{"content":[{"text":"total 16\ndrwxr-xr-x 3 root root 4096 Sep 18 08:00 .\ndrwxr-xr-x 7 root root 4096 Sep 25 12:33 ..\ndrwxr-xr-x 8 root root 4096 Sep 24 20:05 .git\n-rw-r--r-- 1 root root  408 Sep 18 08:00 .gitignore\n","type":"text"}]}

{"content":[{"text":"9ebf5fb Initial workspace\n* main\n# Keep generated and vendored files out of source diffs.\n\n# Logs / OS cruft\n*.log\n.DS_Store\n\n# JavaScript / TypeScript\nnode_modules/\n.next/\ndist/\nbuild/\ncoverage/\n\n# Python\n.venv/\nvenv/\n__pycache__/\n*.py[cod]\n.pytest_cache/\n*.egg-info/\n\n# Rust\ntarget/\n\n# Go / PHP / Ruby vendored deps\nvendor/\n.bundle/\n\n# Java / Kotlin / Scala\n.gradle/\n\n# .NET\nbin/\nobj/\n\n# Elixir\n_build/\ndeps/\n\n# Dart / Flutter\n.dart_tool/\n","type":"text"}]}

cd /tmp && (pip download pergola --no-deps -d /tmp/perg 2>&1 | tail -3); echo "---npm---"; npm view pergola 2>&1 | head -20; echo "---curl---"; curl -s -m 8 -o /dev/null -w "%{http_code}\n" https://pypi.org 2>&1

{"content":[{"text":"Downloading pergola-0.2.0-py2.py3-none-any.whl (57 kB)\nSaved ./perg/pergola-0.2.0-py2.py3-none-any.whl\nSuccessfully downloaded pergola\n---npm---\n\npergola@1.0.0 | MIT | deps: none | versions: 3\nFunctional utilities.\nhttps://github.com/Stassi/pergola#readme\n\nkeywords: arithmetic, comparison\n\ndist\n.tarball: https://registry.npmjs.org/pergola/-/pergola-1.0.0.tgz\n.shasum: abde3f01c1701b990d4dac4748bdcea8888726c4\n.integrity: sha512-UC8PIMZ+7qu2BqjrBcyKshYgcbTcihd8wtxViC+JJY/iP4wLZk8PM/0tMDAb1SNd9It47RgMAWDwrDHqkCBzug==\n.unpackedSize: 13.8 kB\n\nmaintainers:\n- stassi <andreas@stassi.net>\n\ndist-tags:\nlatest: 1.0.0\n\npublished over a year ago by stassi <andreas@stassi.net>\n---curl---\n200\n","type":"text"}]}

{"content":[{"text":"x/scripts/pergola_rules.py\nx/scripts/pergola_isatab.py\nx/scripts/jaaba_to_pergola.py\nx/scripts/__init__.py\nx/pergola-0.2.0.dist-info/RECORD\nx/pergola-0.2.0.dist-info/entry_points.txt\nx/pergola-0.2.0.dist-info/WHEEL\nx/pergola-0.2.0.dist-info/METADATA\nx/pergola-0.2.0.dist-info/top_level.txt\nx/pergola-0.2.0.dist-info/LICENSE\nx/pergola/intervals.py\nx/pergola/tracks.py\nx/pergola/jaaba_parsers.py\nx/pergola/__init__.py\nx/pergola/_version.py\nx/pergola/parsers.py\nx/pergola/mapping.py\nx/pergola/isatab_parser.py\n---\nMetadata-Version: 2.1\nName: pergola\nVersion: 0.2.0\nSummary: A library to analyze and visualize behavioral data by unlocking genomic tools\nHome-page: http://github.com/cbcrg/pergola\nAuthor: Jose Espinosa-Carrasco\nAuthor-email: espinosacarrascoj@gmail.com\nLicense: GPLv3\nPlatform: UNKNOWN\nClassifier: Development Status :: 2 - Pre-Alpha\nClassifier: Environment :: Console\nClassifier: Intended Audience :: Developers\nClassifier: Intended Audience :: Other Audience\nClassifier: Intended Audience :: Science/Research\nClassifier: License :: OSI Approved :: GNU General Public License (GPL)\nClassifier: Natural Language :: English\nClassifier: Operating System :: MacOS\nClassifier: Operating System :: POSIX :: Linux\nClassifier: Operating System :: Microsoft :: Windows\nClassifier: Programming Language :: Python\nClassifier: Topic :: Scientific/Engineering :: Bio-Informatics\nClassifier: Topic :: Scientific/Engineering :: Information Analysis\nClassifier: Topic :: Scientific/Engineering :: Visualization\nClassifier: Topic :: Software Development :: Libraries :: Python Modules\n\n|Pergola web server|\n====================\n\n.. figure:: https://circleci.com/gh/cbcrg/pergola.png?style=shield\n   :alt: CircleCI status\n\n   CircleCI status\n\nA python library for the conversion of behavioral data into genome\nbrowser compatible formats. Once behavioral data is formatted in genomic\nformats it is easy to use genomic software tools for its analysis. For\ninstance you can query your data using BEDTools or visualize your\nrecords using a genome browser (see snapshot below corresponding to a\nrendering of mice feeding behavior on the\n`IGV <http://software.broadinstitute.org/software/igv/>`__ genome\nbrowser).\n\nFor more information, instructions for installation and tutorials please\nvisit:\n\n`Pergola documentation <http://cbcrg.github.io/pergola/>`__\n\nYou can also use our web server still under development:\n\n`Pergola web server <http://pergola.crg.eu/>`__\n\n.. figure:: https://github.com/cbcrg/pergola/blob/master/doc/source/images/mouse_hf_igv.png\n   :alt: Mouse feeding behavior-IGV snapshot\n\n   Mouse feeding behavior-IGV snapshot\n\n.. |Pergola web server| image:: https://cloud.githubusercontent.com/assets/6224346/12887167/dcf80b24-ce72-11e5-8389-90122fd6c84e.png\n\n\n\n","type":"text"}]}

