-
Notifications
You must be signed in to change notification settings - Fork 7
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
1 parent
ca721a4
commit 335a4ef
Showing
12 changed files
with
662 additions
and
98 deletions.
There are no files selected for viewing
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 |
|---|---|---|
|
|
@@ -9,7 +9,7 @@ | |
| Copyright (C) 2016 Miguel Machado <[email protected]> | ||
| Last modified: August 31, 2016 | ||
| Last modified: September 30, 2016 | ||
| This program is free software: you can redistribute it and/or modify | ||
| it under the terms of the GNU General Public License as published by | ||
|
|
@@ -33,13 +33,14 @@ | |
| import modules.spades as spades | ||
| import modules.pilon as pilon | ||
| import modules.mlst as mlst | ||
| import modules.assembly_mapping as assembly_mapping | ||
| import time | ||
| import os | ||
| import sys | ||
|
|
||
|
|
||
| def main(): | ||
| version = '1.7' | ||
| version = '1.8' | ||
| args = utils.parseArguments(version) | ||
|
|
||
| general_start_time = time.time() | ||
|
|
@@ -73,11 +74,8 @@ def main(): | |
| print '\n' + 'VERSION INNUca.py:' | ||
| utils.scriptVersionGit(version, os.getcwd(), script_path) | ||
|
|
||
| # Save CPU information | ||
| with open(os.path.join(outdir, 'cpu_information.' + time_str + '.cpu.txt'), 'wt') as reader: | ||
| command = ['cat', '/proc/cpuinfo'] | ||
| run_successfully, stdout, stderr = utils.runCommandPopenCommunicate(command, False, None) | ||
| reader.write(stdout) | ||
| # Get CPU information | ||
| utils.get_cpu_information(outdir, time_str) | ||
|
|
||
| # Set and print PATH variable | ||
| utils.setPATHvariable(args.doNotUseProvidedSoftware, script_path) | ||
|
|
@@ -106,8 +104,13 @@ def main(): | |
| sys.exit('\n' + 'Errors:' + '\n' + '\n'.join(missingPrograms)) | ||
|
|
||
| # .jar paths | ||
| jar_path_trimmomatic = programs_version_dictionary['trimmomatic-0.36.jar'][3] | ||
| jar_path_pilon = programs_version_dictionary['pilon-1.18.jar'][3] | ||
| jar_path_trimmomatic = None | ||
| if not args.skipTrimmomatic: | ||
| jar_path_trimmomatic = programs_version_dictionary['trimmomatic-0.36.jar'][3] | ||
|
|
||
| jar_path_pilon = None | ||
| if not args.skipPilon and not args.skipSPAdes: | ||
| jar_path_pilon = programs_version_dictionary['pilon-1.18.jar'][3] | ||
|
|
||
| # Check if input directory exists with fastq files and store samples name that have fastq files | ||
| inputDirectory = os.path.abspath(os.path.join(args.inputDirectory, '')) | ||
|
|
@@ -133,13 +136,14 @@ def main(): | |
| # Determine SPAdes maximum memory | ||
| spadesMaxMemory = None | ||
| if not args.skipSPAdes: | ||
| print '' | ||
| spadesMaxMemory = spades.define_memory(args.spadesMaxMemory, args.threads) | ||
|
|
||
| # Run comparisons for each sample | ||
| for sample in samples: | ||
| sample_start_time = time.time() | ||
|
|
||
| print '\n' + 'Sample: ' + sample | ||
| print '\n' + 'Sample: ' + sample + '\n' | ||
|
|
||
| # Create sample outdir | ||
| sample_outdir = os.path.abspath(os.path.join(outdir, sample, '')) | ||
|
|
@@ -154,7 +158,7 @@ def main(): | |
| continue | ||
|
|
||
| print 'The following files will be used:' | ||
| print str(fastq_files) | ||
| print str(fastq_files) + '\n' | ||
|
|
||
| # Run INNUca.py analysis | ||
