_len(config['test']['commentsmaxlen']))
|
||||
# elif v_to_clone is not None :
|
||||
# infos['view'] = infos['dms'].clone_view(random_unique_name(infos), v_to_clone, comments=random_str_with_max_len(config['test']['commentsmaxlen']))
|
||||
# else :
|
||||
# infos['view'] = infos['dms'].new_view(random_unique_name(infos), view_type=v_type, comments=random_str_with_max_len(config['test']['commentsmaxlen']), quality_column=quality_col)
|
||||
#
|
||||
# print_test(config, repr(infos['view']))
|
||||
# if v_to_clone is not None :
|
||||
# if line_selection is None:
|
||||
# assert v_to_clone.line_count == infos['view'].line_count, "New view and cloned view don't have the same line count"
|
||||
# else :
|
||||
# assert len(line_selection) == infos['view'].line_count, "New view with new line selection does not have the right line count"
|
||||
# v_to_clone.close()
|
||||
# if first :
|
||||
# fill_view(config, infos)
|
||||
#
|
||||
#
|
||||
# def create_test_obidms(config, infos):
|
||||
# infos['dms'] = OBIDMS(config['obi']['defaultdms'])
|
||||
#
|
||||
#
|
||||
# def ini_dms_and_first_view(config, infos):
|
||||
# create_test_obidms(config, infos)
|
||||
# random_new_view(config, infos, first=True)
|
||||
# infos['view_names'] = []
|
||||
#
|
||||
#
|
||||
# def addOptions(parser):
|
||||
#
|
||||
# # TODO put this common group somewhere else but I don't know where
|
||||
# group=parser.add_argument_group('DMS and view options')
|
||||
#
|
||||
# group.add_argument('--default-dms','-d',
|
||||
# action="store", dest="obi:defaultdms",
|
||||
# metavar='<DMS NAME>',
|
||||
# default="/tmp/test_dms",
|
||||
# type=str,
|
||||
# help="Name of the default DMS for reading and writing data. "
|
||||
# "Default: /tmp/test_dms")
|
||||
#
|
||||
# group=parser.add_argument_group('obi test specific options')
|
||||
#
|
||||
# group.add_argument('--nb_tests','-n',
|
||||
# action="store", dest="test:nbtests",
|
||||
# metavar='<NB_TESTS>',
|
||||
# default=1000,
|
||||
# type=int,
|
||||
# help="Number of tests to carry out. "
|
||||
# "Default: 1000")
|
||||
#
|
||||
# group.add_argument('--seq_max_len','-s',
|
||||
# action="store", dest="test:seqmaxlen",
|
||||
# metavar='<SEQ_MAX_LEN>',
|
||||
# default=200,
|
||||
# type=int,
|
||||
# help="Maximum length of DNA sequences. "
|
||||
# "Default: 200")
|
||||
#
|
||||
# group.add_argument('--str_max_len','-t',
|
||||
# action="store", dest="test:strmaxlen",
|
||||
# metavar='<STR_MAX_LEN>',
|
||||
# default=200,
|
||||
# type=int,
|
||||
# help="Maximum length of character strings. "
|
||||
# "Default: 200")
|
||||
#
|
||||
# group.add_argument('--comments_max_len','-c',
|
||||
# action="store", dest="test:commentsmaxlen",
|
||||
# metavar='<COMMENTS_MAX_LEN>',
|
||||
# default=10000,
|
||||
# type=int,
|
||||
# help="Maximum length of view comments. "
|
||||
# "Default: 10000")
|
||||
#
|
||||
# group.add_argument('--max_ini_col_count','-o',
|
||||
# action="store", dest="test:maxinicolcount",
|
||||
# metavar='<MAX_INI_COL_COUNT>',
|
||||
# default=10,
|
||||
# type=int,
|
||||
# help="Maximum number of columns in the initial view. "
|
||||
# "Default: 10")
|
||||
#
|
||||
# group.add_argument('--max_line_nb','-l',
|
||||
# action="store", dest="test:maxlinenb",
|
||||
# metavar='<MAX_LINE_NB>',
|
||||
# default=10000,
|
||||
# type=int,
|
||||
# help="Maximum number of lines in a column. "
|
||||
# "Default: 10000")
|
||||
#
|
||||
# group.add_argument('--max_elts_per_line','-e',
|
||||
# action="store", dest="test:maxelts",
|
||||
# metavar='<MAX_ELTS_PER_LINE>',
|
||||
# default=20,
|
||||
# type=int,
|
||||
# help="Maximum number of elements per line in a column. "
|
||||
# "Default: 20")
|
||||
#
|
||||
# group.add_argument('--verbose','-v',
|
||||
# action="store_true", dest="test:verbose",
|
||||
# default=False,
|
||||
# help="Print the tests. "
|
||||
# "Default: Don't print the tests")
|
||||
#
|
||||
# group.add_argument('--seed','-g',
|
||||
# action="store", dest="test:seed",
|
||||
# metavar='<SEED>',
|
||||
# default=None,
|
||||
# help="Seed (use for reproducible tests). "
|
||||
# "Default: Seed is determined by Python")
|
||||
#
|
||||
# def run(config):
|
||||
#
|
||||
# if 'seed' in config['test'] :
|
||||
# random.seed(config['test']['seed'])
|
||||
#
|
||||
# infos = {'dms': None,
|
||||
# 'view': None,
|
||||
# 'view_names': None,
|
||||
# 'unique_names': [],
|
||||
# 'random_generator': {"OBI_BOOL": random_bool, "OBI_CHAR": random_char, "OBI_FLOAT": random_float, "OBI_INT": random_int, "OBI_SEQ": random_seq, "OBI_STR": random_str},
|
||||
# 'tests': [test_set_and_get, test_add_col, test_delete_col, test_col_alias, test_new_view]
|
||||
# }
|
||||
#
|
||||
# config['test']['elt_name_max_len'] = int((COL_COMMENTS_MAX_LEN - config['test']['maxelts']) / config['test']['maxelts'])