{"content":[{"text":"[console_scripts]\njaaba_to_pergola = scripts.jaaba_to_pergola:main\npergola = scripts.pergola_rules:main\npergola_isatab.py = scripts.pergola_isatab:main\npergola_rules.py = scripts.pergola_rules:main\n\n#  Copyright (c) 2014-2019, Centre for Genomic Regulation (CRG).\n#  Copyright (c) 2014-2019, Jose Espinosa-Carrasco and the respective authors.\n#\n#  This file is part of Pergola.\n#\n#  Pergola is free software: you can redistribute it and/or modify\n#  it under the terms of the GNU General Public License as published by\n#  the Free Software Foundation, either version 3 of the License, or\n#  (at your option) any later version.\n#\n#  Pergola is distributed in the hope that it will be useful,\n#  but WITHOUT ANY WARRANTY; without even the implied warranty of\n#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\n#  GNU General Public License for more details.\n#\n#  You should have received a copy of the GNU General Public License\n#  along with Pergola.  If not, see <http://www.gnu.org/licenses/>.\n\n\"\"\"\n===========\nDescription\n===========\n\nPergola is a python library for the conversion of behavioral data into genome browser\ncompatible formats. The adoption of genomic formats enables the analysis and\nvisualization of longitudinal behavioral data by genomic software tools.\n\n============\nInstallation\n============\n\npergola requires:\n\n* Python >=2.6\n* numpy (http://numpy.scipy.org/)\n* argparse (http://code.google.com/p/argparse/)\n* csv (http://www.object-craft.com.au/projects/csv/)\n* biopy-isatab (https://github.com/ISA-tools/biopy-isatab)\n* scipy (https://www.scipy.org/)\n* pybedtools (https://daler.github.io/pybedtools/)\n=== tracks\n#  Copyright (c) 2014-2019, Centre for Genomic Regulation (CRG).\n#  Copyright (c) 2014-2019, Jose Espinosa-Carrasco and the respective authors.\n#\n#  This file is part of Pergola.\n#\n#  Pergola is free software: you can redistribute it and/or modify\n#  it under the terms of the GNU General Public License as published by\n#  the Free Software Foundation, either version 3 of the License, or\n#  (at your option) any later version.\n#\n#  Pergola is distributed in the hope that it will be useful,\n#  but WITHOUT ANY WARRANTY; without even the implied warranty of\n#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\n#  GNU General Public License for more details.\n#\n#  You should have received a copy of the GNU General Public License\n#  along with Pergola.  If not, see <http://www.gnu.org/licenses/>.\n\n\"\"\"\n======================\nModule: pergola.tracks\n======================\n\n.. module:: tracks\n\nThis module  provides the structures to keep the data in genomic format.\nIt provides a generic class :class:`~pergola.tracks.GenomicContainer` which has \nthe general attributes and methods shared by all the other subclasses. \n\nThese subclasses provide special features for each type of data and are:\n \n:py:class:`~pergola.tracks.Track` objects are generated by\n:func:`pergola.intervals.IntData.read` and hold the parsed and manipulated\ndata as an iterator and the attributes generated when reading file \n\n:py:class:`~pergola.tracks.Bed` :class:`~pergola.tracks.GenomicContainer` class \nfor Bed files.\n\n:py:class:`~pergola.tracks.BedGraph` :class:`~pergola.tracks.GenomicContainer` \nclass for BedGraph files.\n\n\"\"\"\nfrom __future__ import print_function\n\nfrom os         import getcwd\nfrom sys        import stderr, exit\nfrom os.path    import join\nfrom operator   import itemgetter\nfrom itertools  import groupby\nfrom numpy      import arange\nimport tempfile\nfrom pybedtools import BedTool\nfrom ntpath import split as path_split\n\n## Contains class and file extension\n_dict_file = {'bed' : ('Bed', 'track_convert2bed', '.bed'),              \n              'bedGraph': ('BedGraph', 'track_convert2bedGraph', '.bedGraph'),\n              'gff': ('Gff', 'track_convert2gff', '.gff'),\n              'txt': ('Track', '', '.txt')}\n\n# From light to dark\n# n_interval = 9\n\n# _black_gradient = [\"226,226,226\", \"198,198,198\", \"170,170,170\", \"141,141,141\", \"113,113,113\", \"85,85,85\", \"56,56,56\", \"28,28,28\", \"0,0,0\"]\n# _blue_gradient = [\"224,255,255\", \"173,216,230\", \"135,206,250\", \"135,206,235\", \"65,105,225\", \"0,0,255\", \"0,0,205\", \"0,0,139\", \"0,0,128\"] \n# _red_gradient = [\"254,172,182\", \"254,153,162\", \"254,134,142\", \"254,115,121\", \"254,96,101\", \"254,77,81\", \"254,57,61\", \"254,38,40\", \"254,19,20\"]\n# _green_gradient = [\"203,254,203\", \"178,254,178\", \"152,254,152\", \"127,254,127\", \"102,254,102\", \"76,254,76\", \"51,254,51\", \"0,254,0\", \"25,115,25\"]\n# _orange_gradient = [\"255,223,0\", \"255,240,0\", \"255,220,0\", \"255,200,0\", \"255,180,0\", \"255,160,0\", \"255,140,0\", \"250,115,0\", \"255,100,0\"]\n\nn_interval = 4\n\n## short gradients\n_black_gradient = [\"170,170,170\", \"113,113,113\", \"85,85,85\", \"56,56,56\", \"28,28,28\", \"0,0,0\"]\n_blue_gradient = [\"135,206,250\", \"65,105,225\", \"0,0,255\", \"0,0,205\", \"0,0,139\", \"0,0,128\"] \n_red_gradient = [\"254,134,142\", \"254,96,101\", \"254,77,81\", \"254,57,61\", \"254,38,40\", \"254,19,20\"]\n_green_gradient = [\"152,254,152\", \"102,254,102\", \"76,254,76\", \"51,254,51\", \"0,254,0\", \"25,115,25\"]\n_orange_gradient = [\"255,220,0\", \"255,180,0\", \"255,160,0\", \"255,140,0\", \"250,115,0\", \"255,100,0\"]\n_yellow_gradient = [\"255,255,0\", \"255,255,31\", \"255,255,51\", \"255,255,102\", \"255,255,153\", \"255,255,204\"]\n_pink_gradient = [\"229,0,174\", \"234,38,190\", \"239,77,206\", \"244,116,222\", \"246,135,230\", \"254,194,254\"]\n_cyan_gradient = [\"0,186,229\", \"38,199,234\", \"58,205,236\", \"116,225,244\", \"135,231,246\", \"174,244,251\"]\n","type":"text"}]}

{"content":[{"text":"#  Copyright (c) 2014-2019, Centre for Genomic Regulation (CRG).\n#  Copyright (c) 2014-2019, Jose Espinosa-Carrasco and the respective authors.\n#\n#  This file is part of Pergola.\n#\n#  Pergola is free software: you can redistribute it and/or modify\n#  it under the terms of the GNU General Public License as published by\n#  the Free Software Foundation, either version 3 of the License, or\n#  (at your option) any later version.\n#\n#  Pergola is distributed in the hope that it will be useful,\n#  but WITHOUT ANY WARRANTY; without even the implied warranty of\n#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\n#  GNU General Public License for more details.\n#\n#  You should have received a copy of the GNU General Public License\n#  along with Pergola.  If not, see <http://www.gnu.org/licenses/>.\n\n\"\"\"\n=========================\nModule: pergola.parsers\n=========================\n\n.. module:: parsers\n\nThis module provides the way to read scripts options provided by pergola library.\n\n\n\"\"\"\nfrom __future__ import print_function\nfrom __future__ import absolute_import\n\nfrom ._version  import __version__\nfrom sys       import stderr\nfrom argparse  import ArgumentParser, ArgumentTypeError\nfrom re        import match\nfrom os.path   import abspath, split, realpath\nfrom .mapping   import check_path\n\n_csv_file_ext = \".csv\"\n\n_dt_act_options = ['all', 'one_per_channel']\n_tr_act_options = ['split_all', 'join_all', 'join_odd', 'join_even']\n_starting_phase_options = ['light', 'dark']\n\nPATH = abspath(split(realpath(__file__))[0])\n\n\ndef parse_num_range(string):\n    \"\"\" \n    This function generate a numeric range from a string containing the boundaries\n    From 1-4 generates a string  \n    \n    :param tracks: :py:func:`set` of tracks to which track_action should be applied set([1,2])\n    :param delimiter: :py:func:`str` option to join tracks (join_all, split_all, join_odd, join_evens)\n            \n    :return: :py:func:`set` with all the numbers in range as strings\n    \n    \"\"\"\n    \n    m = match(r'(\\d+)(?:-(\\d+))?$', string)\n\n    if not m:\n        raise ArgumentTypeError(\"'\" + string + \"' is not a range of number. Expected '0-5' or '2'.\")\n    start = m.group(1)\n    end = m.group(2) or start\n    list_range=list(range(int(start,10), int(end,10)+1))\n    set_range=set(['{0}'.format(t) for t in list_range]) #str because track can be set in the form of track_1 for instance\n    \n    return set_range\n\n\ndef read_track_actions (tracks, track_action = \"split_all\"):\n    \"\"\" \n    Read track actions and returns a set with the tracks to be joined\n    \n    :param tracks: :py:func:`set` of tracks to which track_action should be applied set([1,2])\n    :param track_action: :py:func:`str` option to join tracks (join_all, split_all, join_odd, join_evens)\n    \n    :return: :py:func:`set` of tracks to be joined\n     \n    \"\"\"\n    \n    if track_action not in _tr_act_options:\n        raise ValueError(\"Track_action \\'%s\\' not allowed. Possible values are %s\"%(track_action,', '.join(['{}'.format(m) for m in _tr_act_options])))\n    \n    tracks2merge = \"\"\n    \n    if track_action == \"join_all\":\n        tracks2merge = tracks\n    elif track_action == 'join_odd':\n        tracks2merge = set([t for t in tracks if int(t) % 2])\n    elif track_action == 'join_even':\n        tracks2merge = set([t for t in tracks if not int(t) % 2])\n    else:\n        tracks2merge = \"\"\n        \n    print(\"Tracks to merge are: \", \",\".join(\"'{0}'\".format(t) for t in tracks2merge), file=stderr)\n       \n    if not tracks2merge:\n        print((\"No track action applied as track actions \\'%s\\' can not be applied to list of tracks provided \\'%s\\'\"%(track_action, \" \".join(tracks))), file=stderr)\n        \n    return (tracks2merge)\n\n\ndef read_colors (path_color_file):\n    \"\"\"     \n    Reads user colors for each data_type  \n    \n    :param None path_color_file: :py:func:`str` path to read user color for data_types     \n       \n    :returns: d_user_color dictionary {'data_type_1': 'orange', 'data_type_2':'blue'}\n    \n    \"\"\"\n\n    check_path(path_color_file)\n    comment_tag_t = \"#\"    \n    d_user_color = {}                            \n    \n    with open(path_color_file) as f:    \n       \n       for row in f:\n           \n           if(row.startswith(comment_tag_t) or row.startswith('\\n')):               \n                continue\n                       \n           row_split = row.rstrip('\\n').split('\\t') \n           (data_type, color) = row_split\n           \n           # colors are checked inside tracks.assign_color\n           d_user_color[data_type] = color\n    \n    return d_user_color\n\n\"\"\"\"   \nParsers arguments of pergola_rules.py script (aka pergola)\n\n\"\"\"\n\nparent_parser = ArgumentParser(description = 'Script to transform behavioral data into GB readable data', add_help=False)\n","type":"text"}]}