| run_successfully, pass_qc, run_report = run_INNUca(sample, sample_outdir, fastq_files, args, script_path, scheme, spadesMaxMemory, jar_path_trimmomatic, jar_path_pilon) | ||
|
|
@@ -218,7 +222,7 @@ def run_INNUca(sampleName, outdir, fastq_files, args, script_path, scheme, spade | |
| if os.path.isfile(report_file): | ||
| os.remove(report_file) | ||
| # Run getEstimatedCoverage | ||
| runs['first_Coverage'] = coverage.getEstimatedCoverage(fastq_files, genomeSize, outdir) | ||
| runs['first_Coverage'] = coverage.getEstimatedCoverage(fastq_files, genomeSize, outdir, threads) | ||
| else: | ||
| print '--skipEstimatedCoverage set. Skipping First Estimated Coverage analysis' | ||
| runs['first_Coverage'] = skipped | ||
|
|
@@ -242,14 +246,15 @@ def run_INNUca(sampleName, outdir, fastq_files, args, script_path, scheme, spade | |
|
|
||
| # Run second Estimated Coverage | ||
| if not args.skipEstimatedCoverage: | ||
| runs['second_Coverage'] = coverage.getEstimatedCoverage(fastq_files, genomeSize, outdir) | ||
| runs['second_Coverage'] = coverage.getEstimatedCoverage(fastq_files, genomeSize, outdir, threads) | ||
| else: | ||
| print '--skipEstimatedCoverage set. Skipping Second Estimated Coverage analysis' | ||
| runs['second_Coverage'] = skipped | ||
|
|
||
| # Run second FastQC | ||
| if not args.skipFastQC: | ||
| runs['second_FastQC'] = fastqc.runFastQCanalysis(outdir, threads, adaptersFasta, fastq_files)[0:4] | ||
| run_successfully, pass_qc, time_taken, failing, maximumReadsLength, nts2clip_based_ntsContent = fastqc.runFastQCanalysis(outdir, threads, adaptersFasta, fastq_files) | ||
| runs['second_FastQC'] = [run_successfully, pass_qc, time_taken, failing] | ||
| else: | ||
| print '--skipFastQC set. Skipping Second FastQC analysis' | ||
| runs['second_FastQC'] = skipped | ||
|
|
@@ -266,20 +271,47 @@ def run_INNUca(sampleName, outdir, fastq_files, args, script_path, scheme, spade | |
|
|
||
| # Run SPAdes | ||
| if not args.skipSPAdes: | ||
| run_successfully, pass_qc, time_taken, failing, contigs = spades.runSpades(sampleName, outdir, threads, fastq_files, args.spadesNotUseCareful, spadesMaxMemory, args.spadesMinCoverageAssembly, args.spadesMinContigsLength, genomeSize, args.spadesKmers, maximumReadsLength, args.spadesDefaultKmers, args.spadesMinCoverageContigs) | ||
| run_successfully, pass_qc, time_taken, failing, contigs_spades = spades.runSpades(sampleName, outdir, threads, fastq_files, args.spadesNotUseCareful, spadesMaxMemory, args.spadesMinCoverageAssembly, args.spadesMinContigsLength, genomeSize, args.spadesKmers, maximumReadsLength, args.spadesDefaultKmers, args.spadesMinCoverageContigs) | ||
| runs['SPAdes'] = [run_successfully, pass_qc, time_taken, failing] | ||
|
|
||
| if run_successfully: | ||
| # Run Pilon | ||
| contigs = contigs_spades | ||
|
|
||
| if not args.skipPilon: | ||
| run_successfully, _, time_taken, failing, assembly_polished = pilon.runPilon(jar_path_pilon, contigs, fastq_files, threads, outdir, args.pilonKeepFiles, args.pilonKeepSPAdesAssembly) | ||
| run_successfully, _, time_taken, failing, assembly_polished, bam_file, pilon_folder = pilon.runPilon(jar_path_pilon, contigs_spades, fastq_files, threads, outdir) | ||
| runs['Pilon'] = [run_successfully, None, time_taken, failing] | ||
|
|
||
| if run_successfully: | ||
| contigs = assembly_polished | ||
|
|
||
| # Run Assembly Mapping check | ||
| if bam_file is not None: | ||
