def test_only_one_time_point(self):
"""
Testing if files with just one coordinate for time are read correctly
"""
# print >> stderr,"====================== test 9"
global int_data_electro, mappings_electro
msg_mappings = "Equivalences set in electrophysiology mapping file are not correct."
mappings_electro = mapping.MappingInfo(PATH +
"/electrophysiology/e2p.txt")
keys_electro = ['track', 'data_types', 'data_value', 'start']
fields = mappings_electro.correspondence.values()
self.assertEqual(keys_electro, fields, msg_mappings)
min = 0
max = 0.3
msg_int_data_min = "Min value in electrophysiology data intData not correctly read."
msg_int_data_max = "Max value in electrophysiology data intData not correctly read."
int_data_electro = intervals.IntData(
PATH + "/electrophysiology/electroTest_2f.txt",
map_dict=mappings_electro.correspondence)
self.assertEqual(int_data_electro.min, min, msg_int_data_min)
self.assertEqual(int_data_electro.max, max, msg_int_data_max)
def test_01_correspondence_info(self):
"""
Testing that ontology file is correctly read
"""
# print >> stderr,"====================== test 1"
global mappings_tutorial, exp2, exp3, exp4
mappings_tutorial = mapping.MappingInfo(PATH + "/feeding/f2p.txt")
msg_mappings = "Equivalences set in tutorial mapping file are not correct."
self.assertEqual(mappings_tutorial.correspondence['EndT'], 'end',
msg_mappings)
def pergola_rules(path, map_file_path, sel_tracks=None, list=None, range=None, track_actions=None,
data_types_actions=None, data_types_list=None, write_format=None, relative_coord=False,
intervals_gen=False, multiply_f=None, no_header=False, fields2read=None, window_size=None,
no_track_line=False, separator=None, bed_lab_sw=False, color_dict=None, window_mean=False,
value_mean=False, min_t=None, max_t=None, interval_step=None):
print >> stderr, "@@@Pergola_rules.py: Input file: %s" % path
print >> stderr, "@@@Pergola_rules.py: Configuration file: %s" % map_file_path
# Tracks selected by user
print >> stderr, "@@@Pergola_rules.py: Selected tracks are: ", sel_tracks
# Configuration file
map_file_dict = mapping.MappingInfo(map_file_path)
# Reading color dictionary to set data_types
if color_dict:
print >> stderr, "@@@Pergola_rules.py: Color for data_types in file............ %s" % color_dict
d_colors_data_types = parsers.read_colors (color_dict)
else:
d_colors_data_types = None
# Handling list or range of tracks to join if set
if list and range:
raise ValueError("@@@Pergola_rules.py: Argument -l/--list and -r/--range are not compatible. " \
"As both arguments set tracks to be joined.")
elif (list):
tracks2merge = list
elif (range):
tracks2merge = range
else:
tracks2merge = ""
if tracks2merge: print >> stderr, "@@@Pergola_rules.py: Tracks to join are............ ", tracks2merge
# Handling argument track actions
if tracks2merge and track_actions:
raise ValueError ("Options --list -l or --range -r are incompatible with " \
"--track_actions -a, please change your options")
track_act = track_actions
print >> stderr, "@@@Pergola_rules.py: Track actions are.............................. ", track_act
data_types_list = data_types_list
print >> stderr, "@@@Pergola_rules.py: data_types list is: ", data_types_list
# Handling argument data_types actions
data_types_act = data_types_actions
print >> stderr, "@@@Pergola_rules.py: data_types actions are......................... ", data_types_act
# Handling argument format
if write_format:
print >> stderr, "@@@Pergola_rules.py format to write files....................... ", write_format
else:
write_format = 'bed'
print >>stderr, "@@@Pergola_rules.py format to write files has been set" \
" to default value:", write_format
# Handling relative coordinates
print >> stderr, "@@@Pergola_rules.py: Relative coordinates set to................. %s" % relative_coord
# Handling intervals_gen
print >> stderr, "@@@Pergola_rules.py: Intervals parameter set to.................. %s" % intervals_gen
# Handling interval_step
if interval_step:
if intervals_gen:
print >> stderr, "@@@Pergola_rules.py: Interval step set to........................ %s" % interval_step
else:
raise ValueError("Interval step needs intervals paramater to be set -n/--intervals_gen")
# Handling multiply_intervals
if multiply_f:
print >>stderr, "@@@Pergola_rules.py: Multiply intervals parameter set to...... %s" % multiply_f
else:
multiply_f = 1
print >> stderr, "@@@Pergola_rules.py: Selected tracks are......................... ", sel_tracks
# Setting whether input file has header or not
header_sw = True
if no_header:
header_sw = False
print >> stderr, "@@@Pergola_rules.py: Data file has header set to............. ", header_sw
# Handling fields to read
if fields2read:
print >>stderr, "@@@Pergola_rules.py: Fields to read from the file are......... %s" % fields2read
else:
fields2read = None
# When binning data setting the window of time used in seconds
# if not size provided set to False
if window_size:
print >>stderr, "@@@Pergola_rules.py: Window size set to....................... %d" % window_size
else:
# window_size = 300
window_size = False
print >>stderr, "@@@Pergola_rules.py: Window size set by default to............ %d" % window_size
if window_mean:
print >>stderr, "@@@Pergola_rules.py: Window mean set to....................... %d" % window_mean
else:
window_mean = False
if value_mean:
print >> stderr, "@@@Pergola_rules.py: Value mean set to....................... %d" % value_mean
else:
value_mean = False
if no_track_line:
track_line=False
else:
track_line=True
print >>stderr, "@@@Pergola_rules.py: track_line set to............................ %s" % track_line
# Handling input file field delimiter
if not separator:
separator = "\t"
print >> stderr, "@@@Pergola_rules.py input file field separator set by default to...... \"\\t\"."
