Pergola provides a series of scripts that are available in your system after its installation installation.

These scripts try to wrap up the most common functionalities of Pergola library.

## pergola¶

pergola enables the user to execute many of the main pergola functionalities.

If you prefer to code your own scripts you can see some examples at the tutorials section.

Tip

To reproduce all pergola commands shown in this section you can download the following data set:

The data consists of a series of recordings corresponding to three weeks of the feeding behavior of C57BL/6 mice fed either with a high-fat or a standard chow. To download and uncompress the data you can use the following commands:

mkdir data
wget -O- https://zenodo.org/record/1168982/files/feeding_behavior_C57BL6_mice_HF.tar.gz | tar xz -C data


If you install pergola from GitHub or use the Docker image you can also find this data set on:

/path_to_installation/pergola/sample_data.


Pergola options allow the user to use the main features of Pergola library in a ready-to-use script.

We divided in the five following sections the available arguments:

Note

All the command line examples can be reproduce using the files found in the feeding_behavior_C57BL6_mice_HF.tar.gz tarball file.

### Data input¶

Available data input parameters are listed on the table below:

Argument short Description Example
--input -i Path of input data file -i /foo/feeding_behavior_HF_mice.csv.csv
--mapping_file -m Path of mapping file -m /foo/my_mappings.txt
--field_separator -fs Field separator of mapping file -fs " "
--no_header -nh The input file has not header (column names) -nh
--fields_read -s List of columns name (used in mappping file) -s 'CAGE' 'EndT' 'Nature' 'StartT' 'Value'

Only two of the data input arguments are mandatory to run pergola:

• the -i, --input argument specifies the file to convert.
• the -m, --mapping_file argument contains the mappings between the input file fields and the terms defined in the pergola ontology.

Tip

pergola can take as input files in CSV and xlsx format. You can see examples of both in the input data section.

In this manner, the minimal command to run pergola provided that the input and mappings file are correctly formatted would be:

pergola -i ./data/feeding_behavior_HF_mice.csv -m ./data/b2p.txt


As mentioned before you can also use a xlsx file as input instead:

pergola -i ./data/feeding_behavior_HF_mice.xlsx -m ./data/b2p.txt


Note

The format of the mapping file consists in a text file containing in each line the correspondence between a field in the input data field and the pergola ontology. For more details, refer to the pergola ontology section and to the example of a mapping file.

Tip

Any field on the input data that should not be used by pergola must be set to dummy term in the mapping file.

The rest of arguments are optional and enable the user to provide additional information about the input data in the cases it does not entirely fits the default pergola input data format.

For instance, the -fs, --field_separator sets the delimiter that separates fields inside the input data file when it is not set to tabs (default). As an example if fields are delimited by ,, you can specify it as shown below:

pergola -i ./data/feeding_behavior_HF_mice_commas.csv -m ./data/b2p.txt -fs ","


Pergola needs that input files columns are mapped into pergola ontology terms and thus, if the input file has not header you should provide an ordered list with the corresponding fields of your file as in the example below, using the -nh, --no_header argument together with the -s, --fields_read:

pergola -i ./data/feeding_behavior_HF_mice_no_header.csv -m ./data/b2p.txt -nh -s 'CAGE' 'EndT' 'Nature' 'StartT' 'Value'


Tip

To avoid setting fields names you can use the reserved word ordinal with -s argument. This allows to use numbers instead of terms in the mapping file. Below you can see an example of a assignation of the mapping file using this option:

behavioral_file:1 > pergola:track


The command would result in:

pergola -i ./data/feeding_behavior_HF_mice_no_header.csv -m ./data/b2p_ordinal.txt -nh -s 'ordinal'


### File formats¶

Pergola can convert your data to several genomic file formats. The BED (default option) and GFF file formats provide the perfect scaffold to encode events in the form of discrete time intervals such as for instance a meal. In the other hand, BedGraph format provides a perfect structure to store continuous data such as for instance any behavioral feature measure continuously along time (speed along a trajectory), or any score derived from the original data (cumulative values applying a binning or statitiscal parameter).

Argument short Options Description Example
--format -f bed Converts data to BED format -f bed
gff Converts data to BedGraph format -f gff
bedGraph Converts data to format -f bedGraph

Following our previous example the command line to convert our data to BedGraph format will be:

pergola -i ./data/feeding_behavior_HF_mice.csv -m ./data/b2p.txt -f bedGraph


Note

Pergola converts data by default to BED file format. Refer to the mapping file section to see pergola’s adapted genomic formats.

### Filtering¶

Filtering arguments allow you to select a part of your input data based on pergola assigned fields.

