.. \_getting_start:
===================
You can code your own scripts using ``pergola`` as a Python library.
Here we summarize some examples of how you can use it on your scripts.
.. raw:: html
Tip: This page is available as a Jupyter Notebook on
/pergola/doc/notebooks under pergola GitHub repository. Should you want,
you can interactively execute the code using Jupyter.
.. raw:: html
Input data
----------
The two basics data inputs ``pergola`` uses is a file with longitudinal
recordings (sequence of temporal events) in the form of a ``CSV`` or
``xlsx`` file and a mapping file containing the correspondence between
the fields in this previous file and the ``pergola`` ontology.
Sequence of temporal events
---------------------------
Pergola can process any sequence of temporal events contained in a
character-separated file as in the example below:
::
Animal StartT EndT Behavior Value
1 137 156 eat 0.06
1 168 192 drink 0.02
1 250 281 eat 0.07
1 311 333 eat 0.08
1 457 482 drink 0.02
1 569 601 drink 0.03
.. raw:: html
Note: This example loads a sequence of eating and drinking events from a
experiment where mice were used to study feeding behavior.
.. raw:: html
Mapping file
------------
Pergola needs that you set the equivalences between the fields of the
input data and a controled vocabular defined by Pergola ontology. The
format of the mapping file is `the external mapping file
format `__
from the Gene Ontology Consortium, you can see an example below:
::
! Mapping of behavioural fields into genome browser fields
!
behavioural_file:Animal > pergola:track
behavioural_file:StartT > pergola:chromStart
behavioural_file:EndT > pergola:chromEnd
behavioural_file:Behavior > pergola:dataTypes
behavioural_file:Value > pergola:dataValue
.. code:: ipython2
# You might have to set the path to run this notebook directly from ipython notebook
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)
MappingInfo objects
-------------------
Mappings between the input data and pergola ontology are loaded in
MappingInfo objects:
.. code:: ipython2
from pergola import mapping
# load mapping file
mapping_info = mapping.MappingInfo("../../sample_data/feeding_behavior/b2p.txt")
To view the mappings MappingInfo objects provide the
:func:``pergola.mapping.Mapping.write`` method
.. code:: ipython2
mapping_info.write()
.. parsed-literal::
EndT end
Nature data_types
Value data_value
StartT start
Phase chrom
CAGE track
MappingInfo objects are needed to load data into IntData objects as it
will be explained in the lines below.
IntData objects
---------------
IntData objects load all the intervals of a file:
.. code:: ipython2
from pergola import parsers
from pergola import intervals
# load the data into an IntData object that will store the sequence of events
int_data = intervals.IntData("../../sample_data/feeding_behavior/feeding_behavior_HF_mice.csv", map_dict=mapping_info.correspondence)
.. parsed-literal::
Input file format identified as csv
Intervals when loaded are stored in a list of tuples that can be
accessed by data attribute:
.. code:: ipython2
#Displays first 10 tuples of data list
int_data.data[:10]
.. parsed-literal::
[('1', 1335985232, 'food_sc', 1335985200, '0.02'),
('1', 1335986427, 'food_sc', 1335986151, '0.1'),
('1', 1335986451, 'water', 1335986420, '0.08'),
('1', 1335986553, 'water', 1335986541, '0.02'),
('1', 1335986844, 'water', 1335986832, '0.02'),
('1', 1335986947, 'food_sc', 1335986845, '0.02'),
('1', 1335987059, 'water', 1335987044, '0.02'),
('1', 1335987223, 'food_sc', 1335987089, '0.02'),
('1', 1335987495, 'food_sc', 1335987424, '0.02'),
('1', 1335987574, 'water', 1335987546, '0.04')]
IntData objects also provide some other attributes like the set of
different tracks (term for IDs in pergola ontology) contained in the
data:
.. code:: ipython2
int_data.data_types
.. parsed-literal::
{'food_fat', 'food_sc', 'water'}
The minimun value present in the data:
.. code:: ipython2
int_data.min
.. parsed-literal::
1335985200
The maximun value:
.. code:: ipython2
int_data.max
.. parsed-literal::
1337799586
The set of different tracks present in the data (term for different IDs
in pergola ontology). In this case the different IDs for each mice:
.. code:: ipython2
int_data.tracks
