BoghdadyJR/codesearch_python · Datasets at Hugging Face

text stringlengths 75 104k
def insanity_checks(pipeline_str): """Wrapper that performs all sanity checks on the pipeline string Parameters ---------- pipeline_str : str String with the pipeline definition """ # Gets rid of all spaces in string p_string = pipeline_str.replace(" ", "").strip() # some of t...
def parse_pipeline(pipeline_str): """Parses a pipeline string into a list of dictionaries with the connections between processes Parameters ---------- pipeline_str : str String with the definition of the pipeline, e.g.:: 'processA processB processC(ProcessD \| ProcessE)' Re...
def get_source_lane(fork_process, pipeline_list): """Returns the lane of the last process that matches fork_process Parameters ---------- fork_process : list List of processes before the fork. pipeline_list : list List with the pipeline connection dictionaries. Returns ----...
def get_lanes(lanes_str): """From a raw pipeline string, get a list of lanes from the start of the current fork. When the pipeline is being parsed, it will be split at every fork position. The string at the right of the fork position will be provided to this function. It's job is to retrieve the la...
def linear_connection(plist, lane): """Connects a linear list of processes into a list of dictionaries Parameters ---------- plist : list List with process names. This list should contain at least two entries. lane : int Corresponding lane of the processes Returns ------- ...
def fork_connection(source, sink, source_lane, lane): """Makes the connection between a process and the first processes in the lanes to which it forks. The ``lane`` argument should correspond to the lane of the source process. For each lane in ``sink``, the lane counter will increase. Parameters ...
def add_unique_identifiers(pipeline_str): """Returns the pipeline string with unique identifiers and a dictionary with references between the unique keys and the original values Parameters ---------- pipeline_str : str Pipeline string Returns ------- str Pipeline strin...
def remove_unique_identifiers(identifiers_to_tags, pipeline_links): """Removes unique identifiers and add the original process names to the already parsed pipelines Parameters ---------- identifiers_to_tags : dict Match between unique process identifiers and process names pipeline_links...
def signal_handler(screen): """This function is bound to the SIGINT signal (like ctrl+c) to graciously exit the program and reset the curses options. """ if screen: screen.clear() screen.refresh() curses.nocbreak() screen.keypad(0) curses.echo() curses.e...
def _check_required_files(self): """Checks whetner the trace and log files are available """ if not os.path.exists(self.trace_file): raise eh.InspectionError("The provided trace file could not be " "opened: {}".format(self.trace_file)) i...
def _header_mapping(header): """Parses the trace file header and retrieves the positions of each column key. Parameters ---------- header : str The header line of nextflow's trace file Returns ------- dict Mapping the column ID to...
def _expand_path(hash_str): """Expands the hash string of a process (ae/1dasjdm) into a full working directory Parameters ---------- hash_str : str Nextflow process hash with the beggining of the work directory Returns ------- str ...
def _hms(s): """Converts a hms string into seconds. Parameters ---------- s : str The hms string can be something like '20s', '1m30s' or '300ms'. Returns ------- float Time in seconds. """ if s == "-": return...
def _size_coverter(s): """Converts size string into megabytes Parameters ---------- s : str The size string can be '30KB', '20MB' or '1GB' Returns ------- float With the size in bytes """ if s.upper().endswith("KB"): ...
def _get_pipeline_processes(self): """Parses the .nextflow.log file and retrieves the complete list of processes This method searches for specific signatures at the beginning of the .nextflow.log file:: Apr-19 19:07:32.660 [main] DEBUG nextflow.processor TaskP...
def _clear_inspect(self): """Clears inspect attributes when re-executing a pipeline""" self.trace_info = defaultdict(list) self.process_tags = {} self.process_stats = {} self.samples = [] self.stored_ids = [] self.stored_log_ids = [] self.time_start = Non...
def _update_pipeline_status(self): """Parses the .nextflow.log file for signatures of pipeline status. It sets the :attr:`status_info` attribute. """ with open(self.log_file) as fh: try: first_line = next(fh) except: raise eh.Insp...
def _update_tag_status(self, process, vals): """ Updates the 'submitted', 'finished', 'failed' and 'retry' status of each process/tag combination. Process/tag combinations provided to this method already appear on the trace file, so their submission status is updated based on their ...
def _update_barrier_status(self): """Checks whether the channels to each process have been closed. """ with open(self.log_file) as fh: for line in fh: # Exit barrier update after session abort signal if "Session aborted" in line: ...
def _retrieve_log(path): """Method used to retrieve the contents of a log file into a list. Parameters ---------- path Returns ------- list or None Contents of the provided file, each line as a list entry """ if not os.path.exists(pa...
def _update_trace_info(self, fields, hm): """Parses a trace line and updates the :attr:`status_info` attribute. Parameters ---------- fields : list List of the tab-seperated elements of the trace line hm : dict Maps the column IDs to their position in the...
def _update_process_resources(self, process, vals): """Updates the resources info in :attr:`processes` dictionary. """ resources = ["cpus"] for r in resources: if not self.processes[process][r]: try: self.processes[process][r] = vals[0]["...
def _cpu_load_parser(self, cpus, cpu_per, t): """Parses the cpu load from the number of cpus and its usage percentage and returnsde cpu/hour measure Parameters ---------- cpus : str Number of cpus allocated. cpu_per : str Percentage of cpu load me...
def _assess_resource_warnings(self, process, vals): """Assess whether the cpu load or memory usage is above the allocation Parameters ---------- process : str Process name vals : vals List of trace information for each tag of that process Returns...
def _update_process_stats(self): """Updates the process stats with the information from the processes This method is called at the end of each static parsing of the nextflow trace file. It re-populates the :attr:`process_stats` dictionary with the new stat metrics. """ ...