Argument short Description Example
--tracks -t List of tracks to keep -t track_id_1 track_id_2
--range -r Track range to keep (numerical) -r 1 10
--track_actions -a Action to perform on selected tracks -t track_id_1 track_id_2 -a split_all
--data_types_list -dl List of data types to keep -dl data_type_one data_type_2
--data_types_actions -d Action to perform on selected data types -dl data_type_one data_type_2 -d one_per_channel

Pergola allows you to filter a subset of your data input based on the field set as track in your mapping file.

The example below shows how to get the data only from animal 1 4 7 (tracks):

pergola -i ./data/feeding_behavior_HF_mice.csv -m ./data/b2p.txt -t 1 4  7 -dl food_sc food_fat


If you want to get all tracks from 1 to 4 you can then use the -r option provided your track field is numeric:

pergola -i ./data/feeding_behavior_HF_mice.csv -m ./data/b2p.txt -r 1-4


Tip

By default tracks selected by -r option are joined together in a single output track. You can use -a option to change this behavior.

The -a option allows to join together tracks in the same file. Available -a options are:

track_actions Description
split_all Split all tracks into different files
join_all Join all tracks in a single file
join_odd Join only odd tracks in a single file
join_even Join only even tracks in a single file

An example of how to join all tracks in the same file would be:

pergola -i ./data/feeding_behavior_HF_mice.csv -m ./data/b2p.txt -a join_all


Tip

You can combine -t or -r options with -a in order to filter tracks and join them as you prefer

pergola -i ./data/feeding_behavior_HF_mice.csv -m ./data/b2p.txt -t 1 2 3 -a join_all


It is possible to provide pergola with a list of the field assigned to data_type pergola ontology term to be kept using -dl argument. For instance, in the code below only events assigned to “food_fat” data_type term are kept:

pergola -i ./data/feeding_behavior_HF_mice.csv -m ./data/b2p.txt -dl food_fat


Besides -d option allows to combine all data types into a single output file or split them in different files:

track_actions Description
all Join all data_type into a single file
one_per_channel Split each data_type into different files

Both -dl and -d options can be combined into a single command, in the example below only events tagged as food_sc and food_fat will be kept and joined for each mice id (track):

pergola -i ./data/feeding_behavior_HF_mice.csv -m ./data/b2p.txt -dl food_sc food_fat -d all


### Temporal arguments¶

Given the prominent temporal nature of longitudinal data, pergola provides several arguments to obtain time-based features or to process time intervals.

Argument short Options Description Example
--relative_coord -e   Time relative to first time point -e
--window_size -w integer Bins the data in time windows of the selected size -w 300
--window_mean -wm   Averages by the window size -wm
--value_mean -vm   Averages by the data items within the window -vm
--min_time -min integer Min time point from which data will be processed -min 10
--max_time -max integer Max time point from which data will be processed -max 1000
--intervals_gen -n   Creates two time points from an original input with a single one -n
--interval_step -ns   Sets the step to create end time points when -n option is set -ns 100
--multiply_intervals -mi integer Multiple time points by the selected value -mi 1000

It is possible that input files do not start at time 0. The relative_coord transforms the time points relative to the first time point inside the file.

For instance, if time inside the file is expressed as epoch time as in the example below:

CAGE  StartT      EndT        Value Nature
1     1335986151  1335986261  0.06  food_sc
1     1335986275  1335986330  0.02  food_sc
1     1335986341  1335986427  0.02  food_sc


Applying the -e it will result into the time coordinates below:

pergola -i ./data/file_0.csv -m data/b2p.txt -e

0     110
124   179
190   276


Pergola enables the user to bin the data using equidistant time windows when formatting data to BedGraph files. The -w arguments sets the size of these windows.

For example:

pergola -i ./data/feeding_behavior_HF_mice.csv -m ./data/b2p.txt -f bedGraph -w 300


Note

The -w argument can be only used together with -f bedGraph option

The -wm argument calculates the mean value inside each of the window of time.

pergola -i ./data/feeding_behavior_HF_mice.csv -m ./data/b2p.txt -f bedGraph -w 300 -wm


The -min and -max arguments set which is the first and the last time point to be present in pergola output file. This can be used for instance to unify the beginning (example below) or end of files:

file_1.csv

CAGE    StartT  EndT    Value Nature
1       20      30      0.02  food_sc
1       50      60      0.02  food_fat

pergola -i ./data/file_1.csv -m ./data/b2p.txt -f bedGraph -w 10 -min 0


Note

The time points inserted at the beginning of the file using -min and -max will be set to zero value. In the example above the beginning of the output file will then look as follows:

chr1        0       10      0
chr1        10      20      0.0
chr1        20      30      0.02


If the input file has only a single time point, pergola can process it using the -n argument. This situation is common in files encoding data that are in equidistant time points, as the following one:

id    time value
1     1    8
1     2    13
1     3    21


In this case the -n argument generates an interval for each of the items of the file:

pergola -i ./data/file_2.csv -m ./data/file_2_to_p.txt -f bedGraph -n


In the case were the time inside the input file is encode as decimal values (for instance tenth of seconds).

