#!/usr/bin/env python3 """Create input table and config for Rhea.""" import argparse from functools import partial import gzip import logging import math import os import sys from typing import Tuple from Bio import SeqIO import labkey import pandas as pd logger = logging.getLogger(__name__) def parse_cli_args() -> argparse.Namespace: """ Parses command line arguments. :returns: parsed CLI arguments """ parser = argparse.ArgumentParser( description=__doc__, ) parser.add_argument( "table", type=str, default=None, help="either local file path of input table *or* name of table on " "LabKey instance (see 'LabKey API' options below)", metavar="TABLE", ) api = parser.add_argument_group("LabKey API") api.add_argument( "--labkey-domain", type=str, default=None, help="domain of LabKey instance to query; required for obtaining " "input table via LabKey API", metavar="STR", ) api.add_argument( "--labkey-path", type=str, default=None, help="path to LabKey container that includes specified input table; " "required for obtaining input table via LabKey API", metavar="STR", ) io = parser.add_argument_group("input/output") io.add_argument( "--input-to-output-mapping", type=argparse.FileType('r'), default=os.path.join( os.path.dirname(__file__), 'prepare_inputs.dict.tsv', ), help="lookup table with mappings from input (LabKey or LabKey-like) " "to output (Snakemake) table; default: '%(default)s'", metavar="FILE", ) io.add_argument( "--resources-dir", type=str, default=os.getcwd(), help="path containing the genome resources for all organisms " "(default: %(default)s)", metavar="DIR", ) io.add_argument( "--output-table", type=argparse.FileType('w'), default="samples.tsv", help="output sample table for use in Rhea (default: %(default)s)", metavar="FILE", ) io.add_argument( "--config-file", type=argparse.FileType('w'), default="config.yaml", help="output Snakemake configuration file for use in Rhea (default: " "%(default)s)", metavar="FILE", ) io.add_argument( "--output-dir", type=str, default=os.getcwd(), help="directory to which Rhea results and logs are to be written " "(default: %(default)s)", metavar="DIR", ) parser.add_argument( "--no-process-paths", action="store_true", default=False, help="do not attempt to create absolute paths in output files", ) behavior = parser.add_argument_group("workflow behavior") behavior.add_argument( "--trim-polya", type=int, choices=[True, False], default=True, help="cutadapt: trim poly(A) tails option (default: %(default)s)", ) behavior.add_argument( "--multimappers", type=int, default=100, help="STAR: number of multimappers to report (default: %(default)s)", metavar='INT', ) behavior.add_argument( "--soft-clip", type=str, default="EndToEnd", help="STAR: soft-clipping option (default: %(default)s)", choices=['EndToEnd', 'Local'], ) behavior.add_argument( "--pass-mode", type=str, default="None", help="STAR: 2-pass mode option (default: %(default)s)", choices=["None", "Basic"], ) behavior.add_argument( "--libtype", type=str, default="A", help="Salmon: library type (default: %(default)s)", metavar="STR", ) report = parser.add_argument_group("report") report.add_argument( "--description", type=str, default="N/A", help="short description to be added to the report (default: " "%(default)s)", metavar="STR", ) report.add_argument( "--logo", type=argparse.FileType('r'), default=None, help="path to image file to be added to the report (default: " "%(default)s)", metavar="FILE", ) report.add_argument( "--url", type=str, default="N/A", help="contact URL to be added to the report (default: %(default)s)", metavar="STR", ) parser.add_argument( "-v", "--verbose", action="store_true", default=False, help="print log messages to STDERR", ) parser.add_argument( "--debug", action="store_true", default=False, help="print log and debug messages to STDERR", ) args = parser.parse_args() if args.logo: args.logo.close() args.logo = args.logo.name else: args.logo = "" if (args.labkey_domain and not args.labkey_path) or \ (args.labkey_path and not args.labkey_domain): parser.print_help() sys.exit( "\n[ERROR] Either none or both of '--labkey-domain' and " "'--labkey-path' are required." ) return args def setup_logging( logger: logging.Logger, verbose: bool = False, debug: bool = False, ) -> None: """ Configure logger. :param logger: the `logging.Logger` object to configure :param