def trace_parser(self): """Method that parses the trace file once and updates the :attr:`status_info` attribute with the new entries. """ # Check the timestamp of the tracefile. Only proceed with the parsing # if it changed from the previous time. size_stamp = os.path.ge...
def log_parser(self): """Method that parses the nextflow log file once and updates the submitted number of samples for each process """ # Check the timestamp of the log file. Only proceed with the parsing # if it changed from the previous time. size_stamp = os.path.getsi...
def update_inspection(self): """Wrapper method that calls the appropriate main updating methods of the inspection. It is meant to be used inside a loop (like while), so that it can continuously update the class attributes from the trace and log files. It already implements check...
def display_overview(self): """Displays the default pipeline inspection overview """ stay_alive = True self.screen = curses.initscr() self.screen.keypad(True) self.screen.nodelay(-1) curses.cbreak() curses.noecho() curses.start_color() ...
def _updown(self, direction): """Provides curses scroll functionality. """ if direction == "up" and self.top_line != 0: self.top_line -= 1 elif direction == "down" and \ self.screen.getmaxyx()[0] + self.top_line\ <= self.content_lines + 3: ...
def _rightleft(self, direction): """Provides curses horizontal padding""" if direction == "left" and self.padding != 0: self.padding -= 1 if direction == "right" and \ self.screen.getmaxyx()[1] + self.padding < self.max_width: self.padding += 1
def flush_overview(self): """Displays the default overview of the pipeline execution from the :attr:`status_info`, :attr:`processes` and :attr:`run_status` attributes into stdout. """ colors = { "W": 1, "R": 2, "C": 3 } pc = {...
def _get_log_lines(self, n=300): """Returns a list with the last ``n`` lines of the nextflow log file Parameters ---------- n : int Number of last lines from the log file Returns ------- list List of strings with the nextflow log ...
def _prepare_static_info(self): """Prepares the first batch of information, containing static information such as the pipeline file, and configuration files Returns ------- dict Dict with the static information for the first POST request """ pipeline...
def _dag_file_to_dict(self): """Function that opens the dotfile named .treeDag.json in the current working directory Returns ------- Returns a dictionary with the dag object to be used in the post instance available through the method _establish_connection """ ...
def _get_run_hash(self): """Gets the hash of the nextflow file""" # Get name and path of the pipeline from the log file pipeline_path = get_nextflow_filepath(self.log_file) # Get hash from the entire pipeline file pipeline_hash = hashlib.md5() with open(pipeline_path, "...
def get_nextflow_filepath(log_file): """Gets the nextflow file path from the nextflow log file. It searches for the nextflow run command throughout the file. Parameters ---------- log_file : str Path for the .nextflow.log file Returns ------- str Path for the nextflow f...
def main(sample_id, assembly, min_size): """Main executor of the split_fasta template. Parameters ---------- sample_id : str Sample Identification string. assembly : list Assembly file. min_size : int Minimum contig size. """ logger.info("Starting script") ...
def main(sample_id, trace_file, workdir): """ Parses a nextflow trace file, searches for processes with a specific tag and sends a JSON report with the relevant information The expected fields for the trace file are:: 0. task_id 1. process 2. tag 3. status 4. ex...
def brew_innuendo(args): """Brews a given list of processes according to the recipe Parameters ---------- args : argparse.Namespace The arguments passed through argparser that will be used to check the the recipe, tasks and brew the process Returns ------- str The f...
def brew_recipe(recipe_name): """Returns a pipeline string from a recipe name. Parameters ---------- recipe_name : str Name of the recipe. Must match the name attribute in one of the classes defined in :mod:`flowcraft.generator.recipes` Returns ------- str Pipeline ...
def list_recipes(full=False): """Method that iterates over all available recipes and prints their information to the standard output Parameters ---------- full : bool If true, it will provide the pipeline string along with the recipe name """ logger.info(colored_print( "\n=...
def validate_pipeline(pipeline_string): """Validate pipeline string Validates the pipeline string by searching for forbidden characters Parameters ---------- pipeline_string : str STring with the processes provided Returns ------- """ ...
def build_upstream(self, process_descriptions, task, all_tasks, task_pipeline, count_forks, total_tasks, forks): """Builds the upstream pipeline of the current process Checks for the upstream processes to the current process and adds them to the cur...
def build_downstream(self, process_descriptions, task, all_tasks, task_pipeline, count_forks, total_tasks, forks): """Builds the downstream pipeline of the current process Checks for the downstream processes to the current process and adds them ...
def define_pipeline_string(self, process_descriptions, tasks, check_upstream, check_downstream, count_forks, total_tasks, forks): """Builds the possible forks and connections between the provided processes ...
def build_pipeline_string(self, forks): """Parses, filters and merge all possible pipeline forks into the final pipeline string This method checks for shared start and end sections between forks and merges them according to the shared processes:: [[spades, ...], [skesa, ......
def run_auto_pipeline(self, tasks): """Main method to run the automatic pipeline creation This method aggregates the functions required to build the pipeline string that can be used as input for the workflow generator. Parameters ---------- tasks : str A str...
def _get_component_str(component, params=None, directives=None): """ Generates a component string based on the provided parameters and directives Parameters ---------- component : str Component name params : dict Dictionary with parameter informat...
def write_report(storage_dic, output_file, sample_id): """ Writes a report from multiple samples. Parameters ---------- storage_dic : dict or :py:class:`OrderedDict` Storage containing the trimming statistics. See :py:func:`parse_log` for its generation. output_file : str Pa...
def main(log_files): """ Main executor of the trimmomatic_report template. Parameters ---------- log_files : list List of paths to the trimmomatic log files. """ log_storage = OrderedDict() for log in log_files: log_id = log.rstrip("_trimlog.txt") # Populate stor...
