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Merge pull request #6 from cmmr/patch_v0.2.2
Patch v0.2.2
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,161 @@ | ||
| #!/usr/bin/env python | ||
|
|
||
| import argparse | ||
| import sys, os | ||
| import subprocess | ||
|
|
||
| def str2bool(v): | ||
| if isinstance(v, bool): | ||
| return v | ||
| if v.lower() in ('yes', 'true', 't', 'y', '1'): | ||
| return True | ||
| elif v.lower() in ('no', 'false', 'f', 'n', '0'): | ||
| return False | ||
| else: | ||
| raise argparse.ArgumentTypeError('Boolean value expected.') | ||
|
|
||
| pathname = os.path.dirname(__file__) | ||
| esviritu_script_path = os.path.abspath(pathname) | ||
| print(esviritu_script_path) | ||
|
|
||
| __version__='0.2.1' | ||
|
|
||
| def EsViritu(): | ||
| parser = argparse.ArgumentParser(description='EsViritu is a read mapping pipeline for detection and measurement of human and animal virus pathogens from short read metagenomic or clinical samples. Version ' + str(__version__)) | ||
|
|
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| required_args = parser.add_argument_group(' REQUIRED ARGUMENTS for EsViritu ') | ||
|
|
||
| required_args.add_argument("-r", "--reads", nargs="+", | ||
| dest="READS", required=True, | ||
| help='read file(s) in .fastq format. You can specify more than one separated by a space') | ||
| required_args.add_argument("-s", "--sample", | ||
| dest="SAMPLE", type=str, required=True, | ||
| help='Sample name. No space characters, please.') | ||
| required_args.add_argument("-t", "--cpu", | ||
| dest="CPU", type=int, required=True, | ||
| help='Example: 32 -- Number of CPUs available for EsViritu. ') | ||
| required_args.add_argument("-o", "--output_dir", | ||
| dest="OUTPUT_DIR", type=str, required=True, | ||
| help='Output directory name. Will be created if it does not exist. Can be shared with other samples. No space characters, please. ') | ||
|
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||
|
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||
|
|
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| optional_args = parser.add_argument_group(' OPTIONAL ARGUMENTS for EsViritu.') | ||
|
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||
| optional_args.add_argument('--version', action='version', version=str(__version__)) | ||
| optional_args.add_argument('-q', "--qual", dest="QUAL", type=str2bool, default='False', | ||
| help='True or False. Remove low-quality reads with fastp?') | ||
| optional_args.add_argument('-f', "--filter_seqs", dest="FILTER_SEQS", type=str2bool, default='False', | ||
| help='True or False. Remove reads aligning to sequences at filter_seqs/filter_seqs.fna ?') | ||
| optional_args.add_argument("--filter_dir", | ||
| dest="FILTER_DIR", type=str, default='default', | ||
| help='path to directory of sequences to filter. If not set, EsViritu looks for environmental variable ESVIRITU_FILTER. Then, if this variable is unset, it this is unset, DB path is assumed to be ' + esviritu_script_path.replace("src/EsViritu", "filter_seqs")) | ||
| optional_args.add_argument('-i', "--compare", dest="COMPARE", type=str2bool, default='True', | ||
| help='True or False. Calculate percent identity between sample consensus and reference sequences?') | ||
| optional_args.add_argument("-m", "--mode", | ||
| dest="MODE", type=str, default='general', | ||
| help='Placeholder for future development. Do not change.') | ||
| optional_args.add_argument("--temp", | ||
| dest="TEMP_DIR", type=str, default='default', | ||
| help='path of temporary directory. Default is {OUTPUT_DIR}/{SAMPLE}_temp/') | ||
| optional_args.add_argument("--keep", | ||
| dest="KEEP", type=str2bool, default='False', | ||
| help='True of False. Keep the intermediate files, located in the temporary directory? These can add up, so it is not recommended if space is a concern.') | ||
