def test_08_jaaba_to_pergola(self):
"""
Testing jaaba_to_pergola script
"""
# print >> stderr,"====================== test 8"
data_in = PATH + "/jaaba_data/scores_chase.mat"
jaaba_scores_to_csv(input_file=data_in, path_w=TEST, name_file="file_out", norm=True, data_type="chase")
map_j = PATH + "/jaaba_data/jaaba2pergola.txt"
int_data_j = jaaba_scores_to_intData(input_file=data_in, map_jaaba=map_j, name_file="JAABA_scores", delimiter="\t", norm=True, data_type="a")
print >> stderr, "Min value jaaba====== %d" % int_data_j.min
def test_08_jaaba_to_pergola(self):
"""
Testing jaaba_to_pergola script
"""
# print >> stderr,"====================== test 8"
data_in = PATH + "/jaaba_data/scores_chase.mat"
jaaba_scores_to_csv(input_file=data_in,
path_w=TEST,
name_file="file_out",
norm=True,
data_type="chase")
map_j = PATH + "/jaaba_data/jaaba2pergola.txt"
int_data_j = jaaba_scores_to_intData(input_file=data_in,
map_jaaba=map_j,
name_file="JAABA_scores",
delimiter="\t",
norm=True,
data_type="a")
print >> stderr, "Min value jaaba====== %d" % int_data_j.min
def jaaba_to_pergola(option, args):
"""
main function
sc: scores to csv
sp: scores to pergola
fc: features to csv
fp: features to pergola
"""
for input_file in args.input:
if option == "sc" or option =="sp":
print >> stderr, "@@@jaaba_to_pergola.py: Input file is %s" % input_file
tmp_track = NamedTemporaryFile(prefix='jaaba_csv', suffix='.csv', delete=True)
name_tmp = splitext(basename(tmp_track.name))[0]
path_out = dirname(abspath(tmp_track.name))
jaaba_parsers.jaaba_scores_to_csv(input_file=input_file, path_w=path_out, name_file=name_tmp, norm=True, data_type="chase")
output_file = tmp_track.name
if option == "sc":
path_w = dirname(abspath(input_file))
f_out = path_w + '/' + 'JAABA_scores.csv'
copy (tmp_track.name, f_out)
print >> stderr, "@@@jaaba_to_pergola.py: Scores dumped in %s" % f_out
elif option == "sp":
pergola_rules.pergola_rules(path=output_file, map_file_path=args.mapping_file, sel_tracks=args.tracks,
list=args.list, range=args.range, track_actions=args.track_actions,
data_types_actions=args.data_types_actions, data_types_list=args.data_types_list,
write_format=args.format, relative_coord=args.relative_coord,
intervals_gen=args.intervals_gen, multiply_f=args.multiply_intervals,
no_header=args.no_header, fields2read=args.fields_read, window_size=args.window_size,
no_track_line=args.no_track_line, separator=args.field_separator,
bed_lab_sw=args.bed_label, color_dict=args.color_file, window_mean=args.window_mean)
elif option == "fc" or option == "fp":
print >> stderr, "@@@jaaba_to_pergola.py: Extracting Jaaba features from %s" % input_file
print >> stderr, "@@@jaaba_to_pergola.py: Selected feature/s %s" %args.feature
if not args.dumping_dir:
dumping_dir = getcwd()
print >> stderr, "@@@jaaba_to_pergola.py: No path selected, files dump into path: ", dumping_dir
else:
dumping_dir = args.dumping_dir
print >> stderr, "@@@jaaba_to_pergola.py: Files dump into path: ", dumping_dir
path_tmp = mkdtemp()
for f in args.feature:
jaaba_parsers.extract_jaaba_features(dir_perframe=input_file, map_jaaba="", delimiter="\t",
feature=f, output="csv", path_w=path_tmp)
tmp_file = path_tmp + '/' + f + '.csv'
if option == "fc":
f_out = dumping_dir + '/' + f + '.csv'
copy (tmp_file, f_out)
elif option == "fp":
chdir(dumping_dir)
# pergola_rules.main(path=tmp_file, map_file_path=args.mapping_file, sel_tracks=args.tracks,
pergola_rules.pergola_rules(path=tmp_file, map_file_path=args.mapping_file, sel_tracks=args.tracks,
list=args.list, range=args.range, track_actions=args.track_actions,
data_types_actions=args.data_types_actions, data_types_list=args.data_types_list,
write_format=args.format, relative_coord=args.relative_coord,
intervals_gen=args.intervals_gen, multiply_f=args.multiply_intervals,
no_header=args.no_header, fields2read=args.fields_read, window_size=args.window_size,
no_track_line=args.no_track_line, separator=args.field_separator,
bed_lab_sw=args.bed_label, color_dict=args.color_file, window_mean=args.window_mean)
rmtree(path_tmp)
def jaaba_to_pergola(option, args):
"""
main function
sc: scores to csv
sp: scores to pergola
fc: features to csv
fp: features to pergola
"""
for input_file in args.input:
if option == "sc" or option == "sp":
print >> stderr, "@@@jaaba_to_pergola.py: Input file is %s" % input_file
tmp_track = NamedTemporaryFile(prefix='jaaba_csv',
suffix='.csv',
delete=True)
name_tmp = splitext(basename(tmp_track.name))[0]
path_out = dirname(abspath(tmp_track.name))
jaaba_parsers.jaaba_scores_to_csv(input_file=input_file,
