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| Original file line number | Diff line number | Diff line change |
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| # ----------------------------------------------------------------------------- | ||
| # Copyright (c) 2014--, The Qiita Development Team. | ||
| # | ||
| # Distributed under the terms of the BSD 3-clause License. | ||
| # | ||
| # The full license is in the file LICENSE, distributed with this software. | ||
| # ----------------------------------------------------------------------------- | ||
|
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| from qiita_client import QiitaCommand | ||
| from .shogun import shogun | ||
| from .utils import (generate_shogun_dflt_params, get_dbs_list) | ||
| from os.path import join | ||
| from os import environ | ||
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| __all__ = ['Shogun'] | ||
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| # Define the shogun command | ||
| default_db = join(environ["QC_SHOGUN_DB_DP"], 'shogun') | ||
| default_db_list = get_dbs_list(environ["QC_SHOGUN_DB_DP"]) | ||
| req_params = {'input': ('artifact', ['per_sample_FASTQ'])} | ||
| opt_params = { | ||
| # database | ||
| 'Database': ["choice: [%s]" % default_db_list, | ||
| default_db], | ||
| # aligner | ||
| 'Aligner tool': ['choice:["utree", "burst", "bowtie2"]', 'bowtie2'], | ||
| # taxonomic levels | ||
| 'Taxonomy Level': ['choice:["kingdom", "phylum", "class", "order", ' | ||
| '"family", "genus", "species", "strain", "all"]', | ||
| 'all'], | ||
| # threads | ||
| 'Number of threads': ['integer', '1'], | ||
| } | ||
| outputs = {'Functional Predictions': 'BIOM', 'Taxonomic Predictions': 'BIOM'} | ||
| dflt_param_set = generate_shogun_dflt_params() | ||
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| shogun_cmd = QiitaCommand( | ||
| 'Shogun', "Functional and Taxonomic Predictions", shogun, | ||
| req_params, opt_params, outputs, dflt_param_set) |
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| # ----------------------------------------------------------------------------- | ||
| # Copyright (c) 2014--, The Qiita Development Team. | ||
| # | ||
| # Distributed under the terms of the BSD 3-clause License. | ||
| # | ||
| # The full license is in the file LICENSE, distributed with this software. | ||
| # ----------------------------------------------------------------------------- | ||
| from os.path import join | ||
| from tempfile import TemporaryDirectory | ||
| from .utils import readfq | ||
| from qp_shotgun.utils import (make_read_pairs_per_sample) | ||
| import gzip | ||
|
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| SHOGUN_PARAMS = { | ||
| 'Database': 'database', 'Aligner tool': 'aligner', | ||
| 'Taxonomic Level': 'levels', 'Number of threads': 'threads'} | ||
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| def generate_fna_file(temp_path, samples): | ||
| # Combines reverse and forward seqs per sample | ||
| # Returns filepaths of new combined files | ||
| output_fp = join(temp_path, 'combined.fna') | ||
| output = open(output_fp, "a") | ||
| count = 0 | ||
| for run_prefix, sample, f_fp, r_fp in samples: | ||
| with gzip.open(f_fp, 'rt') as fp: | ||
| # Loop through forward file | ||
| for header, seq, qual in readfq(fp): | ||
| output.write("%s_%d\n" % (sample, count)) | ||
| output.write("%s\n" % seq) | ||
| count += 1 | ||
| with gzip.open(r_fp, 'rt') as fp: | ||
| # Loop through reverse file | ||
| for header, seq, qual in readfq(fp): | ||
| output.write("%s_%d\n" % (sample, count)) | ||
| output.write("%s\n" % seq) | ||
| count += 1 | ||
| output.close() | ||
|
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| return output_fp | ||
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| def _format_params(parameters, func_params): | ||
| params = {} | ||
| # Loop through all of the commands alphabetically | ||
| for param in func_params: | ||
| # Find the value using long parameter names | ||
| parameter = func_params[param] | ||
| value = parameters[param] | ||
| params[parameter] = value | ||
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| return params | ||
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| def generate_shogun_align_commands(input_fp, temp_dir, parameters): | ||
| cmds = [] | ||
| cmds.append( | ||
| 'shogun align --aligner {aligner} --threads {threads} ' | ||
| '--database {database} --input {input} --output {output}'.format( | ||
| aligner=parameters['aligner'], | ||
| threads=parameters['threads'], | ||
| database=parameters['database'], | ||
| input=input_fp, | ||
| output=temp_dir)) | ||
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| return cmds | ||
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| def generate_shogun_assign_taxonomy_commands(temp_dir, parameters): | ||
| cmds = [] | ||
| aln2ext = {'utree': 'tsv', 'burst': 'b6', 'bowtie2': 'sam'} | ||
| ext = aln2ext[parameters['aligner']] | ||
| output_fp = join(temp_dir, 'profile.tsv') | ||