{"content":[{"text":"393:    def read(self, fields=None, relative_coord=False, intervals=False, int_step=None, fields2rel=None, multiply_t=None,\n394-             **kwargs):\n395-        \"\"\"        \n396-        Reads the data and converts it depending on selected options\n397-        \n398-        :param None fields: :py:func:`list` with data columns to read\n399-        :param False relative_coord: If true all coordinates in start and end are\n400-            make relative to the minimal value\n401-        :param False intervals: if set to true intervals will be inferred from timepoints in\n402-            start\n403-        :param None int_step: :py:func:`int` :param None int_step: :py:func:`int` time step value to create \n404-            the end of intervals\n405-        :param None fields2rel: :py:func:`list` with data columns to make relative\n406-        :param None multiply_t: :py:func:`int` multiplies the values of the field set as start and \n407-            end        \n408-        \n409-        :returns: Track object\n410-        \n411-        TODO: By the moment I make this function as a method of the class eventually I would make this a\n412-        separated function\n413-        Eventually do not change self.data but a list inside read and return the Track object with the modifications\n414-        this way data is always the original one.\n415-        \n416-        \"\"\"\n417-\n418-        _f_rel_mand = \"start\"\n419-        _f_int_end = \"end\"\n420-        _f2rel = [\"start\",\"end\"]\n421-        _f2mult = [\"start\",\"end\"]\n422-        i_time_f = [10000000000000]\n423-\n424-        # If fields is not set then all the data columns are read\n425-        if fields is None:\n426-            fields = self.fieldsG\n427-            indexL = range(len(self.fieldsG))\n428-        else:\n429-            try:\n430-                indexL = [self.fieldsG.index(f) for f in fields]\n431-\n432-            except ValueError:\n433-                raise ValueError(\"Field '%s' not in file %s.\" % (f, self.path))\n434-\n435-        # If start not present out     \n436-        try:\n437-            idx_fields2int = self.fieldsG_dict[_f_rel_mand]\n438-        except ValueError:\n439-            raise ValueError(\"Parameter intervals=True needs that field '%s' is not missing in file %s.\"\n440-                             % (_f_rel_mand, self.path))\n441-\n442-        ##################################\n443-        # If there are several tracks we order by track\n444-        # Control for interval change bw tracks        \n445-        _f_track = \"track\"\n446-        i_track = None\n447-\n448-        if _f_track in self.fieldsG_dict:\n449-            i_track = self.fieldsG_dict[_f_track]\n450-\n451-            if all(row[i_track].isdigit() for row in self.data):\n452-                self.data = sorted(self.data, key=lambda x: (int(x[i_track]), x[idx_fields2int]))\n453-            else:\n","type":"text"}]}

cd /sandbox/repo && python3 -m venv .venv && . .venv/bin/activate && pip install -q --upgrade pip 2>&1 | tail -2 && timeout 600 pip install -q pergola 2>&1 | tail -20; python -c "import pergola, pybedtools, numpy, scipy; print('ok', pergola.__file__)"

{"content":[{"text":"Traceback (most recent call last):\n  File \"<string>\", line 1, in <module>\nModuleNotFoundError: No module named 'pybedtools'\n\n\nCommand exited with code 1","type":"text"}],"details":{}}

cd /sandbox/repo && . .venv/bin/activate && pip list 2>/dev/null | head -30 && timeout 600 pip install -q pybedtools 2>&1 | tail -5; python -c "
import pybedtools, pergola
from pergola import intervals
print('pergola import ok')
"

{"content":[{"text":"parent_parser = ArgumentParser(description = 'Script to transform behavioral data into GB readable data', add_help=False)\n\nparent_parser.add_argument('-i', '--input', required=True, metavar=\"PATH\", nargs='+', help='Input file path')\nparent_parser.add_argument('-m', '--mapping_file', required=True, metavar=\"MAPPING_FILE\",\n                    help='File to set the reciprocity between fields in behavioral file and terms used by Pergola' + \\\n                    ' and genome browser grammar')\nparent_parser.add_argument('-t', '--tracks', required=False, metavar=\"TRACKS\", type=int, nargs='+', \n                    help='List of selected tracks')\nparent_parser.add_argument('-l','--list', required=False, metavar=\"LIST_OF_TRACKS\", type=str, nargs='+',\n                           help='Numeric list of tracks to be joined in a single genomic like file')### string allowed as some tracks could be named as: track_1, track2....\nparent_parser.add_argument('-r', '--range', required=False, type=parse_num_range,\n                           help='Numeric range of tracks to be joined in a single genomic like file')\nparent_parser.add_argument('-a', '-ta', '--track_actions', required=False, choices=_tr_act_options,\n                           help='Option of action with tracks selected, split_all, join_all,' + \\\n                           ' join_odd, join_even, join_range or join_list')\nparent_parser.add_argument('-dl', '--data_types_list', required=False, metavar=\"LIST_OF_DATA_TYPES\", type=str, nargs='+',\n                           help='List of data_types to be joined')\nparent_parser.add_argument('-d', '--data_types_actions', required=False, choices=_dt_act_options,\n                           help='Unique values of data_types field should be dumped on' + \\\n                           ' different data structures or not')\nparent_parser.add_argument('-f', '--format', required=False, type=str, default='bed',\n                           help='Write file output format (bed or bedGraph)')\nparent_parser.add_argument('-e', '-rel', '--relative_coord', required=False, action='store_true',\n                           default=False, help='Sets first timepoint' \\\n                           ' to 0 and make all the others relative to this timepoint')\nparent_parser.add_argument('-n', '-int', '--intervals_gen', required=False, action='store_true',\n                           default=None, help='Set startChrom and endChrom from just a timepoint in the file ' \\\n                           'using field set as startChrom')\nparent_parser.add_argument('-ns', '-int_s', '--interval_step', required=False, metavar=\"INTERVAL_STEP\", type=int,\n                           default=False, help='Set step to generate intervals from a single time point')\nparent_parser.add_argument('-mi', '--multiply_intervals', metavar='N', type=int, required=False,\n                           help='Multiplies value in data_value by the given factor')\nparent_parser.add_argument('-nh', '--no_header', required=False, action='store_true', \n                           default=False, help='Data file contains no header')\nparent_parser.add_argument('-s', '-fr', '--fields_read', metavar='FIELDS2READ', type=str, nargs='+',\n                           help='List of fields to read from input file')\nparent_parser.add_argument('-w', '--window_size', required=False, metavar=\"WINDOW_SIZE\", type=int, \n                           help='Window size for bedGraph intervals, default value 300')\nparent_parser.add_argument('-nt', '--no_track_line', required=False, action='store_true',\n                           default=False, help='Track line no included in the bed file')\nparent_parser.add_argument('-fs', '--field_separator', required=False, type=str,\n                           default=False, help='Input file field separator')\nparent_parser.add_argument('-bl', '--bed_label', required=False, action='store_true',\n                           default=False, help='Show data_types as name field in bed file')\nparent_parser.add_argument('-c', '--color_file', required=False, metavar=\"PATH_COLOR_FILE\", \n                           help='Dictionary assigning colors of data_types path')\nparent_parser.add_argument('-wm', '--window_mean', required=False, action='store_true',\n                           default=False, help='Window values averaged by the window size')\nparent_parser.add_argument('-vm', '--value_mean', required=False, action='store_true',\n                           help='Window values averaged by number of items within window')\nparent_parser.add_argument('-min', '--min_time', type=int, required=False,\n                           help='Initial time point to extract')\nparent_parser.add_argument('-max', '--max_time', type=int, required=False,\n                           help='Last time point to extract')\nparent_parser.add_argument('-ng', '--no_genome', required=False, dest='genome', action='store_false',\n                           help='Avoinds the creation of a FASTA file which allows to render a longitudinal trajectory' \\\n                           ' in a genome browser')\nparent_parser.add_argument('-np', '--no_phases', required=False, dest='phases', action='store_false',\n                           help='Avoids the creation of a phases bed file')\nparent_parser.set_defaults(genome=True)\nparent_parser.set_defaults(phases=True)\nparent_parser.add_argument('-o', '--output_file_name', help='File name for output files')\nparent_parser.add_argument('-sp', '--starting_phase', type=str, required=False, choices=_starting_phase_options,\n                           help='Sets the first phase to appear in the phases and cytoband file: light or dark\\n')\nparent_parser.add_argument('-sh', '--shift', required=False, metavar=\"TIME_SHIFT\", type=int,\n                           help='Time shift to be set for the first phase')\nparent_parser.add_argument('-v', '--version', action='version', version='%(prog)s {version}'.format(version=__version__))\n\n\"\"\"\"   \nParsers argument of jaaba_to_pergola.py script\n\n\"\"\"\n\njaaba_parser = ArgumentParser(description = 'Script to transform Jaaba annotations into Pergola readable formats', \n                              add_help=False)\njaaba_parser.add_argument('-v', '--version', action='version', version='%(prog)s {version}'.format(version=__version__))\n\nsubparsers = jaaba_parser.add_subparsers(help='Calls pergola_rules.py', dest='command')\njaaba_parser_sp = subparsers.add_parser('sp', help=\"Converts Jaaba data and process it using pergola\", parents=[parent_parser])\njaaba_parser_sc = subparsers.add_parser('sc', add_help='Converts scores Jaaba files into csv files')\njaaba_parser_fp = subparsers.add_parser('fp', add_help='Converts Jaaba features using pergola', parents=[parent_parser])\njaaba_parser_fc = subparsers.add_parser('fc', add_help='Converts Jaaba features into csv files')\n\njaaba_parser_sc.add_argument('-i', '--input', required=True, metavar=\"PATH\", help='Input file path')\n\njaaba_parser_fc.add_argument('-i', '--input', required=True, metavar=\"PATH\", help='Path to jaaba features')\njaaba_parser_fc.add_argument('-jf', '--feature', required=True, metavar=\"LIST_OF_FEATURES\", type=str, nargs='+',\n                            help='List of features to be extracted, e.g. velmag')\njaaba_parser_fc.add_argument('-dd', '--dumping_dir', required=False, metavar=\"DUMPING_DIR\", help='Input file path')\n# jaaba_parser_fp.add_argument('-i', '--input_jaaba_dir', required=True, metavar=\"PATH\", help='Input file path')\n# jaaba_parser_fp.add_argument('-jd', '--jaaba_dir', required=True, metavar=\"PATH\", help='Path to jaaba features')\njaaba_parser_fp.add_argument('-jf', '--feature', required=True, metavar=\"LIST_OF_FEATURES\", type=str, nargs='+',\n                            help='List of features to be extracted, e.g. velmag')\njaaba_parser_fp.add_argument('-dd', '--dumping_dir', required=False, metavar=\"DUMPING_DIR\", help='Input file path')\n","type":"text"}]}