time  value
1     -30.98
2     -5.19
3     23.96
4     -2.75


It is possible to multiply the time stamp inside this input file by a given factor using the -mi argument and for instance getting the time stamps in milliseconds:

pergola -i ./data/file_3.csv -m ./data/file_2_to_p.txt -n -mi 1000 -f bedGraph


As a result two time point intervals will be returned in output file:

chr1        0       9       -30.98
chr1        10      19      -5.19
chr1        20      29      23.96
chr1        30      31      -2.75


Note

This last argument is useful because provided that genomic tools are always expressed as integer values, if our time points are expressed as decimals sometimes it will be necessary to convert them to integer values.

### Data output¶

There are several arguments related to optional fields inside the genomic file formats. These arguments are related to the data visualization in genomic tools.

Argument short Options Description Example
--no_track_line -nt   When set bed file does not include a track line (Browser configuration) -nt
--bed_label -bl   BED files include labels describing each interval (data type) -bl
--color_file -c   Path to a file setting a color for the different data types to be displayed -c /your_path/color.txt

Some genomic software as for example genome browsers use the track line to get parameters about the visualization of the data. To avoid the track line you can use the -nt option.

pergola -i ./data/feeding_behavior_HF_mice.csv -m ./data/b2p.txt -nt


The name field of the BED file enables to display a label for each record encoded inside the file. Pergola uses this field to display the data_type of each file line when the option is set:

pergola -i ./data/feeding_behavior_HF_mice.csv -m ./data/b2p.txt -bl


The header of a BED file resulting of this option will look as the following one:

track name="1_food_sc" description="1 food_sc" visibility=2 itemRgb="On" priority=20
chr1        1335986151      1335986261      food_sc 0.06    +       1335986151      1335986261      113,113,113
chr1        1335986275      1335986330      food_sc 0.02    +       1335986275      1335986330      170,170,170


To choose which color will be use to display each of the data types inside the file, it is possible to provide pergola with a file coding the colors to be used. The file will consists:

food_sc     orange
food_fat    blue


How to use it is shown in the following example:

pergola -i ./data/feeding_behavior_HF_mice.csv -m ./data/b2p.txt -c ./data/color_code.txt


Tip

In order to see all available options up you can simply type pergola -h

## jaaba_to_pergola¶

Jaaba annotates behavior using video recordings of animals. jaaba_to_pergola is available in your system after you installed pergola. This script allows user to adapt Jaaba data using Pergola for its visualization and analysis.

The available jaaba_to_pergola modes allow to deal with two types of jaaba data:

Note

In order to see all available options up you can simply type jaaba_to_pergola -h

### Jaaba features¶

Jaaba uses a series of features or variables derived from the video-based trajectories of behaving animals to annotate behavior. Pergola allows to obtain these features.

Pergola allows to obtain these features as csv files using the fc mode. Users can also directly process them using pergola by using the fp mode.

Available arguments are:

Argument short Description
--input -i Directory where jaaba features files are placed
--jaaba_features -jf Features to extract
--dumping_directory -dd Directory for dumping csv files

For example it is possible to obtain JAABA features formatted as CSV files using fc mode:

$jaaba_to_pergola fc -i "/jaaba_data/perframe/" -jf velmag dtheta -dd "/output_dir/"  Note The above example shows how to obtain velmag and dtheta features from the perframe folder where jaaba MAT features files are stored and dump them in a directory output_dir. The fp mode makes it possible to convert the selected features into bed or bedGraph files. At the same time it is possible to process the data using any of the pergola options: $jaaba_to_pergola fp -i "/jaaba_data/perframe/" -jf velmag dtheta -dd "/output_dir/" -m "jaaba2pergola_mapping.txt" -f bedGraph -w 300


### Jaaba scores¶

Pergola can convert Jaaba annotations of animal behavior for its visualization and analysis. Jaaba predicts the periods of time within which animals are having a given behavior along a trajectory. These predictions can be dumped into a MAT-file format that contain both the behavioral events predicted and the scores of the reliability of each event.

Jaaba predictions can be also stored in CSV files or process to bed or bedGraph files applying any pergola option. To choose between these two options users can set the sc or the sp mode respectively.

The possible arguments for this modes are:

Argument short Description
--input -i Path to jaaba scores file

Hence, the command line to process a scores Jaaba file into a CSV formatted file using sc mode will be:

$jaaba_to_pergola sc -i predicted_behavior.mat  In the case of sp mode, besides we can use any pergola option: $jaaba_to_pergola sc -i predicted_behavior.mat -m jaaba_scores2pergola_mapping.txt -f bed
`