| optional_args.add_argument("-p", "--read_format", | ||
| dest="READ_FMT", type=str, default='unpaired', | ||
| help='unpaired or paired. Format of input reads. If paired, must provide 2 files (R1, then R2) after -r argument.') | ||
|
|
||
| optional_args.add_argument("--db", | ||
| dest="DB", type=str, default='default', | ||
| help='path to sequence database. If not set, EsViritu looks for environmental variable ESVIRITU_DB. Then, if this variable is unset, it this is unset, DB path is assumed to be ' + esviritu_script_path.replace("src/EsViritu", "DBs/v2.0.2")) | ||
| args = parser.parse_args() | ||
|
|
||
| READS = ' '.join(map(str,args.READS)) | ||
|
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||
|
|
||
| if len(READS.split()) == 2 and str(args.READ_FMT).lower() == "paired": | ||
| print(len(READS.split()), str(args.READ_FMT).lower(), "read files") | ||
| elif len(READS.split()) != 2 and str(args.READ_FMT).lower() == "paired": | ||
| print ("if stating --read_format paired, must provide exactly 2 read files") | ||
| quit() | ||
|
|
||
| if args.DB == "default" and os.getenv('ESVIRITU_DB') != None: | ||
| args.DB = os.getenv('ESVIRITU_DB') | ||
| elif args.DB == "default": | ||
| args.DB = esviritu_script_path.replace("src/EsViritu", "DBs/v2.0.2") | ||
|
|
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| if args.FILTER_DIR == "default" and os.getenv('ESVIRITU_FILTER') != None: | ||
| args.FILTER_DIR = os.getenv('ESVIRITU_FILTER') | ||
| elif args.FILTER_DIR == "default": | ||
| args.FILTER_DIR = esviritu_script_path.replace("src/EsViritu", "filter_seqs") | ||
|
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|
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| print("DB: ", str(args.DB)) | ||
|
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| print("filter seqs: ", str(args.FILTER_DIR)) | ||
|
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| print("version ", str(__version__)) | ||
|
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| # check if R script with libraries returns good exit code | ||
| completedProc = subprocess.run(['Rscript', str(esviritu_script_path) + '/check_R_libraries1.R']) | ||
|
|
||
| print(completedProc.returncode) | ||
| if completedProc.returncode != 0 : | ||
| print ("some required R packages are not found. Required:") | ||
| print ("reactable, htmltools, dplyr, reactablefmtr, dataui, data.table, RColorBrewer, viridis, scales, knitr") | ||
| print ("Did you activate the conda environment?") | ||
| print ("see yml. Exiting") | ||
| quit() | ||
|
|
||
|
|
||
| def is_tool(name): | ||
| """Check whether `name` is on PATH.""" | ||
| from distutils.spawn import find_executable | ||
| return find_executable(name) is not None | ||
|
|
||
| if is_tool("coverm") : | ||
| print ("coverm found") | ||
| else: | ||
| print ("coverm is not found. Exiting.") | ||
| quit() | ||
| if is_tool("minimap2") : | ||
| print ("minimap2 found") | ||
| else: | ||
| print ("minimap2 is not found. Exiting.") | ||
| quit() | ||
| if is_tool("samtools") : | ||
| print ("samtools found") | ||
| else: | ||
| print ("samtools is not found. Exiting.") | ||
| quit() | ||
| if is_tool("bioawk") : | ||
| print ("bioawk found") | ||
| else: | ||
| print ("bioawk is not found. Exiting.") | ||
| quit() | ||
| if is_tool("seqkit") : | ||
| print ("seqkit found") | ||
| else: | ||
| print ("seqkit is not found. Exiting.") | ||
| quit() | ||
| if is_tool("bedtools") : | ||
| print ("bedtools found") | ||
| else: | ||
| print ("bedtools is not found. Exiting.") | ||
| quit() | ||
| if is_tool("fastp") : | ||
| print ("fastp found") | ||
| else: | ||
| print ("fastp is not found. Exiting.") | ||
| quit() | ||
| if is_tool("seqfu") : | ||
| print ("seqfu found") | ||
| else: | ||
| print ("seqfu is not found. Exiting.") | ||
| quit() | ||
|
|
||
| subprocess.call(['bash', str(esviritu_script_path) + '/EsViritu_general.sh', | ||