verbose: whether `logging.INFO` messages shall be logged :param debug: whether `logging.DEBUG` messages shall be logged :returns: None :raises ?: TODO """ if debug: logger.setLevel(logging.DEBUG) elif verbose: logger.setLevel(logging.INFO) else: logger.setLevel(logging.WARNING) handler = logging.StreamHandler() handler.setFormatter(logging.Formatter( "[%(asctime)-15s: %(levelname)-8s @ %(funcName)s] %(message)s" )) logger.addHandler(handler) def fetch_labkey_table( domain: str, container_path: str, query_name: str, context_path: str = "labkey", schema_name: str = "lists", ) -> pd.DataFrame: """ Export LabKey table as Pandas data frame. :param domain: domain of LabKey instance :param container_path: path to LabKey container that includes the table of interest :param query_name: name of LabKey table to export :context_path: required by API; usage unclear TODO :schema_name: required by API; usage unclear TODO :returns: Pandas data frame :raises ?: TODO """ server_context = labkey.utils.create_server_context( domain=domain, container_path=container_path, context_path=context_path, use_ssl=True, ) results = labkey.query.select_rows( server_context=server_context, schema_name=schema_name, query_name=query_name, ) input_table = pd.DataFrame(results["rows"]) return input_table def get_read_length(file: str) -> int: """ Returns read length of first entry of gzipped FASTQ file. :param file: path to gzipped FASTQ file :returns: read length :raises FileNotFoundError: file does not exist :raises IsADirectoryError: file is a directory :raises OSError: file is not gzipped :raises PermissionError: file cannot be read :raises ValueError: not a valid FASTQ file """ with gzip.open(file, "rt") as handle: return len(next(SeqIO.parse(handle, "fastq"))) def kmer_from_read_length( length: int, k_max: int = 31, k_min: int = 11, ) -> int: """ Given a read length, returns appropriate kmer parameter size for Salmon (https://salmon.readthedocs.io/) or similar k-mer-based quantification tools. References for implementation: https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode https://groups.google.com/d/msg/sailfish-users/fphjX7OIGzY/bMBwlCaZAgAJ :param length: length of read in nucleotides :param k_max: maximum allowed k-mer size :param k_min: minimum allowed k-mer size :returns: k_max for l > 2 * k_max, or else the maximum of k and k_min, where k is biggest odd integer that fulfills k < l / 2 """ k = k_max if length < 2 * k_max + 1: # ensure kmer is smaller than half of read length k = math.floor((length - 1) / 2) # ensure kmer is odd if not k % 2: k -= 1 if k < k_min: k = k_min return k def get_strand_param_kallisto(directionality: str) -> str: """ Returns appropriate strand info parameter for kallisto (https://pachterlab.github.io/kallisto/), given a string indicating the "directionality" of a sequencing library. :param directionality: direction in which library was sequenced (one of "SENSE" and "ANTISENSE") :returns: appropriate kallisto option for specified directionality; an empty string is returned if the directionality value is empty or not recognized """ if directionality == "SENSE": option = "--fr" elif directionality == "ANTISENSE": option = "--rf" else: option = "" return option def get_strand_param_alfa(directionality: str) -> str: """ Returns appropriate strand info parameter for ALFA (https://github.com/biocompibens/ALFA), given a string indicating the "directionality" of a sequencing library. :param directionality: direction in which library was sequenced (one of "SENSE" and "ANTISENSE") :returns: appropriate ALFA option for specified directionality; an empty string is returned if the directionality value is empty or not recognized """ if directionality == 'SENSE': option = 'fr-firststrand' elif directionality == 'ANTISENSE': option = 'fr-secondstrand' else: option = '' return option def get_strand_names_alfa(directionality: str) -> Tuple[str, str]: """ Returns appropriate strand name suffixes for ALFA (https://github.com/biocompibens/ALFA), given a string indicating the "directionality" of a sequencing library. :param directionality: direction in which library was sequenced (one of "SENSE" and "ANTISENSE") :returns: tuple of ALFA strand name suffixes for two coverage tracks of a paired-end sequencing library """ if directionality == "SENSE": plus = "str1" minus = "str2" elif directionality == "ANTISENSE": minus = "str1" plus = "str2" else: plus = "" minus = "" return (plus, minus) def get_polya_adapter_seqs(directionality: str) -> Tuple[str, str]: """ Returns repeat oligomers for detecting and trimming of poly(A) signals from a sequencing library, given a string indicating the library's "directionality". :param directionality: direction in which library was sequenced (one of "SENSE" and "ANTISENSE") :returns: tuple of two 15-mers to be used to detect and trim poly(A) signals from the 3' and 5' ends of the reads of sequencing library, respectively """ if directionality == 'SENSE': three = 'AAAAAAAAAAAAAAA' five = 'XXXXXXXXXXXXXXX' elif directionality == 'ANTISENSE': three = 'XXXXXXXXXXXXXXX' five = 'TTTTTTTTTTTTTTT' else: three = 'XXXXXXXXXXXXXXX' five = 'XXXXXXXXXXXXXXX' return (three, five) def expand_path( *args: str, anchor: str = os.getcwd(), expand: bool = True, no_abs: bool = False, ) -> str: """ Constructs absolute path. Not tested with symbolic links. :param args: path fragments which will be joined to the anchor from left to right :param anchor: path relative to which the path fragments in *args shall be interpreted; can be absolute or relative; in the latter case, it is interpreted relative to the current working directory; if path fragments evaluate to absolute path (either before or after expansion), the path will be returned without considering the anchor :param expand: whether environment variables and user directories (e.g, `~`) shall be expanded :param join_only: path fragments in args are joined, but no further processing is done :returns: absolute path """ suffix = os.path.join(*args) if no_abs: return suffix if os.path.isabs(suffix): return os.path.normpath(suffix) if expand: suffix = os.path.expanduser( os.path.expandvars( suffix ) ) if os.path.isabs(suffix): return os.path.normpath(suffix) anchor = os.path.expanduser( os.path.expandvars( anchor ) ) path = os.path.join(anchor, suffix) return os.path.normpath(path) def main(args): """ Create input table and config for Rhea. """ setup_logging( logger=logger, verbose=args.verbose, debug=args.debug, ) # get input table from LabKey or CLI if args.labkey_domain: logger.info( f"Fetching input table from LabKey instance " "'{args.labkey_domain}'..." ) input_table = fetch_labkey_table( domain=args.labkey_domain, container_path=args.labkey_path, query_name=args.table, ) labkey_table = expand_path( '.'.join([args.output_table.name, "labkey"]) ) input_table.to_csv( labkey_table, sep='\t', index=False, ) from_api = True else: logger.info(f"Reading input table from file '{args.table}'...") input_table = pd.read_csv( args.table, header=0, sep='\t', index_col=None, comment='#', engine='python', ) from_api = False # get LabKey to Snakemake sample table field mappings input_dict = pd.read_csv( args.input_to_output_mapping, header=0, sep='\t', index_col=None, comment='#', engine='python', ) args.input_to_output_mapping.close() input_dict.set_index('snakemake', inplace=True, drop=True) # create Snakemake table logger.info("Creating Snakemake input table...") snakemake_table = pd.DataFrame() for index, row in input_table.iterrows(): # extract data from LabKey-like table lk_replicate_name = row[input_dict.loc['replicate_name', 'labkey']] lk_condition = row[input_dict.loc['condition', 'labkey']] lk_seqmode = row[input_dict.loc['seqmode', 'labkey']] lk_fastq_path = row[input_dict.loc['fastq_path', 'labkey']] lk_fq1 = row[input_dict.loc['fq1', 'labkey']] lk_fq2 = row[input_dict.loc['fq2', 'labkey']] lk_fq1_3p = row[input_dict.loc['fq1_3p', 'labkey']] lk_fq1_5p = row[input_dict.loc['fq1_5p', 'labkey']] lk_fq2_3p = row[input_dict.loc['fq2_3p', 'labkey']] lk_fq2_5p = row[input_dict.loc['fq2_5p', 'labkey']] lk_organism = row[input_dict.loc['organism', 'labkey']] lk_sd = row[input_dict.loc['sd', 'labkey']] lk_mean = row[input_dict.loc['mean', 'labkey']] lk_mate1_direction = row[input_dict.loc['mate1_direction', 'labkey']] lk_mate2_direction = row[input_dict.loc['mate2_direction', 'labkey']] # extract, infer or convert to Snakemake input format if from_api and not os.path.isabs(lk_fastq_path): anchor = os.getcwd() logger.warning( f"[WARNING] Don't know how to interpret relative paths " "inside LabKey table. Trying with current working directory " f"'{anchor}' as an anchor, but it may be