|
||||
#
|
||||
# print("Initializing the DMS and the first view...")
|
||||
#
|
||||
# shutil.rmtree(config['obi']['defaultdms']+'.obidms', ignore_errors=True)
|
||||
#
|
||||
# ini_dms_and_first_view(config, infos)
|
||||
# print_test(config, repr(infos['view']))
|
||||
#
|
||||
# i = 0
|
||||
# for t in range(config['test']['nbtests']):
|
||||
# random_test(config, infos)
|
||||
# print_test(config, repr(infos['view']))
|
||||
# i+=1
|
||||
# if (i%(config['test']['nbtests']/10)) == 0 :
|
||||
# print("Testing......"+str(i*100/config['test']['nbtests'])+"%")
|
||||
#
|
||||
# #print(infos)
|
||||
#
|
||||
# infos['view'].close()
|
||||
# infos['dms'].close()
|
||||
# shutil.rmtree(config['obi']['defaultdms']+'.obidms', ignore_errors=True)
|
||||
#
|
||||
# print("Done.")
|
||||
|
||||
|
||||
@ -1,96 +0,0 @@
|
||||
from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
|
||||
from obitools3.obidms._obidms import OBIDMS, OBIView, OBIView_line_selection # TODO cimport doesn't work
|
||||
|
||||
from functools import reduce
|
||||
import time
|
||||
|
||||
__title__="Grep view lines that match the given predicates"
|
||||
|
||||
|
||||
default_config = { 'inputview' : None,
|
||||
'outputview' : None
|
||||
}
|
||||
|
||||
def addOptions(parser):
|
||||
|
||||
# TODO put this common group somewhere else but I don't know where
|
||||
group=parser.add_argument_group('DMS and view options')
|
||||
|
||||
group.add_argument('--default-dms','-d',
|
||||
action="store", dest="obi:defaultdms",
|
||||
metavar='<DMS NAME>',
|
||||
default=None,
|
||||
type=str,
|
||||
help="Name of the default DMS for reading and writing data.")
|
||||
|
||||
group.add_argument('--input-view','-i',
|
||||
action="store", dest="obi:inputview",
|
||||
metavar='<INPUT VIEW NAME>',
|
||||
default=None,
|
||||
type=str,
|
||||
help="Name of the input view, either raw if the view is in the default DMS,"
|
||||
" or in the form 'dms:view' if it is in another DMS.")
|
||||
|
||||
group.add_argument('--output-view','-o',
|
||||
action="store", dest="obi:outputview",
|
||||
metavar='<OUTPUT VIEW NAME>',
|
||||
default=None,
|
||||
type=str,
|
||||
help="Name of the output view, either raw if the view is in the default DMS,"
|
||||
" or in the form 'dms:view' if it is in another DMS.")
|
||||
|
||||
|
||||
group=parser.add_argument_group('obi grep specific options')
|
||||
|
||||
group.add_argument('--predicate','-p',
|
||||
action="append", dest="grep:predicates",
|
||||
metavar='<PREDICATE>',
|
||||
default=None,
|
||||
type=str,
|
||||
help="Grep lines that match the given python expression on <line> or <sequence>.")
|
||||
|
||||
|
||||
def run(config):
|
||||
|
||||
# Open DMS
|
||||
d = OBIDMS(config['obi']['defaultdms'])
|
||||
|
||||
# Open input view 1
|
||||
iview = d.open_view(config['obi']['inputview'])
|
||||
|
||||
# Initialize the progress bar
|
||||
pb = ProgressBar(len(iview), config, seconde=5)
|
||||
|
||||
# Apply filter
|
||||
selection = OBIView_line_selection(iview)
|
||||
for i in range(len(iview)) :
|
||||
pb(i)
|
||||
line = iview[i]
|
||||
|
||||
loc_env = {'sequence': line, 'line': line} # TODO add taxonomy
|
||||
|
||||
good = (reduce(lambda bint x, bint y: x and y,
|
||||
(bool(eval(p, loc_env, line))
|
||||
for p in config['grep']['predicates']), True))
|
||||
|
||||
if good :
|
||||
selection.append(i)
|
||||
|
||||
# Create output view with the line selection
|
||||
oview = d.new_view(config['obi']['outputview'], line_selection=selection, comments="obi grep: "+str(config['grep']['predicates'])+"\n")
|
||||
|
||||
#print("\n")
|
||||
#print(repr(oview))
|
||||
|
||||
iview.close()
|
||||
oview.close()
|
||||
d.close()
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
Reference in New Issue
Block a user