else:
print >>stderr, "@@@Pergola_rules.py input file field separator set to..... \"%s\"" % separator
if bed_lab_sw:
bed_lab = True
print >>stderr, "@@@Pergola_rules.py: bed_label set to......................... %s" % bed_lab
else:
bed_lab = False
intData = intervals.IntData(path, map_dict=map_file_dict.correspondence,
fields_names=fields2read,
header=header_sw, delimiter=separator)
start = intData.min
end = intData.max
if relative_coord:
start = 0
end = intData.max - intData.min
print >> stderr, "@@@Pergola_rules.py: min time in file......................... %d" % start
print >> stderr, "@@@Pergola_rules.py: max time in file......................... %d" % end
if min_t or min_t == 0:
min_time = min_t
print >> stderr, "@@@Pergola_rules.py: min_time set by user to.............. %d" % min_t
else:
min_time = start
if max_t:
max_time = max_t
print >> stderr, "@@@Pergola_rules.py: max_time set by user to............... %d" % max_t
else:
if interval_step:
max_time = end + interval_step
else:
max_time = end + 1
if multiply_f:
min_time = min_time * multiply_f
max_time = max_time * multiply_f
if track_act: tracks2merge = parsers.read_track_actions(tracks=intData.tracks, track_action=track_act)
data_read = intData.read(relative_coord=relative_coord,
intervals=intervals_gen,
multiply_t=multiply_f,
min_time=min_time, max_time=max_time,
int_step=interval_step)
mapping.write_chr(data_read)#mantain
mapping.write_chr_sizes(data_read)
# writes cytoband and light, dark and light_dark bed files
mapping.write_cytoband(end=end, track_line=track_line, lab_bed=False)
# mapping.write_period_seq(start=0, end=intData.max, delta=43200, name_file="phases_dark", track_line=False)
data_read.save_track(name_file="all_intervals")
bed_str = data_read.convert(mode=write_format, tracks=sel_tracks,
tracks_merge=tracks2merge, data_types=data_types_list,
data_types_actions=data_types_act, window=window_size,
mean_win=window_mean, mean_value=value_mean, color_restrictions=d_colors_data_types)
#min_t_trim=min_t, max_t_trim=max_t)
for key in bed_str:
bedSingle = bed_str[key]
bedSingle.save_track(track_line=track_line, bed_label=bed_lab)
### Feeding data
if args.behavioral_type == "feeding":
data_type_1 = "food_sc"
data_type_2 = "food_fat"
data_type_joined = ["food_sc", "food_fat"]
data_type_col = {data_type_1: 'blue', data_type_2: 'red'}
### Drinking data
elif args.behavioral_type == 'drinking':
data_type_1 = "water"
data_type_2 = "saccharin"
data_type_col = {data_type_1: 'blue', data_type_2: 'red'}
else:
print >> stderr, "Behavioral data type not available in script, please try again with \"drinking\" or \"feeding\""
mapping_data = mapping.MappingInfo(args.mapping_file)
behavior_mice = dict()
end_time = -10000
data_read_all_batches = None
for f in args.file_mice_behavior:
int_data = intervals.IntData(f, map_dict=mapping_data.correspondence)
data_read = int_data.read(relative_coord=True)
chr_file_n = "chrom"
mapping.write_chr_sizes(data_read, file_n=chr_file_n)
chr_file = chr_file_n + ".sizes"
if end_time < int_data.max - int_data.min:
# saccharin red
### Feeding data
if args.behavioral_type == "feeding":
data_type_1 = "food_sc"
data_type_2 = "food_fat"
data_type_col = {data_type_1: 'orange', data_type_2: 'black'}
### Drinking data
elif args.behavioral_type == 'drinking':
data_type_1 = "water"
data_type_2 = "saccharin"
data_type_col = {data_type_1: 'blue', data_type_2: 'red'}
else:
print >> stderr, "Behavioral data type not available in script, please try again with \"drinking\" or \"feeding\""
mapping_data = mapping.MappingInfo(
"../../sample_data/feeding_behavior/b2g.txt")
int_data_b1 = intervals.IntData(
"../../sample_data/feeding_beh_CB1_mice/intake_CB1_B1.csv",
