INSTRUCTION stringlengths 1 8.43k | RESPONSE stringlengths 75 104k |
|---|---|
General purpose method that sets the main channels | def set_channels(self, **kwargs):
""" General purpose method that sets the main channels
This method will take a variable number of keyword arguments to
set the :py:attr:`Process._context` attribute with the information
on the main channels for the process. This is done by appending
... |
Updates the forks attribute with the sink channel destination | def update_main_forks(self, sink):
"""Updates the forks attribute with the sink channel destination
Parameters
----------
sink : str
Channel onto which the main input will be forked to
"""
if not self.main_forks:
self.main_forks = [self.output_c... |
General purpose method for setting a secondary channel | def set_secondary_channel(self, source, channel_list):
""" General purpose method for setting a secondary channel
This method allows a given source channel to be forked into one or
more channels and sets those forks in the :py:attr:`Process.forks`
attribute. Both the source and the chan... |
Updates the directives attribute from a dictionary object. | def update_attributes(self, attr_dict):
"""Updates the directives attribute from a dictionary object.
This will only update the directives for processes that have been
defined in the subclass.
Parameters
----------
attr_dict : dict
Dictionary containing the ... |
General method for setting the input channels for the status process | def set_compiler_channels(self, channel_list, operator="mix"):
"""General method for setting the input channels for the status process
Given a list of status channels that are gathered during the pipeline
construction, this method will automatically set the input channel
for the status ... |
Sets the main input channels of the pipeline and their forks. | def set_raw_inputs(self, raw_input):
"""Sets the main input channels of the pipeline and their forks.
The ``raw_input`` dictionary input should contain one entry for each
input type (fastq, fasta, etc). The corresponding value should be a
dictionary/json with the following key:values:
... |
Adds secondary inputs to the start of the pipeline. | def set_secondary_inputs(self, channel_dict):
""" Adds secondary inputs to the start of the pipeline.
This channels are inserted into the pipeline file as they are
provided in the values of the argument.
Parameters
----------
channel_dict : dict
Each entry s... |
Sets the initial definition of the extra input channels. | def set_extra_inputs(self, channel_dict):
"""Sets the initial definition of the extra input channels.
The ``channel_dict`` argument should contain the input type and
destination channel of each parameter (which is the key)::
channel_dict = {
"param1": {
... |
Main executor of the process_mapping template. | def main(sample_id, assembly_file, minsize):
"""Main executor of the process_mapping template.
Parameters
----------
sample_id : str
Sample Identification string.
assembly: str
Path to the fatsa file generated by the assembler.
minsize: str
Min contig size to be consider... |
Attempts to retrieve the coverage value from the header string. | def _parse_coverage(header_str):
"""Attempts to retrieve the coverage value from the header string.
It splits the header by "_" and then screens the list backwards in
search of the first float value. This will be interpreted as the
coverage value. If it cannot find a float value, it ret... |
Parse an assembly fasta file. | def _parse_assembly(self, assembly_file):
"""Parse an assembly fasta file.
This is a Fasta parsing method that populates the
:py:attr:`~Assembly.contigs` attribute with data for each contig in the
assembly.
The insertion of data on the self.contigs is done by the
:py:me... |
Inserts data from a single contig into \: py: attr: ~Assembly. contigs. | def _populate_contigs(self, contig_id, header, cov, sequence):
""" Inserts data from a single contig into\
:py:attr:`~Assembly.contigs`.
By providing a contig id, the original header, the coverage that
is parsed from the header and the sequence, this method will
populate the :p... |
Get GC content and proportions. | def _get_gc_content(sequence, length):
"""Get GC content and proportions.
Parameters
----------
sequence : str
The complete sequence of the contig.
length : int
The length of the sequence contig.
Returns
-------
x : dict
... |
Filters the contigs of the assembly according to user provided \ comparisons. | def filter_contigs(self, *comparisons):
"""Filters the contigs of the assembly according to user provided\
comparisons.