{"content":[{"text":"7:#  it under the terms of the GNU General Public License as published by\n47:_p_ontology_terms = [\"start\", \"data_value\", \"end\", \"data_types\", \"track\", \"chrom\", \"dummy\"]\n68:    def __init__(self, path, **kwargs):\n72:    def _correspondence_from_config(self, path):\n101:    def _tab_config(self, file_tab):\n121:            file_term = row_split[0]\n122:            pergola_term = row_split[1]\n124:            # Validation of the ontology term\n125:            if pergola_term not in _p_ontology_terms:\n126:                raise ValueError(\"Term %s is not a valid pergola term.\" % (pergola_term))\n128:            if pergola_term == \"dummy\": \n129:                    pergola_term = pergola_term + \"_\" + str(dummy_ctr)\n132:            dict_correspondence[file_term] = pergola_term\n136:    def _mapping_config(self, file_map):\n148:        mapping_l_ex = \"tag_file:field_input_file > pergola:pergola_ontology_term\"\n160:                file_term = l[0].split(\":\")[1].rstrip()\n161:                pergola_term = l[1].split(\":\")[1].rstrip('\\t\\n\\r')\n163:                # Validation of the ontology term\n164:                if pergola_term not in _p_ontology_terms:\n165:                    raise ValueError(\"Term %s is not a valid pergola term.\" % (pergola_term))\n167:                if pergola_term == \"dummy\": \n168:                    pergola_term = pergola_term + \"_\" + str(dummy_ctr)\n171:                dict_correspondence[file_term] = pergola_term\n182:    def write(self, indent=0):\n184:        Writes correspondence between the pergola ontology terms and the behavioral data \n199:def check_path(path):\n219:def write_chr(self, mode=\"w\", path_w=None, min_c=None, max_c=None):\n256:def write_chr_sizes(self, mode=\"w\", path_w=None, file_n=None, min_c=None, max_c=None):\n302:def write_cytoband(end, start=0, delta=43200, start_phase=\"light\", mode=\"w\", path_w=None, lab_bed=True, track_line=True):\n426:def write_period_seq (end, start=0, delta=43200, tag=\"day\", mode=\"w\", path_w=None, name_file=\"period_seq\", lab_bed=True, track_line=True):\n","type":"text"}]}

{"content":[{"text":"    \n    .. attribute::  correspondence \n       Dictionary with keys fields in behavioral file and values correspondence in genomic grammar\n    \n    :returns: MappingInfo object\n    \n    \"\"\"\n    \n    def __init__(self, path, **kwargs):\n        self.path = check_path(path)\n        self.correspondence = self._correspondence_from_config(self.path)\n\n    def _correspondence_from_config(self, path):\n        \"\"\"\n        Recognizes the type of mapping file tab separated or the External Mapping File Format\n        from the Gene Ontology Consortium. Deletes comments        \n\n        :param path: :py:func:`str` path to the mapping file aka configuration file\n\n        :returns: dictionary with mappings\n\n        \"\"\"\n\n        with open(path) as config_file:\n            # Eliminates possible empty lines at the end\n            config_file_list = list(filter(lambda x:  not match(r'^\\s*$', x), config_file))\n            \n            file_list_no_comments = [l for l in config_file_list if l[0] != \"!\" if l[0] != \"#\"]\n\n            for i, line in enumerate(file_list_no_comments):\n                if not match(r\"^\\w+\\:[\\\"\\w\\\"]|[\\w]+\\s\\>\\s\\w+\\:\\w+] \", line) and not match(r\"(\\w+)\\s+(\\w+)\", line):\n                    raise TypeError(\"Mapping file format is not recognized: \\\"%s\\\".\" % (path))\n\n            # Checks that files is a tsv and has the desired number of fields\n            if match(r\"^\\w+\\:[\\\"\\w\\\"]|[\\w]+\\s\\>\\s\\w+\\:\\w+] \", file_list_no_comments[0]):\n                return self._mapping_config(file_list_no_comments)\n            elif match(r\"(\\w+)\\s+(\\w+)\", file_list_no_comments[0]):\n                return self._tab_config(file_list_no_comments)\n            else:\n                raise TypeError(\"Mapping file format is not recognized: \\\"%s\\\".\" % (path))\n\n    def _tab_config(self, file_tab):\n        \"\"\"\n        Reads mappings from a tab separated files        \n       \n        :param file_tab: :py:func:`list` with the content of mapping file \n        \n        :returns: dictionary with mappings\n\n        \"\"\"\n\n        dict_correspondence = {}\n        comment_tag_t = \"#\"\n        \n        dummy_ctr=0\n        \n        for row in file_tab:\n            if row.startswith(comment_tag_t):\n                continue\n            row_split = split(r'\\s+', row.rstrip('\\n'))\n\n            file_term = row_split[0]\n            pergola_term = row_split[1]\n            \n            # Validation of the ontology term\n            if pergola_term not in _p_ontology_terms:\n                raise ValueError(\"Term %s is not a valid pergola term.\" % (pergola_term))\n            \n            if pergola_term == \"dummy\": \n                    pergola_term = pergola_term + \"_\" + str(dummy_ctr)\n                    dummy_ctr = dummy_ctr + 1\n            \n            dict_correspondence[file_term] = pergola_term\n\n        return (dict_correspondence)    \n\n    def _mapping_config(self, file_map):\n        \"\"\"\n        Reads mappings from a file formatted following the External Mapping File Format\n        from the Gene Ontology Consortium      \n\n","type":"text"}]}