| str(READS), str(args.SAMPLE), str(args.CPU), str(args.OUTPUT_DIR), | ||
| str(args.QUAL), str(args.FILTER_SEQS), str(args.FILTER_DIR), str(args.COMPARE), | ||
| str(args.TEMP_DIR), str(args.KEEP), str(args.READ_FMT).lower(), | ||
| str(__version__), str(args.DB), str(esviritu_script_path)]) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,161 +1 @@ | ||
| #!/usr/bin/env python | ||
|
|
||
| import argparse | ||
| import sys, os | ||
| import subprocess | ||
|
|
||
| def str2bool(v): | ||
| if isinstance(v, bool): | ||
| return v | ||
| if v.lower() in ('yes', 'true', 't', 'y', '1'): | ||
| return True | ||
| elif v.lower() in ('no', 'false', 'f', 'n', '0'): | ||
| return False | ||
| else: | ||
| raise argparse.ArgumentTypeError('Boolean value expected.') | ||
|
|
||
| pathname = os.path.dirname(__file__) | ||
| esviritu_script_path = os.path.abspath(pathname) | ||
| print(esviritu_script_path) | ||
|
|
||
| __version__='0.2.1' | ||
|
|
||
| def EsViritu(): | ||
| parser = argparse.ArgumentParser(description='EsViritu is a read mapping pipeline for detection and measurement of human and animal virus pathogens from short read metagenomic or clinical samples. Version ' + str(__version__)) | ||
|
|
||
| required_args = parser.add_argument_group(' REQUIRED ARGUMENTS for EsViritu ') | ||
|
|
||
| required_args.add_argument("-r", "--reads", nargs="+", | ||
| dest="READS", required=True, | ||
| help='read file(s) in .fastq format. You can specify more than one separated by a space') | ||
| required_args.add_argument("-s", "--sample", | ||
| dest="SAMPLE", type=str, required=True, | ||
| help='Sample name. No space characters, please.') | ||
| required_args.add_argument("-t", "--cpu", | ||
| dest="CPU", type=int, required=True, | ||
| help='Example: 32 -- Number of CPUs available for EsViritu. ') | ||
| required_args.add_argument("-o", "--output_dir", | ||
| dest="OUTPUT_DIR", type=str, required=True, | ||
| help='Output directory name. Will be created if it does not exist. Can be shared with other samples. No space characters, please. ') | ||
|
|
||
|
|
||
|
|
||
| optional_args = parser.add_argument_group(' OPTIONAL ARGUMENTS for EsViritu.') | ||
|
|
||
| optional_args.add_argument('--version', action='version', version=str(__version__)) | ||
| optional_args.add_argument('-q', "--qual", dest="QUAL", type=str2bool, default='False', | ||
| help='True or False. Remove low-quality reads with fastp?') | ||
| optional_args.add_argument('-f', "--filter_seqs", dest="FILTER_SEQS", type=str2bool, default='False', | ||
| help='True or False. Remove reads aligning to sequences at filter_seqs/filter_seqs.fna ?') | ||
| optional_args.add_argument("--filter_dir", | ||
| dest="FILTER_DIR", type=str, default='default', | ||
| help='path to directory of sequences to filter. If not set, EsViritu looks for environmental variable ESVIRITU_FILTER. Then, if this variable is unset, it this is unset, DB path is assumed to be ' + esviritu_script_path.replace("src/EsViritu", "filter_seqs")) | ||
| optional_args.add_argument('-i', "--compare", dest="COMPARE", type=str2bool, default='True', | ||
| help='True or False. Calculate percent identity between sample consensus and reference sequences?') | ||
| optional_args.add_argument("-m", "--mode", | ||
| dest="MODE", type=str, default='general', | ||
| help='Placeholder for future development. Do not change.') | ||
| optional_args.add_argument("--temp", | ||
| dest="TEMP_DIR", type=str, default='default', | ||
| help='path of temporary directory. Default is {OUTPUT_DIR}/{SAMPLE}_temp/') | ||
| optional_args.add_argument("--keep", | ||
| dest="KEEP", type=str2bool, default='False', | ||
| help='True of False. Keep the intermediate files, located in the temporary directory? These can add up, so it is not recommended if space is a concern.') | ||