better to use" "absolute paths wherever possible..." ) else: anchor = os.path.abspath(os.path.dirname(args.table)) sample = "_".join([lk_replicate_name, lk_condition]) if lk_seqmode == 'PAIRED': seqmode = 'pe' fq2 = expand_path( lk_fastq_path, lk_fq2, anchor=anchor, ) elif lk_seqmode == 'SINGLE': seqmode = 'se' fq2 = "XXXXXXXXXXXXXXX" else: logger.error( f"[ERROR] Illegal sequencing mode '{lk_seqmode}' in row " f"{index+1}." ) sys.exit("Execution aborted.") fq1 = expand_path( lk_fastq_path, lk_fq1, anchor=anchor, ) read_length = get_read_length(fq1) index_size = read_length - 1 kmer = kmer_from_read_length(read_length) fq1_3p = lk_fq1_3p fq1_5p = lk_fq1_5p fq2_3p = lk_fq2_3p fq2_5p = lk_fq2_5p organism = lk_organism.replace(' ', '_').lower() gtf = expand_path( args.resources_dir, organism, 'annotation.gtf', ) genome = expand_path( args.resources_dir, organism, 'genome.fa', ) sd = lk_sd mean = lk_mean fq1_polya_3p, fq1_polya_5p = get_polya_adapter_seqs(lk_mate1_direction) fq2_polya_3p, fq2_polya_5p = get_polya_adapter_seqs(lk_mate2_direction) kallisto_directionality = get_strand_param_kallisto(lk_mate1_direction) alfa_directionality = get_strand_param_alfa(lk_mate1_direction) alfa_plus, alfa_minus = get_strand_names_alfa(lk_mate1_direction) # construct row in Snakemake input table snakemake_table.loc[index, 'sample'] = sample snakemake_table.loc[index, 'seqmode'] = seqmode snakemake_table.loc[index, 'fq1'] = fq1 snakemake_table.loc[index, 'fq2'] = fq2 snakemake_table.loc[index, 'index_size'] = index_size snakemake_table.loc[index, 'kmer'] = kmer snakemake_table.loc[index, 'fq1_3p'] = fq1_3p snakemake_table.loc[index, 'fq1_5p'] = fq1_5p snakemake_table.loc[index, 'fq2_3p'] = fq2_3p snakemake_table.loc[index, 'fq2_5p'] = fq2_5p snakemake_table.loc[index, 'organism'] = organism snakemake_table.loc[index, 'gtf'] = gtf snakemake_table.loc[index, 'genome'] = genome snakemake_table.loc[index, 'sd'] = sd snakemake_table.loc[index, 'mean'] = mean snakemake_table.loc[index, 'kallisto_directionality'] = \ kallisto_directionality snakemake_table.loc[index, 'alfa_directionality'] = alfa_directionality snakemake_table.loc[index, 'alfa_plus'] = alfa_plus snakemake_table.loc[index, 'alfa_minus'] = alfa_minus # add CLI argument-dependent parameters snakemake_table.loc[index, 'multimappers'] = args.multimappers snakemake_table.loc[index, 'soft_clip'] = args.soft_clip snakemake_table.loc[index, 'pass_mode'] = args.pass_mode snakemake_table.loc[index, 'libtype'] = args.libtype if args.trim_polya is True: snakemake_table.loc[index, 'fq1_polya_3p'] = fq1_polya_3p snakemake_table.loc[index, 'fq1_polya_5p'] = fq1_polya_5p snakemake_table.loc[index, 'fq2_polya_3p'] = fq2_polya_3p snakemake_table.loc[index, 'fq2_polya_5p'] = fq2_polya_5p # adjust sample table format snakemake_table.fillna('XXXXXXXXXXXXXXX', inplace=True) snakemake_table = snakemake_table.astype( { "sd": int, "mean": int, "multimappers": int, "kmer": int, "index_size": int, } ) # write Snakemake sample table logger.info("Writing Snakemake input table...") snakemake_table.to_csv( args.output_table, sep='\t', header=True, index=False) args.output_table.close() # compile entries for Snakemake config file logger.info("Creating Snakemake config file...") results_dir = expand_path( args.output_dir, "results", ) log_dir = expand_path( args.output_dir, "logs", ) kallisto_indexes = expand_path( results_dir, "kallisto_indexes", ) salmon_indexes = expand_path( results_dir, "salmon_indexes", ) star_indexes = expand_path( results_dir, "star_indexes", ) alfa_indexes = expand_path( results_dir, "alfa_indexes", ) # write Snakemake config file logger.info("Writing Snakemake config file...") config_file_content = f'''--- samples: "{expand_path(args.output_table.name)}" output_dir: "{results_dir}" log_dir: "{log_dir}" kallisto_indexes: "{kallisto_indexes}" salmon_indexes: "{salmon_indexes}" star_indexes: "{star_indexes}" alfa_indexes: "{alfa_indexes}" report_description: "{args.description}" report_logo: "{args.logo}" report_url: "{args.url}" ... ''' args.config_file.write(config_file_content) args.config_file.close() if __name__ == '__main__': args = parse_cli_args() # Set default according to CLI arg expand_path = partial(expand_path, no_abs=args.no_process_paths) # type: ignore main(args) logger.info("Program completed successfully.") sys.exit(0)