def fix_contig_names(asseembly_path): """Removes whitespace from the assembly contig names Parameters ---------- asseembly_path : path to assembly file Returns ------- str: Path to new assembly file with fixed contig names """ fixed_assembly = "fixed_assembly.fa" with...
def clean_up(fastq): """ Cleans the temporary fastq files. If they are symlinks, the link source is removed Parameters ---------- fastq : list List of fastq files. """ for fq in fastq: # Get real path of fastq files, following symlinks rp = os.path.realpath(fq) ...
def parse_files(self, fls): """Public method for parsing abricate output files. This method is called at at class instantiation for the provided output files. Additional abricate output files can be added using this method after the class instantiation. Parameters -----...
def _parser(self, fl): """Parser for a single abricate output file. This parser will scan a single Abricate output file and populate the :py:attr:`Abricate.storage` attribute. Parameters ---------- fl : str Path to abricate output file Notes ...
def iter_filter(self, filters, databases=None, fields=None, filter_behavior="and"): """General purpose filter iterator. This general filter iterator allows the filtering of entries based on one or more custom filters. These filters must contain an entry of the `stora...
def _get_contig_id(contig_str): """Tries to retrieve contig id. Returns the original string if it is unable to retrieve the id. Parameters ---------- contig_str : str Full contig string (fasta header) Returns ------- str Contig id...
def get_plot_data(self): """ Generates the JSON report to plot the gene boxes Following the convention of the reports platform, this method returns a list of JSON/dict objects with the information about each entry in the abricate file. The information contained in this JSON is:: ...
def write_report_data(self): """Writes the JSON report to a json file """ json_plot = self.get_plot_data() json_table = self.get_table_data() json_dic = {json_plot, json_table} with open(".report.json", "w") as json_report: json_report.write(json.dumps(...
def main(sample_id, assembly_file, coverage_bp_file=None): """Main executor of the assembly_report template. Parameters ---------- sample_id : str Sample Identification string. assembly_file : str Path to assembly file in Fasta format. """ logger.info("Starting assembly re...
def _parse_assembly(self, assembly_file): """Parse an assembly file in fasta format. This is a Fasta parsing method that populates the :py:attr:`Assembly.contigs` attribute with data for each contig in the assembly. Parameters ---------- assembly_file : str ...
def get_summary_stats(self, output_csv=None): """Generates a CSV report with summary statistics about the assembly The calculated statistics are: - Number of contigs - Average contig size - N50 - Total assembly length - Average GC content ...
def _get_window_labels(self, window): """Returns the mapping between sliding window points and their contigs, and the x-axis position of contig Parameters ---------- window : int Size of the window. Returns ------- xbars : list Th...
def _gc_prop(s, length): """Get proportion of GC from a string Parameters ---------- s : str Arbitrary string Returns ------- x : float GC proportion. """ gc = sum(map(s.count, ["c", "g"])) return gc / length
def get_gc_sliding(self, window=2000): """Calculates a sliding window of the GC content for the assembly Returns ------- gc_res : list List of GC proportion floats for each data point in the sliding window """ gc_res = [] # Get complete...
def main(sample_id, fastq_pair, clear): """Main executor of the skesa template. Parameters ---------- sample_id : str Sample Identification string. fastq_pair : list Two element list containing the paired FastQ files. clear : str Can be either 'true' or 'false'. If 'true...
def write_json_report(sample_id, data1, data2): """Writes the report Parameters ---------- data1 data2 Returns ------- """ parser_map = { "base_sequence_quality": ">>Per base sequence quality", "sequence_quality": ">>Per sequence quality scores", "base_gc_...
def get_trim_index(biased_list): """Returns the trim index from a ``bool`` list Provided with a list of ``bool`` elements (``[False, False, True, True]``), this function will assess the index of the list that minimizes the number of True elements (biased positions) at the extremities. To do so, it ...
def trim_range(data_file): """Assess the optimal trim range for a given FastQC data file. This function will parse a single FastQC data file, namely the 'Per base sequence content' category. It will retrieve the A/T and G/C content for each nucleotide position in the reads, and check whether the ...
def get_sample_trim(p1_data, p2_data): """Get the optimal read trim range from data files of paired FastQ reads. Given the FastQC data report files for paired-end FastQ reads, this function will assess the optimal trim range for the 3' and 5' ends of the paired-end reads. This assessment will be based ...
def get_summary(summary_file): """Parses a FastQC summary report file and returns it as a dictionary. This function parses a typical FastQC summary report file, retrieving only the information on the first two columns. For instance, a line could be:: 'PASS Basic Statistics SH10762A_1.fastq.gz'...
def check_summary_health(summary_file, **kwargs): """Checks the health of a sample from the FastQC summary file. Parses the FastQC summary file and tests whether the sample is good or not. There are four categories that cannot fail, and two that must pass in order for the sample pass this check. If the...
def main(sample_id, result_p1, result_p2, opts): """Main executor of the fastqc_report template. If the "--ignore-tests" option is present in the ``opts`` argument, the health check of the sample will be bypassed, and it will pass the check. This option is used in the first run of FastQC. In the second...
def main(sample_id, bowite_log): """Main executor of the process_mapping template. Parameters ---------- sample_id : str Sample Identification string. boetie_log: str Path to the log file generated by bowtie. """ logger.info("Starting mapping file processing") warnings...
def parse_log(self, bowtie_log): """Parse a bowtie log file. This is a bowtie log parsing method that populates the :py:attr:`self.n_reads, self.align_0x, self.align_1x, self.align_mt1x and self.overall_rate` attributes with data from the log file. Disclamer: THIS METHOD IS HOR...