The comparisons must be a list of three elements with the
:py:attr:`~Assembly.contigs` key, operator and test value. For
example, to filter contigs with a mini... |
Returns the length of the assembly without the filtered contigs. | def get_assembly_length(self):
"""Returns the length of the assembly, without the filtered contigs.
Returns
-------
x : int
Total length of the assembly.
"""
return sum(
[vals["length"] for contig_id, vals in self.contigs.items()
if... |
Writes the assembly to a new file. | def write_assembly(self, output_file, filtered=True):
"""Writes the assembly to a new file.
The ``filtered`` option controls whether the new assembly will be
filtered or not.
Parameters
----------
output_file : str
Name of the output assembly file.
f... |
Writes a report with the test results for the current assembly | def write_report(self, output_file):
"""Writes a report with the test results for the current assembly
Parameters
----------
output_file : str
Name of the output assembly file.
"""
logger.debug("Writing the assembly report into: {}".format(
outp... |
Function to guess processes based on strings that are not available in process_map. If the string has typos and is somewhat similar ( 50% ) to any process available in flowcraft it will print info to the terminal suggesting the most similar processes available in flowcraft. | def guess_process(query_str, process_map):
"""
Function to guess processes based on strings that are not available in
process_map. If the string has typos and is somewhat similar (50%) to any
process available in flowcraft it will print info to the terminal,
suggesting the most similar processes ava... |
Recursively removes nested brackets | def remove_inner_forks(text):
"""Recursively removes nested brackets
This function is used to remove nested brackets from fork strings using
regular expressions
Parameters
----------
text: str
The string that contains brackets with inner forks to be removed
Returns
-------
... |
This function performs a check for different number of ( and ) characters which indicates that some forks are poorly constructed. | def brackets_insanity_check(p_string):
"""
This function performs a check for different number of '(' and ')'
characters, which indicates that some forks are poorly constructed.
Parameters
----------
p_string: str
String with the definition of the pipeline, e.g.::
'process... |
This function checks if the pipeline string contains a process between the fork start token or end token and the separator ( lane ) token. Checks for the absence of processes in one of the branches of the fork [ | ) and ( | ] and for the existence of a process before starting a fork ( in an inner fork ) [ | ( ]. | def fork_procs_insanity_check(p_string):
"""
This function checks if the pipeline string contains a process between
the fork start token or end token and the separator (lane) token. Checks for
the absence of processes in one of the branches of the fork ['|)' and '(|']
and for the existence of a proc... |
This function performs two sanity checks in the pipeline string. The first check assures that each fork contains a lane token | while the second check looks for duplicated processes within the same fork. | def inner_fork_insanity_checks(pipeline_string):
"""
This function performs two sanity checks in the pipeline string. The first
check, assures that each fork contains a lane token '|', while the second
check looks for duplicated processes within the same fork.
Parameters
----------
pipeline... |
Wrapper that performs all sanity checks on the pipeline string | 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... |
Parses a pipeline string into a list of dictionaries with the connections between processes | 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... |
Returns the lane of the last process that matches fork_process | 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
----... |
From a raw pipeline string get a list of lanes from the start of the current fork. | 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... |
Connects a linear list of processes into a list of dictionaries | 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
-------
... |
Makes the connection between a process and the first processes in the lanes to which it forks. | 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
... |
Returns the pipeline string with unique identifiers and a dictionary with references between the unique keys and the original values | 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... |
Removes unique identifiers and add the original process names to the already parsed pipelines | 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... |
This function is bound to the SIGINT signal ( like ctrl + c ) to graciously exit the program and reset the curses options. | 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... |
Checks whetner the trace and log files are available | 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... |
Parses the trace file header and retrieves the positions of each column key. | 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... |
Expands the hash string of a process ( ae/ 1dasjdm ) into a full working directory | 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
... |
Converts a hms string into seconds. | 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... |
Converts size string into megabytes | 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"):
... |
Parses the. nextflow. log file and retrieves the complete list of processes | 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... |
Clears inspect attributes when re - executing a pipeline | 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... |
Parses the. nextflow. log file for signatures of pipeline status. It sets the: attr: status_info attribute. | 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... |
Updates the submitted finished failed and retry status of each process/ tag combination. | 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
... |
Checks whether the channels to each process have been closed. | 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:
... |
Method used to retrieve the contents of a log file into a list. | 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... |
Parses a trace line and updates the: attr: status_info attribute. | 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... |
Updates the resources info in: attr: processes dictionary. | 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]["... |
Parses the cpu load from the number of cpus and its usage percentage and returnsde cpu/ hour measure | 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... |
Assess whether the cpu load or memory usage is above the allocation | 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... |
Updates the process stats with the information from the processes | 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.