| cmds.append( | ||
| 'shogun assign_taxonomy ' | ||
| '--aligner {aligner} ' | ||
| '--database {database} ' | ||
| '--input {input} --output {output}'.format( | ||
| aligner=parameters['aligner'], | ||
| database=parameters['database'], | ||
| input=join(temp_dir, 'alignment.%s.%s' % (parameters['aligner'], | ||
| ext)), | ||
| output=output_fp)) | ||
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| return cmds, output_fp | ||
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| def generate_shogun_functional_commands(profile_dir, temp_dir, | ||
| parameters, sel_level): | ||
| cmds = [] | ||
| cmds.append( | ||
| 'shogun functional ' | ||
| '--database {database} ' | ||
| '--input {input} ' | ||
| '--output {output} ' | ||
| '--level {level}'.format( | ||
| database=parameters['database'], | ||
| input=profile_dir, | ||
| output=join(temp_dir, 'profile.functional.%s.tsv' % sel_level), | ||
| level=sel_level)) | ||
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| return cmds | ||
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| def generate_biom_conversion_commands(input_fp, output_dir, level): | ||
| cmds = [] | ||
| cmds.append( | ||
| 'biom convert -i {input} ' | ||
| '-o {output} ' | ||
| '--table-type="OTU table" ' | ||
| '--process-obs-metadata taxonomy --to-hdf5'.format( | ||
| input=input_fp, | ||
| output=join(output_dir, 'otu_table.%s.biom' % level))) | ||
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| return cmds | ||
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| def shogun(qclient, job_id, parameters, out_dir): | ||
| """Run Shogun with the given parameters | ||
| Parameters | ||
| ---------- | ||
| qclient : tgp.qiita_client.QiitaClient | ||
| The Qiita server client | ||
| job_id : str | ||
| The job id | ||
| parameters : dict | ||
| The parameter values to run split libraries | ||
| out_dir : str | ||
| The path to the job's output directory | ||
| Returns | ||
| ------- | ||
| bool, list, str | ||
| The results of the job | ||
| """ | ||
| # Step 1 get the rest of the information need to run Atropos | ||
| qclient.update_job_step(job_id, "Step 1 of 6: Collecting information") | ||
| artifact_id = parameters['input'] | ||
| del parameters['input'] | ||
|
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| # Get the artifact filepath information | ||
| artifact_info = qclient.get("/qiita_db/artifacts/%s/" % artifact_id) | ||
| fps = artifact_info['files'] | ||
|
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| # Get the artifact metadata | ||
| prep_info = qclient.get('/qiita_db/prep_template/%s/' | ||
| % artifact_info['prep_information'][0]) | ||
| qiime_map = prep_info['qiime-map'] | ||
|
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| # Step 2 converting to fna | ||
| qclient.update_job_step( | ||
| job_id, "Step 2 of 6: Converting to FNA for Shogun") | ||
|
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| with TemporaryDirectory(dir=out_dir, prefix='shogun_') as temp_dir: | ||
| rs = fps['raw_reverse_seqs'] if 'raw_reverse_seqs' in fps else [] | ||
| samples = make_read_pairs_per_sample( | ||
| fps['raw_forward_seqs'], rs, qiime_map) | ||
|
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| comb_fp = generate_fna_file(temp_dir, samples) | ||
| # Combining files | ||
| parameters = _format_params(parameters, SHOGUN_PARAMS) | ||
| # Step 3 align | ||
| qclient.update_job_step( | ||
| job_id, "Step 3 of 6: Aligning FNA with Shogun") | ||
| generate_shogun_align_commands( | ||
| comb_fp, temp_dir, parameters) | ||
| # Step 4 taxonomic profile | ||
| qclient.update_job_step( | ||
| job_id, "Step 4 of 6: Taxonomic profile with Shogun") | ||
| cmd, profile_fp = generate_shogun_assign_taxonomy_commands( | ||
| temp_dir, parameters) | ||
| # Step 5 functional profile | ||
| qclient.update_job_step( | ||
| job_id, "Step 5 of 6: Functional profile with Shogun") | ||
| levels = ['genus', 'species', 'level'] | ||
| for level in levels: | ||
| generate_shogun_functional_commands( | ||
| profile_fp, temp_dir, parameters, level) | ||
| # Step 6 functional profile | ||
| qclient.update_job_step( | ||
| job_id, "Step 6 of 6: Converting results to BIOM") | ||
| for level in levels: | ||
| input_fp = ('profile.functional.%s.tsv' % level) | ||
| generate_biom_conversion_commands(input_fp, out_dir, level) | ||
|
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| ainfo = {} | ||
|
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| return True, ainfo, "" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| # ----------------------------------------------------------------------------- | ||
| # Copyright (c) 2014--, The Qiita Development Team. | ||
| # | ||
| # Distributed under the terms of the BSD 3-clause License. | ||
| # | ||
| # The full license is in the file LICENSE, distributed with this software. | ||
| # ----------------------------------------------------------------------------- |
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