| optional_args.add_argument("-p", "--read_format", | ||
| dest="READ_FMT", type=str, default='unpaired', | ||
| help='unpaired or paired. Format of input reads. If paired, must provide 2 files (R1, then R2) after -r argument.') | ||
|
|
||
| optional_args.add_argument("--db", | ||
| dest="DB", type=str, default='default', | ||
| help='path to sequence database. If not set, EsViritu looks for environmental variable ESVIRITU_DB. Then, if this variable is unset, it this is unset, DB path is assumed to be ' + esviritu_script_path.replace("src/EsViritu", "DBs/v2.0.2")) | ||
| args = parser.parse_args() | ||
|
|
||
| READS = ' '.join(map(str,args.READS)) | ||
|
|
||
|
|
||
| if len(READS.split()) == 2 and str(args.READ_FMT).lower() == "paired": | ||
| print(len(READS.split()), str(args.READ_FMT).lower(), "read files") | ||
| elif len(READS.split()) != 2 and str(args.READ_FMT).lower() == "paired": | ||
| print ("if stating --read_format paired, must provide exactly 2 read files") | ||
| quit() | ||
|
|
||
| if args.DB == "default" and os.getenv('ESVIRITU_DB') != None: | ||
| args.DB = os.getenv('ESVIRITU_DB') | ||
| elif args.DB == "default": | ||
| args.DB = esviritu_script_path.replace("src/EsViritu", "DBs/v2.0.2") | ||
|
|
||
| if args.FILTER_DIR == "default" and os.getenv('ESVIRITU_FILTER') != None: | ||
| args.FILTER_DIR = os.getenv('ESVIRITU_FILTER') | ||
| elif args.FILTER_DIR == "default": | ||
| args.FILTER_DIR = esviritu_script_path.replace("src/EsViritu", "filter_seqs") | ||
|
|
||
|
|
||
| print("DB: ", str(args.DB)) | ||
|
|
||
| print("filter seqs: ", str(args.FILTER_DIR)) | ||
|
|
||
| print("version ", str(__version__)) | ||
|
|
||
| # check if R script with libraries returns good exit code | ||
| completedProc = subprocess.run(['Rscript', str(esviritu_script_path) + '/check_R_libraries1.R']) | ||
|
|
||
| print(completedProc.returncode) | ||
| if completedProc.returncode != 0 : | ||
| print ("some required R packages are not found. Required:") | ||
| print ("reactable, htmltools, dplyr, reactablefmtr, dataui, data.table, RColorBrewer, viridis, scales, knitr") | ||
| print ("Did you activate the conda environment?") | ||
| print ("see yml. Exiting") | ||
| quit() | ||
|
|
||
|
|
||
| def is_tool(name): | ||
| """Check whether `name` is on PATH.""" | ||
| from distutils.spawn import find_executable | ||
| return find_executable(name) is not None | ||
|
|
||
| if is_tool("coverm") : | ||
| print ("coverm found") | ||
| else: | ||
| print ("coverm is not found. Exiting.") | ||
| quit() | ||
| if is_tool("minimap2") : | ||
| print ("minimap2 found") | ||
| else: | ||
| print ("minimap2 is not found. Exiting.") | ||
| quit() | ||
| if is_tool("samtools") : | ||
| print ("samtools found") | ||
| else: | ||
| print ("samtools is not found. Exiting.") | ||
| quit() | ||
| if is_tool("bioawk") : | ||
| print ("bioawk found") | ||
| else: | ||
| print ("bioawk is not found. Exiting.") | ||
| quit() | ||
| if is_tool("seqkit") : | ||
| print ("seqkit found") | ||
| else: | ||
| print ("seqkit is not found. Exiting.") | ||
| quit() | ||
| if is_tool("bedtools") : | ||
| print ("bedtools found") | ||
| else: | ||
| print ("bedtools is not found. Exiting.") | ||
| quit() | ||
| if is_tool("fastp") : | ||
| print ("fastp found") | ||
| else: | ||
| print ("fastp is not found. Exiting.") | ||
| quit() | ||
| if is_tool("seqfu") : | ||
| print ("seqfu found") | ||
| else: | ||
| print ("seqfu is not found. Exiting.") | ||
| quit() | ||
|
|
||
| subprocess.call(['bash', str(esviritu_script_path) + '/EsViritu_general.sh', | ||
| str(READS), str(args.SAMPLE), str(args.CPU), str(args.OUTPUT_DIR), | ||
| str(args.QUAL), str(args.FILTER_SEQS), str(args.FILTER_DIR), str(args.COMPARE), | ||
| str(args.TEMP_DIR), str(args.KEEP), str(args.READ_FMT).lower(), | ||
| str(__version__), str(args.DB), str(esviritu_script_path)]) | ||
| from .EsViritu import EsViritu |