{"content":[{"text":"37:def main(args=None):\n38-    parser_pergola_rules = ArgumentParser(parents=[parsers.parent_parser]) \n39-    \n40-    args = parser_pergola_rules.parse_args()\n41-\n42-    multiple_files = False\n43-\n44-    if len(args.input) > 1:\n45-        print(\"@@@Pergola_rules.py: Multiple input files processed\")\n46-        multiple_files = True\n47-\n48-    for idx, input_file in enumerate(args.input):\n49-\n50-        if multiple_files:\n51-            if args.output_file_name is None:\n52-                output_file_n = splitext(basename(input_file))[0]\n53-            else:\n54-                output_file_n = args.output_file_name + \"_\" + str(idx + 1)\n55-        else:\n56-            output_file_n = args.output_file_name\n57-\n58-        pergola_rules(path=input_file, map_file_path=args.mapping_file, sel_tracks=args.tracks,\n59-                      list=args.list, range=args.range, track_actions=args.track_actions,\n60-                      data_types_actions=args.data_types_actions, data_types_list=args.data_types_list,\n61-                      write_format=args.format, relative_coord=args.relative_coord,\n62-                      intervals_gen=args.intervals_gen, interval_step=args.interval_step,\n63-                      multiply_f=args.multiply_intervals, no_header=args.no_header, fields2read=args.fields_read,\n64-                      window_size=args.window_size, no_track_line=args.no_track_line, separator=args.field_separator,\n65-                      bed_lab_sw=args.bed_label, color_dict=args.color_file, window_mean=args.window_mean,\n66-                      value_mean=args.value_mean, min_t=args.min_time, max_t=args.max_time, phases=args.phases,\n67-                      genome=args.genome, output_file_name=output_file_n, starting_phase=args.starting_phase,\n68-                      shift=args.shift)\n69-\n70-def pergola_rules(path, map_file_path, sel_tracks=None, list=None, range=None, track_actions=None, \n71-                  data_types_actions=None, data_types_list=None, write_format=None, relative_coord=False,\n72-                  intervals_gen=False, multiply_f=None, no_header=False, fields2read=None, window_size=None,\n73-                  no_track_line=False, separator=None, bed_lab_sw=False, color_dict=None, window_mean=False,\n74-                  value_mean=False, min_t=None, max_t=None, interval_step=None, phases=False, genome=False,\n75-                  output_file_name=None, starting_phase=False, shift=None):\n76-    \n77-    print(\"@@@Pergola_rules.py: Input file: %s\" % path, file=stderr) \n78-    print(\"@@@Pergola_rules.py: Configuration file: %s\" % map_file_path, file=stderr)\n79-    \n80-    # Tracks selected by user\n81-    print(\"@@@Pergola_rules.py: Selected tracks are: \", sel_tracks, file=stderr)\n82-    \n83-    # Configuration file\n84-    map_file_dict = mapping.MappingInfo(map_file_path)\n85-    \n86-    # Reading color dictionary to set data_types\n87-    if color_dict:\n88-        print(\"@@@Pergola_rules.py: Color for data_types in file............ %s\" % color_dict, file=stderr)\n89-        d_colors_data_types = parsers.read_colors (color_dict)\n90-    else:\n91-        d_colors_data_types = None    \n92-        \n93-    # Handling list or range of tracks to join if set\n94-    if list and range:\n95-        raise ValueError(\"@@@Pergola_rules.py: Argument -l/--list and -r/--range are not compatible. \" \\\n96-                         \"As both arguments set tracks to be joined.\")    \n97-    elif (list):\n98-        tracks2merge = list\n99-    elif (range):\n100-        tracks2merge = range\n101-    else:\n102-        tracks2merge = \"\"\n103-    \n104-    if tracks2merge: print(\"@@@Pergola_rules.py: Tracks to join are............ \", tracks2merge, file=stderr)\n105-    \n106-    # Handling argument track actions\n107-    if tracks2merge and track_actions:\n108-        raise ValueError (\"Options --list -l or --range -r are incompatible with \" \\\n109-                          \"--track_actions -a, please change your options\")\n110-    \n111-    track_act = track_actions\n112-    print(\"@@@Pergola_rules.py: Track actions are.............................. \", track_act, file=stderr)\n113-    \n114-    data_types_list = data_types_list\n115-    print(\"@@@Pergola_rules.py: data_types list is: \", data_types_list, file=stderr)\n116-      \n117-    # Handling argument data_types actions\n","type":"text"}]}

cd /sandbox/repo && mkdir -p data config examples out && python - <<'EOF'
import csv, random
random.seed(7)
behaviors = ["feeding", "resting", "grooming", "walking"]
rows = [("timepoint","behavior","track")]
t = 0
for track in (1,2):
    t = 0
    while t < 60:
        dur = random.randint(1,4)
        rows.append((t, random.choice(behaviors), track))
        t += dur
with open("data/mouse_feeding.csv","w",newline="") as f:
    csv.writer(f).writerows(rows)
EOF
cat > config/mapping.tsv <<'EOF'
# behavioral_file_field   pergola_ontology_term
timepoint	start
behavior	data_types
track	track
EOF
head -6 data/mouse_feeding.csv; wc -l data/mouse_feeding.csv

{"content":[{"text":"timepoint,behavior,track\r\n0,resting,1\r\n3,feeding,1\r\n7,feeding,1\r\n8,feeding,1\r\n11,feeding,1\r\n50 data/mouse_feeding.csv\n","type":"text"}]}

{"content":[{"text":"41:class IntData(object):\n42-    \"\"\"\n43-    Generic class for input data\n44-    \n45-    .. attribute:: path\n46-    \n47-       Name of path to a csv/tab or xlsx (excel) input file\n48-    \n49-    .. attribute:: delimiter\n50-    \n51-       Character use to separate values of the same record in file (default \"\\t\").\n52-    \n53-    .. attribute:: header\n54-    \n55-       Indicates the presence of a header.\n56-       * `False` if there is no header. Fields should the be provided using fields param\n57-       * `True` if the file have a header line with names. This names should match names in map_dict (default).\n58-    \n59-    .. attribute:: fieldsB\n60-    \n61-        List with the behavioral fields corresponding each column in the file\n62-    \n63-    .. attribute:: fieldsG_dict\n64-    \n65-        A dictionary with the equivalence to map fields in the input file and the pergola\n66-        ontology to describe behavioral data    \n67-    \n68-    .. attribute:: min\n69-    \n70-        First time value in the file. Read from field set as \"start\"\n71-    \n72-    .. attribute:: max\n73-    \n74-        Last timepoint in the file. Read from field set as \"end\"\n75-    \n76-    .. attribute:: range_values\n77-    \n78-        Range of values inside data_value field\n79-        \n80-    .. attribute:: data\n81-    \n82-        List of tuples containing the data read from the file\n83-    \n84-    .. attribute:: data_types\n85-    \n86-        All different data_types that appear in the data read from \"data_types\" field.\n87-        If data_types field not in file, all intervals are set as belonging to data_types \"a\"\n88-\n89-    .. attribute:: tracks\n90-    \n91-        Set of tracks in the file. Read from \"tracks\" field.\n92-        If tracks field not in file, all intervals are set as belonging to track \"1\" \n93-        \n94-    :returns: IntData object\n95-    \n96-    \"\"\"\n97-\n98-    def __init__(self, path, map_dict, header=True, **kwargs):\n99-        self.path = check_path(path)\n100-        self._in_file = open(self.path, \"r\")\n101-        self.delimiter = self._check_delimiter(self.path, kwargs.get('delimiter', \"\\t\"))\n","type":"text"}]}