map_dict=mapping_data.correspondence)
int_data_b2 = intervals.IntData(
"../../sample_data/feeding_beh_CB1_mice/intake_CB1_B2.csv",
map_dict=mapping_data.correspondence)
int_data_b3 = intervals.IntData(
"../../sample_data/feeding_beh_CB1_mice/intake_CB1_B3.csv",
map_dict=mapping_data.correspondence)
int_data_b4 = intervals.IntData(
"../../sample_data/feeding_beh_CB1_mice/intake_CB1_B4.csv",
map_dict=mapping_data.correspondence)
mapping_bed = mapping.MappingInfo("../../test/pybed2perg.txt")
else:
tag_file = "mean_speed_i_motionDir"
print >> stderr, "Bed speed file: %s" % args.speed
print >> stderr, "Bed motion file: %s" % args.motion
print >> stderr, "Mapping bed to Pergola file: %s" % args.bed_mapping
print >> stderr, "Output tag file: %s" % tag_file
# base_dir = path.dirname(getcwd())
# dir_development = base_dir + "/c_elegans_data_test/"
# # out_dir = base_dir + "/test/"
# out_dir = base_dir + "/c_elegans_data_test/"
# # mapping_bed = mapping.MappingInfo(base_dir + "/test/" + "bed2pergola.txt")
mapping_bed = mapping.MappingInfo(args.bed_mapping)
## mapping_bed = mapping.MappingInfo("/Users/jespinosa/git/pergola/test/c_elegans_data_test/bed2pergola.txt")
# speed bed file
## read file from input args
# bed_speed_file = dir_development + "midbody.575_JU440_on_food_L_2011_02_17__16_43___3___11_features_speed.csv.bed"
# bed_speed_file ='/Users/jespinosa/git/pergola/test/c_elegans_data_test/results_GB/midbody.575_JU440_on_food_L_2011_02_17__11_00___3___1_features.mat.GB.bed'
## bed_speed_file = '/Users/jespinosa/git/pergola/test/c_elegans_data_test/work/be/c8a7942756ee7053d0f9856e1caa88/bed_speed_no_tr'
## error to debug nextflow Paolo
# bed_speed_file = dir_development + args.speed
bed_speed_file = args.speed
int_data_speed = intervals.IntData(bed_speed_file, map_dict=mapping_bed.correspondence, header=False,
fields_names=['chrm', 'start', 'end', 'nature', 'value', 'strain', 'color'])
################################################################
### ###
### ###
### ###
### ###
### ###
### ###
################################################################
from pergola import mapping, intervals, tracks
from os import path, getcwd
base_dir = path.dirname(getcwd())
out_dir = base_dir + "/test/"
mapping_data = mapping.MappingInfo(base_dir + "/sample_data/feeding_behavior/b2g.txt")
int_data = intervals.IntData(base_dir + "/sample_data/feeding_behavior/feedingBehavior_HF_mice.csv", map_dict=mapping_data.correspondence)
# Dictionary to set colors of each type of food
data_type_col = {'food_sc': 'orange', 'food_fat':'blue'}
data_read = int_data.read(relative_coord=True)
# for i in data_read.data: print i
data_read.data_types
data_read.fields
# bed_str = data_read.convert(mode="bed")
# bedGraph_str = data_read.convert(mode="bedGraph")
### Jose A Espinosa. CSN/CB-CRG Group. Feb 2015 ###
################################################################
### Script creating pybedtools objects directly from pergola ###
################################################################
import pybedtools
# import sys
# my_path_to_modules = "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/"
# sys.path.append(my_path_to_modules)
from pergola import mapping
from pergola import intervals
mapping_data = mapping.MappingInfo(
"/Users/jespinosa/git/pergola/sample_data/feeding_behavior/b2g.txt")
int_data = intervals.IntData(
"/Users/jespinosa/git/pergola/sample_data/feeding_behavior/feedingBehavior_HF_mice.csv",
map_dict=mapping_data.correspondence)
data_read = int_data.read(relative_coord=True)
data_type_col = {'food_sc': 'orange', 'food_fat': 'blue'}
bed_str = data_read.convert(mode="bed",