def _parse_process_name(name_str): """Parses the process string and returns the process name and its directives Process strings my contain directive information with the following syntax:: proc_name={'directive':'val'} This method parses this string and returns the...
def _build_connections(self, process_list, ignore_dependencies, auto_dependency): """Parses the process connections dictionaries into a process list This method is called upon instantiation of the NextflowGenerator class. Essentially, it sets the main input/output cha...
def _get_process_names(self, con, pid): """Returns the input/output process names and output process directives Parameters ---------- con : dict Dictionary with the connection information between two processes. Returns ------- input_name : str ...
def _add_dependency(self, p, template, inlane, outlane, pid): """Automatically Adds a dependency of a process. This method adds a template to the process list attribute as a dependency. It will adapt the input lane, output lane and process id of the process that depends on it. ...
def _search_tree_backwards(self, template, parent_lanes): """Searches the process tree backwards in search of a provided process The search takes into consideration the provided parent lanes and searches only those Parameters ---------- template : str Name o...
def _build_header(self): """Adds the header template to the master template string """ logger.debug("===============") logger.debug("Building header") logger.debug("===============") self.template += hs.header
def _build_footer(self): """Adds the footer template to the master template string""" logger.debug("===============") logger.debug("Building header") logger.debug("===============") self.template += fs.footer
def _update_raw_input(self, p, sink_channel=None, input_type=None): """Given a process, this method updates the :attr:`~Process.main_raw_inputs` attribute with the corresponding raw input channel of that process. The input channel and input type can be overridden if the `input_channel` a...
def _update_extra_inputs(self, p): """Given a process, this method updates the :attr:`~Process.extra_inputs` attribute with the corresponding extra inputs of that process Parameters ---------- p : flowcraft.Process.Process """ if p.extra_input: ...
def _update_secondary_channels(self, p): """Given a process, this method updates the :attr:`~Process.secondary_channels` attribute with the corresponding secondary inputs of that channel. The rationale of the secondary channels is the following: - Start storing any secondar...
def _set_channels(self): """Sets the main channels for the pipeline This method will parse de the :attr:`~Process.processes` attribute and perform the following tasks for each process: - Sets the input/output channels and main input forks and adds them to the process'...
def _set_init_process(self): """Sets the main raw inputs and secondary inputs on the init process This method will fetch the :class:`flowcraft.process.Init` process instance and sets the raw input ( :func:`flowcraft.process.Init.set_raw_inputs`) for that process. This will handl...
def _set_secondary_channels(self): """Sets the secondary channels for the pipeline This will iterate over the :py:attr:`NextflowGenerator.secondary_channels` dictionary that is populated when executing :func:`~NextflowGenerator._update_secondary_channels` method. """ ...
def _set_general_compilers(self): """Adds compiler channels to the :attr:`processes` attribute. This method will iterate over the pipeline's processes and check if any process is feeding channels to a compiler process. If so, that compiler process is added to the pipeline and those chan...
def _set_status_channels(self): """Compiles all status channels for the status compiler process """ status_inst = pc.StatusCompiler(template="status_compiler") report_inst = pc.ReportCompiler(template="report_compiler") # Compile status channels from pipeline process st...
def _get_resources_string(res_dict, pid): """ Returns the nextflow resources string from a dictionary object If the dictionary has at least on of the resource directives, these will be compiled for each process in the dictionary and returned as a string read for injection in the nextflo...
def _get_container_string(cont_dict, pid): """ Returns the nextflow containers string from a dictionary object If the dictionary has at least on of the container directives, these will be compiled for each process in the dictionary and returned as a string read for injection in the next...
def _get_params_string(self): """Returns the nextflow params string from a dictionary object. The params dict should be a set of key:value pairs with the parameter name, and the default parameter value:: self.params = { "genomeSize": 2.1, "minCoverag...
def _get_merged_params_string(self): """Returns the merged nextflow params string from a dictionary object. The params dict should be a set of key:value pairs with the parameter name, and the default parameter value:: self.params = { "genomeSize": 2.1, ...
def _get_manifest_string(self): """Returns the nextflow manifest config string to include in the config file from the information on the pipeline. Returns ------- str Nextflow manifest configuration string """ config_str = "" config_str += '...
def _set_configurations(self): """This method will iterate over all process in the pipeline and populate the nextflow configuration files with the directives of each process in the pipeline. """ logger.debug("======================") logger.debug("Setting configurations"...
def dag_to_file(self, dict_viz, output_file=".treeDag.json"): """Writes dag to output file Parameters ---------- dict_viz: dict Tree like dictionary that is used to export tree data of processes to html file and here for the dotfile .treeDag.json """ ...
def render_pipeline(self): """Write pipeline attributes to json This function writes the pipeline and their attributes to a json file, that is intended to be read by resources/pipeline_graph.html to render a graphical output showing the DAG. """ dict_viz = { ...
def write_configs(self, project_root): """Wrapper method that writes all configuration files to the pipeline directory """ # Write resources config with open(join(project_root, "resources.config"), "w") as fh: fh.write(self.resources) # Write containers conf...
def export_params(self): """Export pipeline params as a JSON to stdout This run mode iterates over the pipeline processes and exports the params dictionary of each component as a JSON to stdout. """ params_json = {} # Skip first init process for p in self.proce...