| if not args.skipAssemblyMapping: | ||
| run_successfully, pass_qc, time_taken, failing, assembly_filtered = assembly_mapping.runAssemblyMapping(bam_file, contigs_spades, threads, outdir, args.assemblyMinCoverageContigs, assembly_polished, args.assemblyKeepPilonContigs) | ||
| runs['Assembly_Mapping'] = [run_successfully, pass_qc, time_taken, failing] | ||
|
|
||
| if run_successfully: | ||
| contigs = assembly_filtered | ||
| else: | ||
| print '--skipAssemblyMapping set. Skipping Assembly Mapping check' | ||
| runs['Assembly_Mapping'] = skipped | ||
| else: | ||
| print 'Pilon did not produce the bam file! Assembly Mapping check' | ||
| runs['Assembly_Mapping'] = skipped | ||
|
|
||
| if assembly_polished is not None and not args.pilonKeepSPAdesAssembly: | ||
| os.remove(contigs_spades) | ||
|
|
||
| if not args.pilonKeepFiles: | ||
| utils.removeDirectory(pilon_folder) | ||
|
|
||
| else: | ||
| print '--skipPilon set. Skipping Pilon correction' | ||
| print '--skipPilon set. Skipping Pilon correction and Assembly Mapping check' | ||
| runs['Pilon'] = skipped | ||
| runs['Assembly_Mapping'] = skipped | ||
|
|
||
| print '\n' + 'Assembly to use: ' + contigs + '\n' | ||
|
|
||
| # Run MLST | ||
| if not args.skipMLST: | ||
|
|
@@ -288,18 +320,20 @@ def run_INNUca(sampleName, outdir, fastq_files, args, script_path, scheme, spade | |
| print '--skipMLST set. Skipping MLST analysis' | ||
| runs['MLST'] = skipped | ||
| else: | ||
| print 'SPAdes did not run successfully! Skipping Pilon correction and MLST analysis' | ||
| print 'SPAdes did not run successfully! Skipping Pilon correction, Assembly Mapping check and MLST analysis' | ||
| runs['Pilon'] = skipped | ||
| runs['Assembly_Mapping'] = skipped | ||
| runs['MLST'] = skipped | ||
|
|
||
| else: | ||
| print '--skipSPAdes set. Skipping SPAdes Pilon correction and MLST analysis' | ||
| print '--skipSPAdes set. Skipping SPAdes Pilon correction, Assembly Mapping check and MLST analysis' | ||
| runs['SPAdes'] = skipped | ||
| runs['Pilon'] = skipped | ||
| runs['Assembly_Mapping'] = skipped | ||
| runs['MLST'] = skipped | ||
| else: | ||
| print 'Moving to the next sample' | ||
| for step in ('first_Coverage', 'first_FastQC', 'Trimmomatic', 'second_Coverage', 'second_FastQC', 'SPAdes', 'Pilon', 'MLST'): | ||
| for step in ('first_Coverage', 'first_FastQC', 'Trimmomatic', 'second_Coverage', 'second_FastQC', 'SPAdes', 'Pilon', 'Assembly_Mapping', 'MLST'): | ||
| runs[step] = not_run | ||
|
|
||
| # Remove Trimmomatic directory with cleaned reads | ||
|
|
@@ -317,8 +351,9 @@ def run_INNUca(sampleName, outdir, fastq_files, args, script_path, scheme, spade | |
| pass_fastqc = runs['second_FastQC'][1] or (runs['second_FastQC'][1] is None and runs['first_FastQC'][1]) | ||
| pass_trimmomatic = runs['Trimmomatic'][1] is not False | ||
| pass_spades = runs['SPAdes'][1] is not False | ||
| pass_assemblyMapping = runs['Assembly_Mapping'][1] is not False | ||
| pass_mlst = runs['MLST'][1] is not False | ||
| pass_qc = all([pass_fastqIntegrity, pass_cov, pass_fastqc, pass_trimmomatic, pass_spades, pass_mlst]) | ||
| pass_qc = all([pass_fastqIntegrity, pass_cov, pass_fastqc, pass_trimmomatic, pass_spades, pass_assemblyMapping, pass_mlst]) | ||
|
|
||
| return run_successfully, pass_qc, runs | ||
|
|
||
|
|
||
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
Oops, something went wrong.