.. parsed-literal::
{'1',
'10',
'11',
'12',
'13',
'14',
'15',
'16',
'17',
'18',
'2',
'3',
'4',
'5',
'7',
'8',
'9'}
And finally the dataTypes (term for different types of data in pergola
ontology) that can be used to encode for example different behaviours:
.. code:: ipython2
mapping_info.write()
.. parsed-literal::
EndT end
Nature data_types
Value data_value
StartT start
Phase chrom
CAGE track
.. code:: ipython2
mapping_info.correspondence['EndT']
.. parsed-literal::
'end'
Data conversion:
----------------
GenomicContainer is a generic class from which three subclasses derive:
Track objects
-------------
Data can be loaded into a Track objects by read function. This function
allows to convert the intervals to relative values using the first time
point as 0:
.. code:: ipython2
int_data_read = int_data.read(relative_coord=True)
.. parsed-literal::
Relative coordinates set to: True
.. code:: ipython2
int_data_read.list_tracks
.. parsed-literal::
{'1',
'10',
'11',
'12',
'13',
'14',
'15',
'16',
'17',
'18',
'2',
'3',
'4',
'5',
'7',
'8',
'9'}
.. code:: ipython2
int_data_read.range_values
.. parsed-literal::
[0.02, 8.82]
.. code:: ipython2
dict_bed = int_data_read.convert(mode='bed')
.. code:: ipython2
#dict_bed = data_read.convert(mode='bed')
for key in dict_bed:
print "key.......: ",key#del
bedSingle = dict_bed [key]
print "::::::::::::::",bedSingle.data_types
.. parsed-literal::
key.......: ('12', 'food_sc')
:::::::::::::: food_sc
key.......: ('7', 'food_sc')
:::::::::::::: food_sc
key.......: ('14', 'water')
:::::::::::::: water
key.......: ('1', 'food_sc')
:::::::::::::: food_sc
key.......: ('12', 'food_fat')
:::::::::::::: food_fat
key.......: ('2', 'food_sc')
:::::::::::::: food_sc
key.......: ('10', 'food_fat')
:::::::::::::: food_fat
key.......: ('15', 'food_sc')
:::::::::::::: food_sc
key.......: ('17', 'water')
:::::::::::::: water
key.......: ('14', 'food_fat')
:::::::::::::: food_fat
key.......: ('5', 'food_sc')
:::::::::::::: food_sc
key.......: ('18', 'food_fat')
:::::::::::::: food_fat
key.......: ('2', 'water')
:::::::::::::: water
key.......: ('11', 'water')
:::::::::::::: water
key.......: ('16', 'food_fat')
:::::::::::::: food_fat
key.......: ('16', 'water')
:::::::::::::: water
key.......: ('14', 'food_sc')
:::::::::::::: food_sc
key.......: ('11', 'food_sc')
:::::::::::::: food_sc
key.......: ('4', 'water')
:::::::::::::: water
key.......: ('3', 'food_sc')
:::::::::::::: food_sc
key.......: ('2', 'food_fat')
:::::::::::::: food_fat
key.......: ('10', 'water')
:::::::::::::: water
key.......: ('9', 'water')
:::::::::::::: water
key.......: ('4', 'food_sc')
:::::::::::::: food_sc
key.......: ('8', 'water')
:::::::::::::: water
key.......: ('7', 'water')
:::::::::::::: water
key.......: ('17', 'food_sc')
:::::::::::::: food_sc
key.......: ('9', 'food_sc')
:::::::::::::: food_sc
key.......: ('12', 'water')
:::::::::::::: water
key.......: ('16', 'food_sc')
:::::::::::::: food_sc
key.......: ('5', 'water')
:::::::::::::: water
key.......: ('10', 'food_sc')
:::::::::::::: food_sc
key.......: ('13', 'water')
:::::::::::::: water
key.......: ('8', 'food_fat')
:::::::::::::: food_fat
key.......: ('1', 'water')
:::::::::::::: water
key.......: ('3', 'water')
:::::::::::::: water
key.......: ('18', 'food_sc')
:::::::::::::: food_sc
key.......: ('15', 'water')
:::::::::::::: water
key.......: ('18', 'water')
:::::::::::::: water
key.......: ('4', 'food_fat')
:::::::::::::: food_fat
key.......: ('13', 'food_sc')
:::::::::::::: food_sc
key.......: ('8', 'food_sc')
:::::::::::::: food_sc
.. code:: ipython2
bed_12_food_sc = dict_bed[('2', 'food_sc')]
.. code:: ipython2
bed_12_food_sc.range_values
.. parsed-literal::
['0.02', '0.540000000000001']
.. code:: ipython2
type(bed_12_food_sc)
.. parsed-literal::
pergola.tracks.Bed
.. code:: ipython2
bed_12_food_sc.data
# Code to print the data inside a bed object (generator object)
#for row in bed_12_food_sc.data:
# print row
.. parsed-literal::
.. code:: ipython2
dict_bedGraph = int_data_read.convert(mode='bedGraph')
.. code:: ipython2
for key in dict_bedGraph:
print "key.......: ",key#del
bedGraphSingle = dict_bedGraph [key]
print "::::::::::::::",bedGraphSingle.data_types
.. parsed-literal::
key.......: ('12', 'food_sc')