{"content":[{"text":"pergola/mapping.py:182:    def write(self, indent=0):\npergola/mapping.py:219:def write_chr(self, mode=\"w\", path_w=None, min_c=None, max_c=None):\npergola/mapping.py:256:def write_chr_sizes(self, mode=\"w\", path_w=None, file_n=None, min_c=None, max_c=None):\npergola/mapping.py:302:def write_cytoband(end, start=0, delta=43200, start_phase=\"light\", mode=\"w\", path_w=None, lab_bed=True, track_line=True):\npergola/mapping.py:426:def write_period_seq (end, start=0, delta=43200, tag=\"day\", mode=\"w\", path_w=None, name_file=\"period_seq\", lab_bed=True, track_line=True):\npergola/tracks.py:158:    def save_track(self, mode=\"w\", path=None, name_file=None, track_line=True, bed_label=False, gff_label=False):\npergola/tracks.py:625:    def track_convert2bed(self, track, in_call=False, **kwargs):\npergola/tracks.py:698:    def track_convert2gff(self, track, in_call=False, **kwargs):\npergola/tracks.py:808:    def track_convert2bedGraph(self, track, in_call=False, window=300, mean_win=False, mean_value=False,  **kwargs):\n","type":"text"}]}

{"content":[{"text":"    # Handling argument data_types actions\n    data_types_act = data_types_actions\n    print(\"@@@Pergola_rules.py: data_types actions are......................... \", data_types_act, file=stderr)\n    \n    # Handling argument format    \n    if write_format:\n        print(\"@@@Pergola_rules.py format to write files....................... \", write_format, file=stderr)\n    else:\n        write_format = 'bed'\n        print(\"@@@Pergola_rules.py format to write files has been set\" \\\n                        \" to default value:\", write_format, file=stderr)\n\n    # Handling relative coordinates\n    print(\"@@@Pergola_rules.py: Relative coordinates set to................. %s\" % relative_coord, file=stderr)\n    \n    # Handling intervals_gen\n    print(\"@@@Pergola_rules.py: Intervals parameter set to.................. %s\" % intervals_gen, file=stderr)\n\n    # Handling interval_step\n    if interval_step:\n        if intervals_gen:\n            print(\"@@@Pergola_rules.py: Interval step set to........................ %s\" % interval_step, file=stderr)\n        else:\n            raise ValueError(\"Interval step needs intervals paramater to be set -n/--intervals_gen\")\n\n    # Handling multiply_intervals\n    if multiply_f:\n        print(\"@@@Pergola_rules.py: Multiply intervals parameter set to...... %s\" % multiply_f, file=stderr)                        \n    else:\n        multiply_f = 1\n    \n    print(\"@@@Pergola_rules.py: Selected tracks are......................... \", sel_tracks, file=stderr)\n    \n    # Setting whether input file has header or not\n    header_sw = True\n    \n    if no_header:\n        header_sw = False\n        print(\"@@@Pergola_rules.py: Data file has header set to............. \", header_sw, file=stderr)\n\n    # Handling fields to read\n    if fields2read:\n        print(\"@@@Pergola_rules.py: Fields to read from the file are......... %s\" % fields2read, file=stderr)                        \n    else:\n        fields2read = None    \n    \n    # When binning data setting the window of time used in seconds\n    # if not size provided set to False\n    if window_size:\n        print(\"@@@Pergola_rules.py: Window size set to....................... %d\" % window_size, file=stderr)\n    else:\n#         window_size = 300\n        window_size = False\n        print(\"@@@Pergola_rules.py: Window size set by default to............ %d\" % window_size, file=stderr)\n    \n    if window_mean:\n        print(\"@@@Pergola_rules.py: Window mean set to....................... %d\" % window_mean, file=stderr)\n    else:      \n        window_mean = False\n\n    if value_mean:\n        print(\"@@@Pergola_rules.py: Value mean set to....................... %d\" % value_mean, file=stderr)\n    else:\n        value_mean = False\n\n    if no_track_line:\n        track_line=False\n    else:\n        track_line=True\n        \n    print(\"@@@Pergola_rules.py: track_line set to............................ %s\" % track_line, file=stderr)\n    \n    # Handling input file field delimiter    \n    if not separator:\n        separator = \"\\t\"\n        print(\"@@@Pergola_rules.py input file field separator set by default to...... \\\"\\\\t\\\".\", file=stderr)\n    else:        \n        print(\"@@@Pergola_rules.py input file field separator set to..... \\\"%s\\\"\" % separator, file=stderr)\n    \n    if bed_lab_sw:\n        bed_lab = True\n        print(\"@@@Pergola_rules.py: bed_label set to......................... %s\" % bed_lab, file=stderr)\n    else:\n        bed_lab = False\n\n    intData = intervals.IntData(path, map_dict=map_file_dict.correspondence,\n                                fields_names=fields2read,\n                                header=header_sw, delimiter=separator)\n\n    start = intData.min\n    end = intData.max\n\n    if relative_coord:\n        start = 0\n        end = intData.max - intData.min\n\n    print(\"@@@Pergola_rules.py: min time in trajectory......................... %d\" % start, file=stderr)\n    print(\"@@@Pergola_rules.py: max time in trajectory......................... %d\" % end, file=stderr)\n\n    if min_t or min_t == 0:\n        min_time = min_t\n        print(\"@@@Pergola_rules.py: min_time set by user to.............. %d\" % min_t, file=stderr)\n    else:\n        min_time = start\n\n    if max_t:\n        max_time = max_t\n        print(\"@@@Pergola_rules.py: max_time set by user to............... %d\" % max_t, file=stderr)\n    else:\n        if interval_step:\n            max_time = end + interval_step\n        else:\n            max_time = end + 1\n\n    # Phases option\n    print(\"@@@Pergola_rules.py: Phases file set to............................%s\" % phases, file=stderr)\n\n    # Genome option\n    print(\"@@@Pergola_rules.py: Genome option set to..........................%s\" % genome, file=stderr)\n\n    # Output file name\n    print(\"@@@Pergola_rules.py: Output file/s name set t......................%s\" % output_file_name, file=stderr)\n\n    # Starting phase option\n    if starting_phase:\n        if phases:\n            print(\"@@@Pergola_rules.py: Starting phase set to.............. %s\" % starting_phase, file=stderr)\n        else:\n            raise ValueError(\"Starting phase needs phases option to be set to true\")\n    else:\n        starting_phase = \"light\"\n    if shift:\n        time_shift = shift\n        print(\"@@@Pergola_rules.py: Time shift set to....................... %d\" % shift, file=stderr)\n    else:\n        #         window_size = 300\n        time_shift = 0\n        print(\"@@@Pergola_rules.py: Window size set by default to............ %d\" % window_size, file=stderr)\n\n    if multiply_f:\n        min_time = min_time * multiply_f\n        max_time = max_time * multiply_f\n\n    if track_act: tracks2merge = parsers.read_track_actions(tracks=intData.tracks, track_action=track_act)\n","type":"text"}]}

cd /sandbox/repo/out && ../.venv/bin/pergola -i ../data/mouse_feeding.csv -m ../config/mapping.tsv -n -ns 1 -f bed -bl -o mouse_feeding 2>&1 | tail -5; ls -la; echo "--- bed ---"; head -8 *.bed 2>/dev/null

{"content":[{"text":"                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n  File \"/sandbox/repo/.venv/lib/python3.12/site-packages/pergola/intervals.py\", line 139, in _check_delimiter\n    else: raise ValueError(\"Input delimiter does not correspond to delimiter found in file \\'%s\\'\"%(delimiter))\n          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\nValueError: Input delimiter does not correspond to delimiter found in file '\t'\ntotal 8\ndrwx------ 2 root root 4096 Sep 25 12:35 .\ndrwxr-xr-x 8 root root 4096 Sep 25 12:35 ..\n--- bed ---\n\n\nCommand exited with code 1","type":"text"}],"details":{}}

cd /sandbox/repo/out && ../.venv/bin/pergola -i ../data/mouse_feeding.csv -m ../config/mapping.tsv -n -ns 1 -f bed -bl -fs , -o mouse_feeding 2>&1 | grep -v "@@@" | tail -8; ls; echo "--- bed ---"; head -6 *.bed; echo "--- cytoband ---"; head -3 *cytoband* 2>/dev/null; echo "--- fasta ---"; head -c 200 *.fa* 2>/dev/null