def insanity_checks(pipeline_str): """Wrapper that performs all sanity checks on the pipeline string Parameters ---------- pipeline_str : str String with the pipeline definition """ # Gets rid of all spaces in string p_string = pipeline_str.replace(" ", "").strip() # some of t...

def parse_pipeline(pipeline_str): """Parses a pipeline string into a list of dictionaries with the connections between processes Parameters ---------- pipeline_str : str String with the definition of the pipeline, e.g.:: 'processA processB processC(ProcessD | ProcessE)' Re...

def get_source_lane(fork_process, pipeline_list): """Returns the lane of the last process that matches fork_process Parameters ---------- fork_process : list List of processes before the fork. pipeline_list : list List with the pipeline connection dictionaries. Returns ----...

def get_lanes(lanes_str): """From a raw pipeline string, get a list of lanes from the start of the current fork. When the pipeline is being parsed, it will be split at every fork position. The string at the right of the fork position will be provided to this function. It's job is to retrieve the la...

def linear_connection(plist, lane): """Connects a linear list of processes into a list of dictionaries Parameters ---------- plist : list List with process names. This list should contain at least two entries. lane : int Corresponding lane of the processes Returns ------- ...

def fork_connection(source, sink, source_lane, lane): """Makes the connection between a process and the first processes in the lanes to which it forks. The ``lane`` argument should correspond to the lane of the source process. For each lane in ``sink``, the lane counter will increase. Parameters ...

def add_unique_identifiers(pipeline_str): """Returns the pipeline string with unique identifiers and a dictionary with references between the unique keys and the original values Parameters ---------- pipeline_str : str Pipeline string Returns ------- str Pipeline strin...

def remove_unique_identifiers(identifiers_to_tags, pipeline_links): """Removes unique identifiers and add the original process names to the already parsed pipelines Parameters ---------- identifiers_to_tags : dict Match between unique process identifiers and process names pipeline_links...

def signal_handler(screen): """This function is bound to the SIGINT signal (like ctrl+c) to graciously exit the program and reset the curses options. """ if screen: screen.clear() screen.refresh() curses.nocbreak() screen.keypad(0) curses.echo() curses.e...

def _check_required_files(self): """Checks whetner the trace and log files are available """ if not os.path.exists(self.trace_file): raise eh.InspectionError("The provided trace file could not be " "opened: {}".format(self.trace_file)) i...

def _header_mapping(header): """Parses the trace file header and retrieves the positions of each column key. Parameters ---------- header : str The header line of nextflow's trace file Returns ------- dict Mapping the column ID to...

def _expand_path(hash_str): """Expands the hash string of a process (ae/1dasjdm) into a full working directory Parameters ---------- hash_str : str Nextflow process hash with the beggining of the work directory Returns ------- str ...

def _hms(s): """Converts a hms string into seconds. Parameters ---------- s : str The hms string can be something like '20s', '1m30s' or '300ms'. Returns ------- float Time in seconds. """ if s == "-": return...

def _size_coverter(s): """Converts size string into megabytes Parameters ---------- s : str The size string can be '30KB', '20MB' or '1GB' Returns ------- float With the size in bytes """ if s.upper().endswith("KB"): ...

def _get_pipeline_processes(self): """Parses the .nextflow.log file and retrieves the complete list of processes This method searches for specific signatures at the beginning of the .nextflow.log file:: Apr-19 19:07:32.660 [main] DEBUG nextflow.processor TaskP...

def _clear_inspect(self): """Clears inspect attributes when re-executing a pipeline""" self.trace_info = defaultdict(list) self.process_tags = {} self.process_stats = {} self.samples = [] self.stored_ids = [] self.stored_log_ids = [] self.time_start = Non...

def _update_pipeline_status(self): """Parses the .nextflow.log file for signatures of pipeline status. It sets the :attr:`status_info` attribute. """ with open(self.log_file) as fh: try: first_line = next(fh) except: raise eh.Insp...

def _update_tag_status(self, process, vals): """ Updates the 'submitted', 'finished', 'failed' and 'retry' status of each process/tag combination. Process/tag combinations provided to this method already appear on the trace file, so their submission status is updated based on their ...

def _update_barrier_status(self): """Checks whether the channels to each process have been closed. """ with open(self.log_file) as fh: for line in fh: # Exit barrier update after session abort signal if "Session aborted" in line: ...

def _retrieve_log(path): """Method used to retrieve the contents of a log file into a list. Parameters ---------- path Returns ------- list or None Contents of the provided file, each line as a list entry """ if not os.path.exists(pa...

def _update_trace_info(self, fields, hm): """Parses a trace line and updates the :attr:`status_info` attribute. Parameters ---------- fields : list List of the tab-seperated elements of the trace line hm : dict Maps the column IDs to their position in the...

def _update_process_resources(self, process, vals): """Updates the resources info in :attr:`processes` dictionary. """ resources = ["cpus"] for r in resources: if not self.processes[process][r]: try: self.processes[process][r] = vals[0]["...

def _cpu_load_parser(self, cpus, cpu_per, t): """Parses the cpu load from the number of cpus and its usage percentage and returnsde cpu/hour measure Parameters ---------- cpus : str Number of cpus allocated. cpu_per : str Percentage of cpu load me...

def _assess_resource_warnings(self, process, vals): """Assess whether the cpu load or memory usage is above the allocation Parameters ---------- process : str Process name vals : vals List of trace information for each tag of that process Returns...

def _update_process_stats(self): """Updates the process stats with the information from the processes This method is called at the end of each static parsing of the nextflow trace file. It re-populates the :attr:`process_stats` dictionary with the new stat metrics. """ ...