data_types=["food_sc", "food_fat"],
dataTypes_actions="all",
color_restrictions=data_type_col)
# bed_tr1_food_sc = bed_str[('1', 'food_sc')]
print >> stderr, "Mapping file: %s" % args.bed_mapping
print >> stderr, "Chrom_sizes file: %s" % args.chrom_sizes
# # Input files
forward_file = args.forward_file
backward_file = args.backward_file
bed_mapping = args.bed_mapping
chrom_sizes = args.chrom_sizes
# forward_file = '/Users/jespinosa/git/pergola/test/c_elegans_data_test/results_motion_GB/575_JU440_on_food_L_2011_02_17__11_00___3___1_features.matfile_worm.backward.csv.motion.bed'
# backward_file = '/Users/jespinosa/git/pergola/test/c_elegans_data_test/results_motion_GB/575_JU440_on_food_L_2011_02_17__11_00___3___1_features.matfile_worm.forward.csv.motion.bed'
# bed_mapping = '/Users/jespinosa/git/pergola/test/c_elegans_data_test/bed2pergola.txt'
chr_file_n = "chrom.sizes"
mapping_bed = mapping.MappingInfo(bed_mapping)
forward = intervals.IntData(forward_file,
map_dict=mapping_bed.correspondence,
header=False,
fields_names=[
'chrm', 'start', 'end', 'nature', 'value',
'strain', 'color'
])
forward_read = forward.read(relative_coord=False)
forward_bed_obj = forward_read.convert(mode="bed")['chr1',
'.'].create_pybedtools()
backward = intervals.IntData(backward_file,
map_dict=mapping_bed.correspondence,
header=False,
'--mapping_file',
help='Mapping file to read JAABA files',
required=True)
parser.add_argument('-t',
'--tag_group',
help='Tag to distinguish data sets',
required=True)
parser.add_argument('-b',
'--behavior',
help='Annotated behavior using JAABA',
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()
### mice feeding behavior and uses tools from pybedtools to ###
### extract intermeals intervals (complement) and intersect ###
### them with day and experimental phases. ###
### Generates a bed file for each track with the result of ###
### the above described operations. ###
################################################################
import pybedtools
from os import path, getcwd
from pergola import mapping
from pergola import intervals
base_dir = path.dirname(getcwd())
out_dir = base_dir + "/test/"
mapping_data = mapping.MappingInfo(base_dir +
"/sample_data/feeding_behavior/b2g.txt")
int_data = intervals.IntData(
base_dir + "/sample_data/feeding_behavior/feedingBehavior_HF_mice.csv",
map_dict=mapping_data.correspondence)
data_read = int_data.read(relative_coord=True)
###################
# Generate to BedTool objects containing light and dark phases
# Write phases file
mapping.write_cytoband(end=int_data.max - int_data.min,
delta=43200,
start_phase="dark")
#!/usr/bin/env python
from pergola import mapping
from pergola import intervals
from pergola import parsers
mapping_info = mapping.MappingInfo(
"/Users/jespinosa/git/pergola/sample_data/feeding_behavior/b2g.txt")
mapping_info.write()
# load the data into an IntData object that will store the sequence of events
int_data = intervals.IntData(
"/Users/jespinosa/git/pergola/sample_data/feeding_behavior/feedingBehavior_HF_mice.csv",
map_dict=mapping_info.correspondence,
delimiter="\t")
print(int_data.data[:12])
print(int_data.fieldsB)
print(int_data.fieldsG_dict)
# print (int_data.fieldsG_dict.keys())
print(int_data.dataTypes)
print(int_data.tracks)
print "debugging_simple_read---- min value in int_data_feeding ------------------------", int_data.min
print "debugging_simple_read---- max value in int_data_feeding ------------------------", int_data.max
track_data = int_data.read(relative_coord=True)
print "track object files are============+++++++++++++++++++", track_data.fields
track_data.convert(mode="bed")
#electro for single time point validation