{"content":[{"text":"  File \"/sandbox/repo/.venv/lib/python3.12/site-packages/pergola/intervals.py\", line 105, in __init__\n    self.fieldsG_dict = self._set_fields_g(map_dict)\n                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n  File \"/sandbox/repo/.venv/lib/python3.12/site-packages/pergola/intervals.py\", line 301, in _set_fields_g\n    raise ValueError(\"Input file mandatory fields  are \\\"start\\\" and \\\"data_value\\\" \\n\" \\\nValueError: Input file mandatory fields  are \"start\" and \"data_value\" \nYour current assigned fields are \"start\",\"data_types\",\"track\"\nTIP: Check your ontology_file\n--- bed ---\nhead: cannot open '*.bed' for reading: No such file or directory\n--- cytoband ---\n--- fasta ---\n\n\nCommand exited with code 1","type":"text"}],"details":{}}

cd /sandbox/repo && python - <<'EOF'
import csv, random
random.seed(7)
behaviors = ["feeding", "resting", "grooming", "walking"]
rows = [("timepoint","behavior","intensity","track")]
for track in (1,2):
    t = 0
    while t < 60:
        b = random.choice(behaviors)
        intensity = random.randint(1,9) if b in ("feeding","walking") else random.randint(0,3)
        rows.append((t, b, intensity, track))
        t += random.randint(1,4)
with open("data/mouse_feeding.csv","w",newline="") as f:
    csv.writer(f).writerows(rows)
EOF
cat > config/mapping.tsv <<'EOF'
# behavioral_file_field   pergola_ontology_term
timepoint	start
intensity	data_value
behavior	data_types
track	track
EOF
head -5 data/mouse_feeding.csv
cd out && ../.venv/bin/pergola -i ../data/mouse_feeding.csv -m ../config/mapping.tsv -n -ns 1 -f bed -bl -fs , -o mouse_feeding 2>&1 | grep -v "@@@" | tail -6; ls; echo "--- bed ---"; head -6 *.bed

{"content":[{"text":"timepoint,behavior,intensity,track\r\n0,grooming,1,1\r\n4,feeding,2,1\r\n5,grooming,0,1\r\n7,feeding,2,1\r\nNo path selected, files dump into path:  /sandbox/repo/out\nFile mouse_feeding.2_grooming.bed generated\nNo path selected, files dump into path:  /sandbox/repo/out\nFile mouse_feeding.2_resting.bed generated\nNo path selected, files dump into path:  /sandbox/repo/out\nFile mouse_feeding.2_walking.bed generated\nchr1.fa\nchrom.sizes\ncytoband_file.txt\nmouse_feeding.1_feeding.bed\nmouse_feeding.1_grooming.bed\nmouse_feeding.1_resting.bed\nmouse_feeding.1_walking.bed\nmouse_feeding.2_feeding.bed\nmouse_feeding.2_grooming.bed\nmouse_feeding.2_resting.bed\nmouse_feeding.2_walking.bed\nphases_dark.bed\nphases_light.bed\n--- bed ---\n==> mouse_feeding.1_feeding.bed <==\ntrack name=\"1_feeding\" description=\"1 feeding\" visibility=2 itemRgb=\"On\" priority=20\nchr1\t4\t5\tfeeding\t2\t+\t4\t5\t254,96,101\nchr1\t7\t8\tfeeding\t2\t+\t7\t8\t254,96,101\nchr1\t13\t14\tfeeding\t9\t+\t13\t14\t254,57,61\nchr1\t17\t18\tfeeding\t2\t+\t17\t18\t254,96,101\nchr1\t19\t20\tfeeding\t7\t+\t19\t20\t254,57,61\n\n==> mouse_feeding.1_grooming.bed <==\ntrack name=\"1_grooming\" description=\"1 grooming\" visibility=2 itemRgb=\"On\" priority=20\nchr1\t0\t1\tgrooming\t1\t+\t0\t1\t113,113,113\nchr1\t5\t6\tgrooming\t0\t+\t5\t6\t170,170,170\nchr1\t22\t23\tgrooming\t3\t+\t22\t23\t85,85,85\nchr1\t47\t48\tgrooming\t3\t+\t47\t48\t85,85,85\n\n==> mouse_feeding.1_resting.bed <==\ntrack name=\"1_resting\" description=\"1 resting\" visibility=2 itemRgb=\"On\" priority=20\nchr1\t20\t21\tresting\t0\t+\t20\t21\t135,206,250\nchr1\t41\t42\tresting\t1\t+\t41\t42\t65,105,225\nchr1\t54\t55\tresting\t2\t+\t54\t55\t65,105,225\n\n==> mouse_feeding.1_walking.bed <==\ntrack name=\"1_walking\" description=\"1 walking\" visibility=2 itemRgb=\"On\" priority=20\nchr1\t11\t12\twalking\t2\t+\t11\t12\t102,254,102\nchr1\t34\t35\twalking\t6\t+\t34\t35\t51,254,51\nchr1\t38\t39\twalking\t6\t+\t38\t39\t51,254,51\nchr1\t56\t57\twalking\t7\t+\t56\t57\t51,254,51\n\n==> mouse_feeding.2_feeding.bed <==\ntrack name=\"2_feeding\" description=\"2 feeding\" visibility=2 itemRgb=\"On\" priority=20\nchr1\t6\t7\tfeeding\t5\t+\t6\t7\t254,57,61\nchr1\t13\t14\tfeeding\t8\t+\t13\t14\t254,57,61\nchr1\t20\t21\tfeeding\t4\t+\t20\t21\t254,77,81\nchr1\t41\t42\tfeeding\t3\t+\t41\t42\t254,77,81\n\n==> mouse_feeding.2_grooming.bed <==\ntrack name=\"2_grooming\" description=\"2 grooming\" visibility=2 itemRgb=\"On\" priority=20\nchr1\t0\t1\tgrooming\t2\t+\t0\t1\t113,113,113\nchr1\t5\t6\tgrooming\t3\t+\t5\t6\t85,85,85\nchr1\t10\t11\tgrooming\t3\t+\t10\t11\t85,85,85\nchr1\t32\t33\tgrooming\t1\t+\t32\t33\t113,113,113\nchr1\t36\t37\tgrooming\t3\t+\t36\t37\t85,85,85\n\n==> mouse_feeding.2_resting.bed <==\ntrack name=\"2_resting\" description=\"2 resting\" visibility=2 itemRgb=\"On\" priority=20\nchr1\t16\t17\tresting\t0\t+\t16\t17\t135,206,250\nchr1\t23\t24\tresting\t1\t+\t23\t24\t65,105,225\nchr1\t28\t29\tresting\t3\t+\t28\t29\t0,0,255\nchr1\t43\t44\tresting\t1\t+\t43\t44\t65,105,225\n\n==> mouse_feeding.2_walking.bed <==\ntrack name=\"2_walking\" description=\"2 walking\" visibility=2 itemRgb=\"On\" priority=20\nchr1\t4\t5\twalking\t2\t+\t4\t5\t102,254,102\nchr1\t27\t28\twalking\t8\t+\t27\t28\t51,254,51\nchr1\t39\t40\twalking\t4\t+\t39\t40\t76,254,76\nchr1\t44\t45\twalking\t3\t+\t44\t45\t76,254,76\nchr1\t49\t50\twalking\t9\t+\t49\t50\t51,254,51\n\n==> phases_dark.bed <==\ntrack name=\"phases\" description=\"Track annotating phases of the experiment\" visibility=2 color=0,0,255 useScore=1 priority=user\n\n==> phases_light.bed <==\ntrack name=\"phases\" description=\"Track annotating phases of the experiment\" visibility=2 color=0,0,255 useScore=1 priority=user\n","type":"text"}]}

{"content":[{"text":"    if track_act: tracks2merge = parsers.read_track_actions(tracks=intData.tracks, track_action=track_act)\n\n    data_read = intData.read(relative_coord=relative_coord,\n                             intervals=intervals_gen,\n                             multiply_t=multiply_f,\n                             min_time=min_time, max_time=max_time,\n                             int_step=interval_step)\n\n    if genome:\n        # whole trajectory\n        # mapping.write_chr(data_read, min_c=start, max_c=end)\n        # mapping.write_chr_sizes(data_read, min_c=start, max_c=end)\n\n        # using min and max set by user\n        mapping.write_chr(data_read)\n        mapping.write_chr_sizes(data_read)\n\n    if phases:\n        # writes cytoband and light, dark and light_dark bed files\n        mapping.write_cytoband(end=end, start=time_shift, start_phase=starting_phase, track_line=track_line,\n                               lab_bed=bed_lab)\n        # mapping.write_period_seq(start=0, end=intData.max, delta=43200, name_file=\"phases_dark\", track_line=False)\n\n    ## all intervals not save, in should be an option if necessary to save it\n    # data_read.save_track(name_file=\"all_intervals\")\n\n    bed_str = data_read.convert(mode=write_format, tracks=sel_tracks,\n                                tracks_merge=tracks2merge, data_types=data_types_list,\n                                data_types_actions=data_types_act, window=window_size,\n                                mean_win=window_mean, mean_value=value_mean, color_restrictions=d_colors_data_types)\n                                #min_t_trim=min_t, max_t_trim=max_t)\n    \n    for key in bed_str:\n        bedSingle = bed_str[key]\n\n        output_file_n = None\n\n        if output_file_name is not None:\n            output_file_n = output_file_name + '.' + '_'.join(key)\n\n        bedSingle.save_track(name_file=output_file_n, track_line=track_line, bed_label=bed_lab)\n\nif __name__ == '__main__':\n    exit(main())","type":"text"}]}

cd /sandbox/repo && sed -i 's/mouse_feading/mouse_feeding/' examples/behavior_to_bed.py && .venv/bin/python examples/behavior_to_bed.py 2>&1 | tail -20 && ls out/api && head -4 out/api/mouse_feeding.1_feeding.bed