def trace_parser(self): """Method that parses the trace file once and updates the :attr:`status_info` attribute with the new entries. """ # Check the timestamp of the tracefile. Only proceed with the parsing # if it changed from the previous time. size_stamp = os.path.ge...

def log_parser(self): """Method that parses the nextflow log file once and updates the submitted number of samples for each process """ # Check the timestamp of the log file. Only proceed with the parsing # if it changed from the previous time. size_stamp = os.path.getsi...

def update_inspection(self): """Wrapper method that calls the appropriate main updating methods of the inspection. It is meant to be used inside a loop (like while), so that it can continuously update the class attributes from the trace and log files. It already implements check...

def display_overview(self): """Displays the default pipeline inspection overview """ stay_alive = True self.screen = curses.initscr() self.screen.keypad(True) self.screen.nodelay(-1) curses.cbreak() curses.noecho() curses.start_color() ...

def _updown(self, direction): """Provides curses scroll functionality. """ if direction == "up" and self.top_line != 0: self.top_line -= 1 elif direction == "down" and \ self.screen.getmaxyx()[0] + self.top_line\ <= self.content_lines + 3: ...

def _rightleft(self, direction): """Provides curses horizontal padding""" if direction == "left" and self.padding != 0: self.padding -= 1 if direction == "right" and \ self.screen.getmaxyx()[1] + self.padding < self.max_width: self.padding += 1

def flush_overview(self): """Displays the default overview of the pipeline execution from the :attr:`status_info`, :attr:`processes` and :attr:`run_status` attributes into stdout. """ colors = { "W": 1, "R": 2, "C": 3 } pc = {...

def _get_log_lines(self, n=300): """Returns a list with the last ``n`` lines of the nextflow log file Parameters ---------- n : int Number of last lines from the log file Returns ------- list List of strings with the nextflow log ...

def _prepare_static_info(self): """Prepares the first batch of information, containing static information such as the pipeline file, and configuration files Returns ------- dict Dict with the static information for the first POST request """ pipeline...

def _dag_file_to_dict(self): """Function that opens the dotfile named .treeDag.json in the current working directory Returns ------- Returns a dictionary with the dag object to be used in the post instance available through the method _establish_connection """ ...

def _get_run_hash(self): """Gets the hash of the nextflow file""" # Get name and path of the pipeline from the log file pipeline_path = get_nextflow_filepath(self.log_file) # Get hash from the entire pipeline file pipeline_hash = hashlib.md5() with open(pipeline_path, "...

def get_nextflow_filepath(log_file): """Gets the nextflow file path from the nextflow log file. It searches for the nextflow run command throughout the file. Parameters ---------- log_file : str Path for the .nextflow.log file Returns ------- str Path for the nextflow f...

def main(sample_id, assembly, min_size): """Main executor of the split_fasta template. Parameters ---------- sample_id : str Sample Identification string. assembly : list Assembly file. min_size : int Minimum contig size. """ logger.info("Starting script") ...

def main(sample_id, trace_file, workdir): """ Parses a nextflow trace file, searches for processes with a specific tag and sends a JSON report with the relevant information The expected fields for the trace file are:: 0. task_id 1. process 2. tag 3. status 4. ex...

def brew_innuendo(args): """Brews a given list of processes according to the recipe Parameters ---------- args : argparse.Namespace The arguments passed through argparser that will be used to check the the recipe, tasks and brew the process Returns ------- str The f...

def brew_recipe(recipe_name): """Returns a pipeline string from a recipe name. Parameters ---------- recipe_name : str Name of the recipe. Must match the name attribute in one of the classes defined in :mod:`flowcraft.generator.recipes` Returns ------- str Pipeline ...

def list_recipes(full=False): """Method that iterates over all available recipes and prints their information to the standard output Parameters ---------- full : bool If true, it will provide the pipeline string along with the recipe name """ logger.info(colored_print( "\n=...

def validate_pipeline(pipeline_string): """Validate pipeline string Validates the pipeline string by searching for forbidden characters Parameters ---------- pipeline_string : str STring with the processes provided Returns ------- """ ...

def build_upstream(self, process_descriptions, task, all_tasks, task_pipeline, count_forks, total_tasks, forks): """Builds the upstream pipeline of the current process Checks for the upstream processes to the current process and adds them to the cur...

def build_downstream(self, process_descriptions, task, all_tasks, task_pipeline, count_forks, total_tasks, forks): """Builds the downstream pipeline of the current process Checks for the downstream processes to the current process and adds them ...

def define_pipeline_string(self, process_descriptions, tasks, check_upstream, check_downstream, count_forks, total_tasks, forks): """Builds the possible forks and connections between the provided processes ...

def build_pipeline_string(self, forks): """Parses, filters and merge all possible pipeline forks into the final pipeline string This method checks for shared start and end sections between forks and merges them according to the shared processes:: [[spades, ...], [skesa, ......

def run_auto_pipeline(self, tasks): """Main method to run the automatic pipeline creation This method aggregates the functions required to build the pipeline string that can be used as input for the workflow generator. Parameters ---------- tasks : str A str...

def _get_component_str(component, params=None, directives=None): """ Generates a component string based on the provided parameters and directives Parameters ---------- component : str Component name params : dict Dictionary with parameter informat...

def write_report(storage_dic, output_file, sample_id): """ Writes a report from multiple samples. Parameters ---------- storage_dic : dict or :py:class:`OrderedDict` Storage containing the trimming statistics. See :py:func:`parse_log` for its generation. output_file : str Pa...