:::::::::::::: food_sc
key.......: ('7', 'food_sc')
:::::::::::::: food_sc
key.......: ('14', 'water')
:::::::::::::: water
key.......: ('1', 'food_sc')
:::::::::::::: food_sc
key.......: ('12', 'food_fat')
:::::::::::::: food_fat
key.......: ('2', 'food_sc')
:::::::::::::: food_sc
key.......: ('10', 'food_fat')
:::::::::::::: food_fat
key.......: ('15', 'food_sc')
:::::::::::::: food_sc
key.......: ('17', 'water')
:::::::::::::: water
key.......: ('14', 'food_fat')
:::::::::::::: food_fat
key.......: ('5', 'food_sc')
:::::::::::::: food_sc
key.......: ('18', 'food_fat')
:::::::::::::: food_fat
key.......: ('2', 'water')
:::::::::::::: water
key.......: ('11', 'water')
:::::::::::::: water
key.......: ('16', 'food_fat')
:::::::::::::: food_fat
key.......: ('16', 'water')
:::::::::::::: water
key.......: ('14', 'food_sc')
:::::::::::::: food_sc
key.......: ('11', 'food_sc')
:::::::::::::: food_sc
key.......: ('4', 'water')
:::::::::::::: water
key.......: ('3', 'food_sc')
:::::::::::::: food_sc
key.......: ('2', 'food_fat')
:::::::::::::: food_fat
key.......: ('10', 'water')
:::::::::::::: water
key.......: ('9', 'water')
:::::::::::::: water
key.......: ('4', 'food_sc')
:::::::::::::: food_sc
key.......: ('8', 'water')
:::::::::::::: water
key.......: ('7', 'water')
:::::::::::::: water
key.......: ('17', 'food_sc')
:::::::::::::: food_sc
key.......: ('9', 'food_sc')
:::::::::::::: food_sc
key.......: ('12', 'water')
:::::::::::::: water
key.......: ('16', 'food_sc')
:::::::::::::: food_sc
key.......: ('5', 'water')
:::::::::::::: water
key.......: ('10', 'food_sc')
:::::::::::::: food_sc
key.......: ('13', 'water')
:::::::::::::: water
key.......: ('8', 'food_fat')
:::::::::::::: food_fat
key.......: ('1', 'water')
:::::::::::::: water
key.......: ('3', 'water')
:::::::::::::: water
key.......: ('18', 'food_sc')
:::::::::::::: food_sc
key.......: ('15', 'water')
:::::::::::::: water
key.......: ('18', 'water')
:::::::::::::: water
key.......: ('4', 'food_fat')
:::::::::::::: food_fat
key.......: ('13', 'food_sc')
:::::::::::::: food_sc
key.......: ('8', 'food_sc')
:::::::::::::: food_sc
.. code:: ipython2
bedG_8_food_sc = dict_bedGraph[('8', 'food_sc')]
Track object
------------
.. code:: ipython2
bedG_8_food_sc.data
# Code to print the data inside a bed object (generator object)
#for row in bedG_8_food_sc:
# print row
.. parsed-literal::
.. code:: ipython2
type(int_data_read)
.. parsed-literal::
pergola.tracks.Track
.. code:: ipython2
type(int_data_read.data)
.. parsed-literal::
list
.. code:: ipython2
int_data_read.range_values
.. parsed-literal::
[0.02, 8.82]
.. code:: ipython2
int_data_read.list_tracks
.. parsed-literal::
{'1',
'10',
'11',
'12',
'13',
'14',
'15',
'16',
'17',
'18',
'2',
'3',
'4',
'5',
'7',
'8',
'9'}
.. code:: ipython2
int_data_read.data[-10]
.. parsed-literal::
('18', 1812042, 'food_fat', 1811948, '0.14')
.. code:: ipython2
int_data_read.data_types
.. parsed-literal::
{'food_fat', 'food_sc', 'water'}
.. code:: ipython2
#data_read.convert(mode=write_format, tracks=sel_tracks, tracks_merge=tracks2merge,
# data_types=data_types_list, dataTypes_actions=dataTypes_act,
# window=window_size)
.. code:: ipython2
mapping.write_chr (int_data_read)
.. parsed-literal::
Chromosome fasta like file will be dump into "/Users/jespinosa/git/pergola/doc/notebooks" as it has not been set using path_w
Genome fasta file created: /Users/jespinosa/git/pergola/doc/notebooks/chr1.fa
.. code:: ipython2
# Generate a cytoband file and a bed file with phases
mapping.write_cytoband(end = int_data.max - int_data.min, delta=43200, start_phase="dark", lab_bed=False)
.. parsed-literal::
Cytoband like file will be dump into "/Users/jespinosa/git/pergola/doc/notebooks" as it has not been set using path_w
Bed files with phases will be dump into "/Users/jespinosa/git/pergola/doc/notebooks" as it has not been set using path_w
.. code:: ipython2
#data_read = intData.read(relative_coord=True, multiply_t=1)
data_read = int_data.read(relative_coord=True)
.. parsed-literal::
Relative coordinates set to: True
.. code:: ipython2
#for i in data_read.data:
# print i
.. code:: ipython2
data_type_col = {'food_sc': 'orange', 'food_fat':'blue'}
.. code:: ipython2