path_w=path_out,
name_file=name_tmp,
norm=True,
data_type="chase")
output_file = tmp_track.name
if option == "sc":
path_w = dirname(abspath(input_file))
f_out = path_w + '/' + 'JAABA_scores.csv'
copy(tmp_track.name, f_out)
print >> stderr, "@@@jaaba_to_pergola.py: Scores dumped in %s" % f_out
elif option == "sp":
pergola_rules.pergola_rules(
path=output_file,
map_file_path=args.mapping_file,
sel_tracks=args.tracks,
list=args.list,
range=args.range,
track_actions=args.track_actions,
data_types_actions=args.data_types_actions,
data_types_list=args.data_types_list,
write_format=args.format,
relative_coord=args.relative_coord,
intervals_gen=args.intervals_gen,
multiply_f=args.multiply_intervals,
no_header=args.no_header,
fields2read=args.fields_read,
window_size=args.window_size,
no_track_line=args.no_track_line,
separator=args.field_separator,
bed_lab_sw=args.bed_label,
color_dict=args.color_file,
window_mean=args.window_mean)
elif option == "fc" or option == "fp":
print >> stderr, "@@@jaaba_to_pergola.py: Extracting Jaaba features from %s" % input_file
print >> stderr, "@@@jaaba_to_pergola.py: Selected feature/s %s" % args.feature
if not args.dumping_dir:
dumping_dir = getcwd()
print >> stderr, "@@@jaaba_to_pergola.py: No path selected, files dump into path: ", dumping_dir
else:
dumping_dir = args.dumping_dir
print >> stderr, "@@@jaaba_to_pergola.py: Files dump into path: ", dumping_dir
path_tmp = mkdtemp()
for f in args.feature:
jaaba_parsers.extract_jaaba_features(dir_perframe=input_file,
map_jaaba="",
delimiter="\t",
feature=f,
output="csv",
path_w=path_tmp)
tmp_file = path_tmp + '/' + f + '.csv'
if option == "fc":
f_out = dumping_dir + '/' + f + '.csv'
copy(tmp_file, f_out)
elif option == "fp":
chdir(dumping_dir)
# pergola_rules.main(path=tmp_file, map_file_path=args.mapping_file, sel_tracks=args.tracks,
pergola_rules.pergola_rules(
path=tmp_file,
map_file_path=args.mapping_file,
sel_tracks=args.tracks,
list=args.list,
range=args.range,
track_actions=args.track_actions,
data_types_actions=args.data_types_actions,
data_types_list=args.data_types_list,
write_format=args.format,
relative_coord=args.relative_coord,
intervals_gen=args.intervals_gen,
multiply_f=args.multiply_intervals,
no_header=args.no_header,
fields2read=args.fields_read,
window_size=args.window_size,
no_track_line=args.no_track_line,
separator=args.field_separator,
bed_lab_sw=args.bed_label,
color_dict=args.color_file,
window_mean=args.window_mean)
rmtree(path_tmp)
required=True)
args = parser.parse_args()
chase_score_f = args.score_file
mappings_jaaba = mapping.MappingInfo(args.mapping_file)
tag_group = args.tag_group
annotated_behavior = args.behavior
tmp_track = NamedTemporaryFile(prefix='jaaba_csv', suffix='.csv', delete=True)
name_tmp = splitext(basename(tmp_track.name))[0]
path_out = dirname(abspath(tmp_track.name))
jaaba_parsers.jaaba_scores_to_csv(input_file=chase_score_f,
path_w=path_out,
name_file=name_tmp,
norm=True,
data_type=annotated_behavior)
scores_chase_int = intervals.IntData(
tmp_track.name, map_dict=mappings_jaaba.correspondence).read()
data_type_col = {annotated_behavior: 'blue'}
if tag_group == "pBDPGAL4":
# data_type_col = {annotated_behavior: 'orange'}
data_type_col = {annotated_behavior: 'red'}
dict_bed_annotated_int = scores_chase_int.convert(
mode="bed", color_restrictions=data_type_col)
# from scipy import io #parsers
# from scipy import nditer
from numpy import hstack #parsers
from numpy import mean #parsers
# from pergola import mapping#parsers
# from pergola import intervals#parsers
from pergola import parsers
from pergola import jaaba_parsers
# from tempfile import NamedTemporaryFile#parsers
# This part has been included in the function
# jaaba_data = io.loadmat('/Users/jespinosa/JAABA_MAC_0.5.1/sampledata/Chase1_TrpA_Rig1Plate15BowlA_20120404T141155/scores_chase.mat')
jaaba_parsers.jaaba_scores_to_csv(
input_file=
'/Users/jespinosa/JAABA_MAC_0.5.1/sampledata_v0.5/Chase1_TrpA_Rig1Plate15BowlA_20120404T141155/scores_chase.mat',
path_w='/Users/jespinosa/git/pergola/test',
norm=True,
data_type="chase")
print("You correctly transform your JAABA scores into a csv file")
input_jaaba_file = '/Users/jespinosa/JAABA_MAC_0.5.1/sampledata_v0.5/Chase1_TrpA_Rig1Plate15BowlA_20120404T141155/scores_chase.mat'
map_file_jaaba = "/Users/jespinosa/git/pergola/test/jaaba2pergola.txt"
int_data_jaaba = jaaba_parsers.jaaba_scores_to_intData(
input_file=input_jaaba_file,
map_jaaba=map_file_jaaba,
norm=True,
data_type="chase")
print int_data_jaaba.min
print int_data_jaaba.max