def main(log_files): """ Main executor of the trimmomatic_report template. Parameters ---------- log_files : list List of paths to the trimmomatic log files. """ log_storage = OrderedDict() for log in log_files: log_id = log.rstrip("_trimlog.txt") # Populate stor...

def fix_contig_names(asseembly_path): """Removes whitespace from the assembly contig names Parameters ---------- asseembly_path : path to assembly file Returns ------- str: Path to new assembly file with fixed contig names """ fixed_assembly = "fixed_assembly.fa" with...

def clean_up(fastq): """ Cleans the temporary fastq files. If they are symlinks, the link source is removed Parameters ---------- fastq : list List of fastq files. """ for fq in fastq: # Get real path of fastq files, following symlinks rp = os.path.realpath(fq) ...

def parse_files(self, fls): """Public method for parsing abricate output files. This method is called at at class instantiation for the provided output files. Additional abricate output files can be added using this method after the class instantiation. Parameters -----...

def _parser(self, fl): """Parser for a single abricate output file. This parser will scan a single Abricate output file and populate the :py:attr:`Abricate.storage` attribute. Parameters ---------- fl : str Path to abricate output file Notes ...

def iter_filter(self, filters, databases=None, fields=None, filter_behavior="and"): """General purpose filter iterator. This general filter iterator allows the filtering of entries based on one or more custom filters. These filters must contain an entry of the `stora...

def _get_contig_id(contig_str): """Tries to retrieve contig id. Returns the original string if it is unable to retrieve the id. Parameters ---------- contig_str : str Full contig string (fasta header) Returns ------- str Contig id...

def get_plot_data(self): """ Generates the JSON report to plot the gene boxes Following the convention of the reports platform, this method returns a list of JSON/dict objects with the information about each entry in the abricate file. The information contained in this JSON is:: ...

def write_report_data(self): """Writes the JSON report to a json file """ json_plot = self.get_plot_data() json_table = self.get_table_data() json_dic = {**json_plot, **json_table} with open(".report.json", "w") as json_report: json_report.write(json.dumps(...

def main(sample_id, assembly_file, coverage_bp_file=None): """Main executor of the assembly_report template. Parameters ---------- sample_id : str Sample Identification string. assembly_file : str Path to assembly file in Fasta format. """ logger.info("Starting assembly re...

def _parse_assembly(self, assembly_file): """Parse an assembly file in fasta format. This is a Fasta parsing method that populates the :py:attr:`Assembly.contigs` attribute with data for each contig in the assembly. Parameters ---------- assembly_file : str ...

def get_summary_stats(self, output_csv=None): """Generates a CSV report with summary statistics about the assembly The calculated statistics are: - Number of contigs - Average contig size - N50 - Total assembly length - Average GC content ...

def _get_window_labels(self, window): """Returns the mapping between sliding window points and their contigs, and the x-axis position of contig Parameters ---------- window : int Size of the window. Returns ------- xbars : list Th...

def _gc_prop(s, length): """Get proportion of GC from a string Parameters ---------- s : str Arbitrary string Returns ------- x : float GC proportion. """ gc = sum(map(s.count, ["c", "g"])) return gc / length

def get_gc_sliding(self, window=2000): """Calculates a sliding window of the GC content for the assembly Returns ------- gc_res : list List of GC proportion floats for each data point in the sliding window """ gc_res = [] # Get complete...

def main(sample_id, fastq_pair, clear): """Main executor of the skesa template. Parameters ---------- sample_id : str Sample Identification string. fastq_pair : list Two element list containing the paired FastQ files. clear : str Can be either 'true' or 'false'. If 'true...

def write_json_report(sample_id, data1, data2): """Writes the report Parameters ---------- data1 data2 Returns ------- """ parser_map = { "base_sequence_quality": ">>Per base sequence quality", "sequence_quality": ">>Per sequence quality scores", "base_gc_...

def get_trim_index(biased_list): """Returns the trim index from a ``bool`` list Provided with a list of ``bool`` elements (``[False, False, True, True]``), this function will assess the index of the list that minimizes the number of True elements (biased positions) at the extremities. To do so, it ...

def trim_range(data_file): """Assess the optimal trim range for a given FastQC data file. This function will parse a single FastQC data file, namely the *'Per base sequence content'* category. It will retrieve the A/T and G/C content for each nucleotide position in the reads, and check whether the ...

def get_sample_trim(p1_data, p2_data): """Get the optimal read trim range from data files of paired FastQ reads. Given the FastQC data report files for paired-end FastQ reads, this function will assess the optimal trim range for the 3' and 5' ends of the paired-end reads. This assessment will be based ...

def get_summary(summary_file): """Parses a FastQC summary report file and returns it as a dictionary. This function parses a typical FastQC summary report file, retrieving only the information on the first two columns. For instance, a line could be:: 'PASS Basic Statistics SH10762A_1.fastq.gz'...

def check_summary_health(summary_file, **kwargs): """Checks the health of a sample from the FastQC summary file. Parses the FastQC summary file and tests whether the sample is good or not. There are four categories that cannot fail, and two that must pass in order for the sample pass this check. If the...

def main(sample_id, result_p1, result_p2, opts): """Main executor of the fastqc_report template. If the "--ignore-tests" option is present in the ``opts`` argument, the health check of the sample will be bypassed, and it will pass the check. This option is used in the first run of FastQC. In the second...

def main(sample_id, bowite_log): """Main executor of the process_mapping template. Parameters ---------- sample_id : str Sample Identification string. boetie_log: str Path to the log file generated by bowtie. """ logger.info("Starting mapping file processing") warnings...