bed_str = data_read.convert(mode="bed", data_types=["food_sc", "food_fat"], dataTypes_actions="all",
color_restrictions=data_type_col)
.. parsed-literal::
Removed data types are: water
.. code:: ipython2
for key in bed_str:
bedSingle = bed_str[key]
bedSingle.save_track()
.. parsed-literal::
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_12_dt_food_sc.bed generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_14_dt_food_fat.bed generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_1_dt_food_sc.bed generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_2_dt_food_sc.bed generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_15_dt_food_sc.bed generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_5_dt_food_sc.bed generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_16_dt_food_fat.bed generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_14_dt_food_sc.bed generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_11_dt_food_sc.bed generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_3_dt_food_sc.bed generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_2_dt_food_fat.bed generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_10_dt_food_fat.bed generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_4_dt_food_sc.bed generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_17_dt_food_sc.bed generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_9_dt_food_sc.bed generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_12_dt_food_fat.bed generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_16_dt_food_sc.bed generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_10_dt_food_sc.bed generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_8_dt_food_fat.bed generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_7_dt_food_sc.bed generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_18_dt_food_sc.bed generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_18_dt_food_fat.bed generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_4_dt_food_fat.bed generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_13_dt_food_sc.bed generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_8_dt_food_sc.bed generated
Output data
-----------
``pergola`` allows the conversion to several genomic formats, here we
summarize some commands and operations as an example of ``pergola``
capabilities:
Bed file
--------
::
track type=bed name="1_eat" description="1 eat" visibility=2 itemRgb="On" priority=20
chr1 137.0 156.0 "" 0.06 + 137.0 156.0 51,254,51
chr1 250.0 281.0 "" 0.07 + 250.0 281.0 0,254,0
chr1 311.0 333.0 "" 0.08 + 311.0 333.0 25,115,25
::
track type=bed name="1_eat" description="1 eat" visibility=2 itemRgb="On" priority=20
chr1 0 19 "" 0.06 + 0 19 51,254,51
chr1 113 144 "" 0.07 + 113 144 0,254,0
chr1 174 196 "" 0.08 + 174 196 25,115,25
.. code:: ipython2
data_type_col_bedGraph = {'food_sc':'orange', 'food_fat_food_sc':'blue'}
.. code:: ipython2
bedGraph_str = data_read.convert(mode="bedGraph", window=1800, data_types=["food_sc", "food_fat"], dataTypes_actions="all", color_restrictions=data_type_col_bedGraph)
.. parsed-literal::
Removed data types are: water
.. code:: ipython2
for key in bedGraph_str:
bedGraph_single = bedGraph_str[key]
bedGraph_single.save_track()
.. parsed-literal::
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_12_dt_food_sc.bedGraph generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_14_dt_food_fat.bedGraph generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_1_dt_food_sc.bedGraph generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_2_dt_food_sc.bedGraph generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_15_dt_food_sc.bedGraph generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_5_dt_food_sc.bedGraph generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_16_dt_food_fat.bedGraph generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_14_dt_food_sc.bedGraph generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_11_dt_food_sc.bedGraph generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_3_dt_food_sc.bedGraph generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_2_dt_food_fat.bedGraph generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_10_dt_food_fat.bedGraph generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_4_dt_food_sc.bedGraph generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_17_dt_food_sc.bedGraph generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_9_dt_food_sc.bedGraph generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_12_dt_food_fat.bedGraph generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_16_dt_food_sc.bedGraph generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_10_dt_food_sc.bedGraph generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_8_dt_food_fat.bedGraph generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_7_dt_food_sc.bedGraph generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_18_dt_food_sc.bedGraph generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_18_dt_food_fat.bedGraph generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_4_dt_food_fat.bedGraph generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_13_dt_food_sc.bedGraph generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File tr_8_dt_food_sc.bedGraph generated
bedGraph files
--------------
::
track type=bedGraph name="1_eat" description="1_eat" visibility=full color=0,254,0 altColor=25,115,25 priority=20
chr1 0 30 0.06
chr1 30 60 0
chr1 60 90 0
chr1 90 120 0.0158064516129
chr1 120 150 0.0541935483871
chr1 150 180 0.0218181818182
chr1 180 210 0.0581818181818
chr1 210 240 0
.. code:: ipython2
## Bed file showing the files (recordings)
# reading correspondence file
mapping_file_data = mapping.MappingInfo("../../sample_data/feeding_behavior/f2g.txt")
.. code:: ipython2
mapping_file_data.write()
.. parsed-literal::
Value data_value
EndT end
StartT start
File track
NameFile data_types
.. code:: ipython2
# Reading file info
files_data = intervals.IntData("../../sample_data/feeding_behavior/files.csv", map_dict=mapping_file_data.correspondence)
data_file_read = files_data.read(relative_coord=True)
.. parsed-literal::
Input file format identified as csv
Relative coordinates set to: True
.. code:: ipython2
bed_file = data_file_read.convert(mode="bed", dataTypes_actions="all", tracks_merge=files_data.tracks)
.. parsed-literal::
Tracks that will be merged are: 1 3 2 5 4 7 6 9 8
.. code:: ipython2
for key in bed_file:
bed_file_single = bed_file[key]
bed_file_single.save_track(name_file = "files_data")
.. parsed-literal::
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File files_data.bed generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File files_data.bed generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File files_data.bed generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File files_data.bed generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File files_data.bed generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File files_data.bed generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File files_data.bed generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File files_data.bed generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File files_data.bed generated
.. code:: ipython2
# Reading phase info
phase_data = intervals.IntData("../../sample_data/feeding_behavior/phases_exp.csv", map_dict=mapping_file_data.correspondence)
data_phase_read = phase_data.read(relative_coord=True)
.. parsed-literal::
Input file format identified as csv
Relative coordinates set to: True
.. code:: ipython2
bed_file = data_phase_read.convert(mode="bed", dataTypes_actions="all", tracks_merge=phase_data.tracks)
.. parsed-literal::
Tracks that will be merged are: 1 2
.. code:: ipython2
for key in bed_file:
bed_file_single = bed_file[key]
bed_file_single.save_track(name_file = "phase_exp")
.. parsed-literal::
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File phase_exp.bed generated
No path selected, files dump into path: /Users/jespinosa/git/pergola/doc/notebooks
File phase_exp.bed generated
means bed file to delete
::
chr1 1 1801 "" 1000 + 0 1 0.06
chr1 137171 138971 "" 1000 + 132936 137171 0
chr1 397442 399242 "" 1000 + 391684 397442 0
chr1 568633 570433 "" 1000 + 563646 568633 0.125714
intermeal to delete
::
chr1 1 30 "" 1000 + 1 30 0
chr1 183 345 "" 1000 + 183 345 0
chr1 502 924 "" 1000 + 502 924 0