{"content":[{"text":"Files dump into path:  /sandbox/repo/out/api\nFile mouse_feeding.2_feeding.bed generated\nFiles dump into path:  /sandbox/repo/out/api\nFile mouse_feeding.2_grooming.bed generated\nFiles dump into path:  /sandbox/repo/out/api\nFile mouse_feeding.2_resting.bed generated\nFiles dump into path:  /sandbox/repo/out/api\nFile mouse_feeding.2_walking.bed generated\nfield mapping: {'timepoint': 'start', 'intensity': 'data_value', 'behavior': 'data_types', 'track': 'track'}\ntracks: ['1', '2']\nbehaviors: ['feeding', 'grooming', 'resting', 'walking']\ntime range: 0 -> 57\nwrote /sandbox/repo/out/api/mouse_feeding.1_feeding.bed\nwrote /sandbox/repo/out/api/mouse_feeding.1_grooming.bed\nwrote /sandbox/repo/out/api/mouse_feeding.1_resting.bed\nwrote /sandbox/repo/out/api/mouse_feeding.1_walking.bed\nwrote /sandbox/repo/out/api/mouse_feeding.2_feeding.bed\nwrote /sandbox/repo/out/api/mouse_feeding.2_grooming.bed\nwrote /sandbox/repo/out/api/mouse_feeding.2_resting.bed\nwrote /sandbox/repo/out/api/mouse_feeding.2_walking.bed\nmouse_feeding.1_feeding.bed\nmouse_feeding.1_grooming.bed\nmouse_feeding.1_resting.bed\nmouse_feeding.1_walking.bed\nmouse_feeding.2_feeding.bed\nmouse_feeding.2_grooming.bed\nmouse_feeding.2_resting.bed\nmouse_feeding.2_walking.bed\ntrack name=\"1_feeding\" description=\"1 feeding\" visibility=2 itemRgb=\"On\" priority=20\nchr1\t4\t5\tfeeding\t2\t+\t4\t5\t113,113,113\nchr1\t7\t8\tfeeding\t2\t+\t7\t8\t113,113,113\nchr1\t13\t14\tfeeding\t9\t+\t13\t14\t56,56,56\n","type":"text"}]}

cd /sandbox/repo/out && rm -rf cli && mkdir cli && cd cli && ../../.venv/bin/pergola -i ../../data/mouse_feeding.csv -m ../../config/mapping.tsv -n -ns 1 -f bed -bl -fs , -a join_all -ng -np -o joined 2>&1 | grep -v "@@@" | tail -3; ls; head -5 joined*.bed | head -12

{"content":[{"text":"File joined.1_2_resting.bed generated\nNo path selected, files dump into path:  /sandbox/repo/out/cli\nFile joined.1_2_walking.bed generated\njoined.1_2_feeding.bed\njoined.1_2_grooming.bed\njoined.1_2_resting.bed\njoined.1_2_walking.bed\n==> joined.1_2_feeding.bed <==\ntrack name=\"1_2_feeding\" description=\"1_2 feeding\" visibility=2 itemRgb=\"On\" priority=20\nchr1\t4\t5\tfeeding\t2\t+\t4\t5\t113,113,113\nchr1\t6\t7\tfeeding\t5\t+\t6\t7\t56,56,56\nchr1\t7\t8\tfeeding\t2\t+\t7\t8\t113,113,113\nchr1\t13\t14\tfeeding\t9\t+\t13\t14\t56,56,56\n\n==> joined.1_2_grooming.bed <==\ntrack name=\"1_2_grooming\" description=\"1_2 grooming\" visibility=2 itemRgb=\"On\" priority=20\nchr1\t0\t1\tgrooming\t1\t+\t0\t1\t102,254,102\nchr1\t0\t1\tgrooming\t2\t+\t0\t1\t102,254,102\nchr1\t5\t6\tgrooming\t0\t+\t5\t6\t152,254,152\n","type":"text"}]}

{"content":[{"text":"Package         Version\n--------------- -----------\nnumpy           2.5.3\npandas          3.0.6\npergola         0.2.0\npip             26.2.1\npybedtools      0.12.1\npysam           0.24.1\npython-dateutil 2.9.0.post0\nsix             1.17.0\n","type":"text"}]}

{"content":[{"text":"Relative coordinates set to: False\nIntervals will be inferred from timepoints\nTracks that will be merged are: 2 1\nNo path selected, files dump into path:  /sandbox/repo/out/cli\nFile joined.2_1_feeding.bed generated\nNo path selected, files dump into path:  /sandbox/repo/out/cli\nFile joined.2_1_grooming.bed generated\nNo path selected, files dump into path:  /sandbox/repo/out/cli\nFile joined.2_1_resting.bed generated\nNo path selected, files dump into path:  /sandbox/repo/out/cli\nFile joined.2_1_walking.bed generated\n\nGenerated:\njoined.2_1_feeding.bed\njoined.2_1_grooming.bed\njoined.2_1_resting.bed\njoined.2_1_walking.bed\n\nSample (joined feeding events; chrom = timeline, coords = timepoints):\nhead: cannot open 'joined.1_2_feeding.bed' for reading: No such file or directory\n","type":"text"}]}

{"content":[{"text":"joined.2_1_resting.bed\njoined.2_1_walking.bed\n\nSample (joined feeding events; chrom = timeline, coords = timepoints):\ntrack name=\"2_1_feeding\" description=\"2_1 feeding\" visibility=2 itemRgb=\"On\" priority=20\nchr1\t4\t5\tfeeding\t2\t+\t4\t5\t254,96,101\nchr1\t6\t7\tfeeding\t5\t+\t6\t7\t254,57,61\nchr1\t7\t8\tfeeding\t2\t+\t7\t8\t254,96,101\n","type":"text"}]}

cd /sandbox/repo && printf '\n# Pergola example outputs\nout/\n' >> .gitignore && curl -s -m 10 https://pypi.org/pypi/pergola/json | python3 -c "import json,sys; d=json.load(sys.stdin); print(d['info']['version'], list(d['releases']['0.2.0'])[0]['upload_time'])"

cd /sandbox/repo && rm -rf out && .venv/bin/python examples/behavior_to_bed.py >/dev/null 2>&1 && bash examples/run_cli.sh >/dev/null 2>&1 && ls out out/api out/cli | head -30 && git add -A && git status --short && git -c user.email=agent@pi -c user.name=agent commit -q -m "Add Pergola quickstart: behavioral CSV -> BED via CLI and Python API" && git log --oneline | head -3

{"content":[{"text":"out:\napi\ncli\n\nout/api:\nmouse_feeding.1_feeding.bed\nmouse_feeding.1_grooming.bed\nmouse_feeding.1_resting.bed\nmouse_feeding.1_walking.bed\nmouse_feeding.2_feeding.bed\nmouse_feeding.2_grooming.bed\nmouse_feeding.2_resting.bed\nmouse_feeding.2_walking.bed\n\nout/cli:\njoined.1_2_feeding.bed\njoined.1_2_grooming.bed\njoined.1_2_resting.bed\njoined.1_2_walking.bed\nM  .gitignore\nA  README.md\nA  config/mapping.tsv\nA  data/mouse_feeding.csv\nA  examples/behavior_to_bed.py\nA  examples/run_cli.sh\nA  requirements.txt\n90df8c0 Add Pergola quickstart: behavioral CSV -> BED via CLI and Python API\n9ebf5fb Initial workspace\n","type":"text"}]}