def parse_log(self, bowtie_log): """Parse a bowtie log file. This is a bowtie log parsing method that populates the :py:attr:`self.n_reads, self.align_0x, self.align_1x, self.align_mt1x and self.overall_rate` attributes with data from the log file. Disclamer: THIS METHOD IS HOR...

def _parse_process_name(name_str): """Parses the process string and returns the process name and its directives Process strings my contain directive information with the following syntax:: proc_name={'directive':'val'} This method parses this string and returns the...

def _build_connections(self, process_list, ignore_dependencies, auto_dependency): """Parses the process connections dictionaries into a process list This method is called upon instantiation of the NextflowGenerator class. Essentially, it sets the main input/output cha...

def _get_process_names(self, con, pid): """Returns the input/output process names and output process directives Parameters ---------- con : dict Dictionary with the connection information between two processes. Returns ------- input_name : str ...

def _add_dependency(self, p, template, inlane, outlane, pid): """Automatically Adds a dependency of a process. This method adds a template to the process list attribute as a dependency. It will adapt the input lane, output lane and process id of the process that depends on it. ...

def _search_tree_backwards(self, template, parent_lanes): """Searches the process tree backwards in search of a provided process The search takes into consideration the provided parent lanes and searches only those Parameters ---------- template : str Name o...

def _build_header(self): """Adds the header template to the master template string """ logger.debug("===============") logger.debug("Building header") logger.debug("===============") self.template += hs.header

def _build_footer(self): """Adds the footer template to the master template string""" logger.debug("===============") logger.debug("Building header") logger.debug("===============") self.template += fs.footer

def _update_raw_input(self, p, sink_channel=None, input_type=None): """Given a process, this method updates the :attr:`~Process.main_raw_inputs` attribute with the corresponding raw input channel of that process. The input channel and input type can be overridden if the `input_channel` a...

def _update_extra_inputs(self, p): """Given a process, this method updates the :attr:`~Process.extra_inputs` attribute with the corresponding extra inputs of that process Parameters ---------- p : flowcraft.Process.Process """ if p.extra_input: ...

def _update_secondary_channels(self, p): """Given a process, this method updates the :attr:`~Process.secondary_channels` attribute with the corresponding secondary inputs of that channel. The rationale of the secondary channels is the following: - Start storing any secondar...

def _set_channels(self): """Sets the main channels for the pipeline This method will parse de the :attr:`~Process.processes` attribute and perform the following tasks for each process: - Sets the input/output channels and main input forks and adds them to the process'...

def _set_init_process(self): """Sets the main raw inputs and secondary inputs on the init process This method will fetch the :class:`flowcraft.process.Init` process instance and sets the raw input ( :func:`flowcraft.process.Init.set_raw_inputs`) for that process. This will handl...

def _set_secondary_channels(self): """Sets the secondary channels for the pipeline This will iterate over the :py:attr:`NextflowGenerator.secondary_channels` dictionary that is populated when executing :func:`~NextflowGenerator._update_secondary_channels` method. """ ...

def _set_general_compilers(self): """Adds compiler channels to the :attr:`processes` attribute. This method will iterate over the pipeline's processes and check if any process is feeding channels to a compiler process. If so, that compiler process is added to the pipeline and those chan...

def _set_status_channels(self): """Compiles all status channels for the status compiler process """ status_inst = pc.StatusCompiler(template="status_compiler") report_inst = pc.ReportCompiler(template="report_compiler") # Compile status channels from pipeline process st...

def _get_resources_string(res_dict, pid): """ Returns the nextflow resources string from a dictionary object If the dictionary has at least on of the resource directives, these will be compiled for each process in the dictionary and returned as a string read for injection in the nextflo...

def _get_container_string(cont_dict, pid): """ Returns the nextflow containers string from a dictionary object If the dictionary has at least on of the container directives, these will be compiled for each process in the dictionary and returned as a string read for injection in the next...

def _get_params_string(self): """Returns the nextflow params string from a dictionary object. The params dict should be a set of key:value pairs with the parameter name, and the default parameter value:: self.params = { "genomeSize": 2.1, "minCoverag...

def _get_merged_params_string(self): """Returns the merged nextflow params string from a dictionary object. The params dict should be a set of key:value pairs with the parameter name, and the default parameter value:: self.params = { "genomeSize": 2.1, ...

def _get_manifest_string(self): """Returns the nextflow manifest config string to include in the config file from the information on the pipeline. Returns ------- str Nextflow manifest configuration string """ config_str = "" config_str += '...

def _set_configurations(self): """This method will iterate over all process in the pipeline and populate the nextflow configuration files with the directives of each process in the pipeline. """ logger.debug("======================") logger.debug("Setting configurations"...

def dag_to_file(self, dict_viz, output_file=".treeDag.json"): """Writes dag to output file Parameters ---------- dict_viz: dict Tree like dictionary that is used to export tree data of processes to html file and here for the dotfile .treeDag.json """ ...

def render_pipeline(self): """Write pipeline attributes to json This function writes the pipeline and their attributes to a json file, that is intended to be read by resources/pipeline_graph.html to render a graphical output showing the DAG. """ dict_viz = { ...

def write_configs(self, project_root): """Wrapper method that writes all configuration files to the pipeline directory """ # Write resources config with open(join(project_root, "resources.config"), "w") as fh: fh.write(self.resources) # Write containers conf...

def export_params(self): """Export pipeline params as a JSON to stdout This run mode iterates over the pipeline processes and exports the params dictionary of each component as a JSON to stdout. """ params_json = {} # Skip first init process for p in self.proce...