"""
... |
Method that parses the trace file once and updates the: attr: status_info attribute with the new entries. | 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... |
Method that parses the nextflow log file once and updates the submitted number of samples for each process | 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... |
Wrapper method that calls the appropriate main updating methods of the inspection. | 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... |
Displays the default pipeline inspection overview | 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()
... |
Provides curses scroll functionality. | 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:
... |
Provides curses horizontal padding | 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 |
Displays the default overview of the pipeline execution from the: attr: status_info: attr: processes and: attr: run_status attributes into stdout. | 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 = {... |
Returns a list with the last n lines of the nextflow log file | 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
... |
Prepares the first batch of information containing static information such as the pipeline file and configuration files | 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... |
Function that opens the dotfile named. treeDag. json in the current working directory | 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
"""
... |
Gets the hash of the nextflow file | 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, "... |
Gets the nextflow file path from the nextflow log file. It searches for the nextflow run command throughout the file. | 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... |
Main executor of the split_fasta template. | 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")
... |
Parses a nextflow trace file searches for processes with a specific tag and sends a JSON report with the relevant information | 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... |
Brews a given list of processes according to the recipe | 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... |
Returns a pipeline string from a recipe name. | 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 ... |
Method that iterates over all available recipes and prints their information to the standard output | 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=... |
Validate pipeline string | 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
-------
"""
... |
Builds the upstream pipeline of the current process | 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... |
Builds the downstream pipeline of the current process | 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 ... |
Builds the possible forks and connections between the provided processes | 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
... |
Parses filters and merge all possible pipeline forks into the final pipeline string | 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, ...... |
Main method to run the automatic pipeline creation | 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... |
Generates a component string based on the provided parameters and directives | 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... |
Writes a report from multiple samples. | 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... |
Main executor of the trimmomatic_report template. | 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... |
Removes whitespace from the assembly contig names | 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... |
Cleans the temporary fastq files. If they are symlinks the link source is removed | 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)
... |
Public method for parsing abricate output files. | 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
-----... |
Parser for a single abricate output file. | 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
... |
General purpose filter iterator. | 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... |
Tries to retrieve contig id. Returns the original string if it is unable to retrieve the id. | 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... |
Generates the JSON report to plot the gene boxes | 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::
... |
Writes the JSON report to a json file | 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(... |
Main executor of the assembly_report template. | 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... |
Parse an assembly file in fasta format. | 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
... |
Generates a CSV report with summary statistics about the assembly | 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
... |
Returns the mapping between sliding window points and their contigs and the x - axis position of contig | 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... |
Get proportion of GC from a string | 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 |
Calculates a sliding window of the GC content for the assembly | 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... |
Main executor of the skesa template. | 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... |
Writes the report | 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_... |
Returns the trim index from a bool list | 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 ... |
Assess the optimal trim range for a given FastQC data file. | 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
... |
Get the optimal read trim range from data files of paired FastQ reads. | 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 ... |
Parses a FastQC summary report file and returns it as a dictionary. | 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'... |
Checks the health of a sample from the FastQC summary file. | 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... |
Main executor of the fastqc_report template. | 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... |
Main executor of the process_mapping template. | 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... |
Parse a bowtie log file. | 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... |
Parses the process string and returns the process name and its directives | 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... |
Parses the process connections dictionaries into a process list | 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... |
Returns the input/ output process names and output process directives | 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
... |
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