def get_extract_otu_tax_rank_command(config, fixed_rank, taxa_otu_rank, otu_taxa_labels, abund_table,
significance_threshold, rdp_database, rdp_depth):
"""Extract OTU-tax-ranks"""
description = 'OTU taxextr'
short = 'te'
command = [config['scripts']['taxrank_extractor'],
'--input', fixed_rank,
'--output', taxa_otu_rank,
'--significance_threshold', significance_threshold,
'--out_taxlabel', otu_taxa_labels,
'--abundance_table', abund_table]
if rdp_database == '16S' and rdp_depth == 'phylum':
command += ['--deeper_taxa', 'proteobacteria']
if rdp_depth == 'phylum':
base_depth = 1
elif rdp_depth == 'class':
base_depth = 2
else:
raise Exception('Unknown RDP depth encountered: {}'.format(rdp_depth))
if rdp_database == '16S':
command += ['--depth', base_depth]
elif rdp_database == '18S':
command += ['--depth', base_depth + 1]
return program_module.ProgramCommand(description, short, command)
def get_prinseq_command(config_file, input_file, good_output, bad_output):
"""
Runs the Prinseq program which performs various cleaning on the reads
Currently performs:
- Quality trimming for both ends
- Evaluating that the remaining length is long enough
- Evaluating the quality of the read
- Evaluating that it contains a low number of Ns
"""
description = 'Prinseq'
short = 'pq'
prinseq = [config_file['programs']['prinseq']]
input_command = ['-fastq', input_file]
output_command = ['-out_good', good_output,
'-out_bad', bad_output]
# phred_command = ['-phred64']
trim_command = ['-trim_qual_left', str(TRIM_QUAL), '-trim_qual_right', str(TRIM_QUAL)]
minlen_command = ['-min_len', str(MIN_LEN)]
minqual_command = ['-min_qual_mean', str(MIN_QUAL)]
ns_command = ['-ns_max_p', str(MAX_NS)]
process_command = prinseq + input_command + output_command\
+ trim_command + minlen_command + minqual_command + ns_command # + derep_command
return program_module.ProgramCommand(description, short, process_command)
def get_timeplot_command(config, log_table_fp, timeplot_fp):
"""Create a taxa barplot using matplotlib"""
description = 'Timeplot'
short = 'tp'
command = [
config['scripts']['time_script'], '-i', log_table_fp, '-o', timeplot_fp
]
return program_module.ProgramCommand(description, short, command)
def get_generate_otu_names_command(config, raw_otus, otu_name_map):
"""Generates mapping table between old and newly generated OTU names"""
description = 'Generate otu names'
short = 'GOn'
command = [
config['scripts']['generate_otu_names'], '--input', raw_otus,
'--output', otu_name_map
]
return program_module.ProgramCommand(description, short, command)
def get_convert_to_phylip_command(config, pynast_alignment_fasta,
pynast_alignment_phylip):
"""Convert fasta-alignment to phylip format"""
description = 'Convert fas/phy'
short = 'Cfp'
command = [
config['scripts']['fasta_to_phylip'], '--input_fasta',
pynast_alignment_fasta, '--output_phylip', pynast_alignment_phylip
]
return program_module.ProgramCommand(description, short, command)
def get_fast_tree_command(config, input_alignment_fp, output_tree_fp):
"""Produces a tree file from a PyNAST alignment using Fast Tree"""
description = 'FastTree'
short = 'FT'
command = [config['scripts']['fasttree'],
'--input', input_alignment_fp,
'--output', output_tree_fp,
'--fasttree_path', config['programs']['fasttree']]
return program_module.ProgramCommand(description, short, command)
def get_create_color_tables_command(config, fixed_rdp_output_fp, otu_color_taxa_table, taxa_color_table):
"""Produces color tables for color strap and color definitions"""
description = 'Create color-tab'
short = 'cct'
command = [config['scripts']['colors_from_phyla'],
'--input', fixed_rdp_output_fp,
'--otu_color_taxa', otu_color_taxa_table,
'--taxa_color', taxa_color_table]
return program_module.ProgramCommand(description, short, command)
def get_reduce_phylip_command(config, phylip_alignment,
phylip_alignment_reduced):
"""Remove empty columns from phylip alignment"""
description = 'Reduce phylip'
short = 'rp'
command = [
config['scripts']['reduce_phylip'], '-i', phylip_alignment, '-o',
phylip_alignment_reduced
]
return program_module.ProgramCommand(description, short, command)
def get_decompression_command(config_file, compressed_input_fp,
decompressed_output_base):
"""Runs the decompression script, targetting .gz files only"""
description = 'decompress'
short = 'dc'
command = [
config_file['scripts']['decompression_script'], '--input',
compressed_input_fp, '--output_base', decompressed_output_base,
'--decompression_mode', 'gz'
]
return program_module.ProgramCommand(description, short, command)
def get_derep_command(config, raw_reads_fp, dereplicated_fp):
"""
Adds the -derep_fulllength execute_test
Dereplicates full-length sequences
Outputs fasta-file with dereplication counts
"""
description = 'Dereplicate'
short = 'dr'
command = [
config['programs']['dereplicate'], raw_reads_fp, dereplicated_fp
]
return program_module.ProgramCommand(description, short, command)
def get_merge_command(config_file, input_fastq_files_fp, merged_output_fp,
labels):
"""Runs the decompression script, targetting .gz files only"""
description = 'merge'
short = 'mr'
print('DEBUG input labels {}'.format(labels))
command = [
config_file['scripts']['merge'], '--input_files', input_fastq_files_fp,
'--output', merged_output_fp, '--labels', labels
]
return program_module.ProgramCommand(description, short, command)
def get_fastq_to_fasta_command(config, fastq_fp, fasta_fp):
"""
Command for converting the input files from fastq to fasta format
This format is needed in the following steps
"""
description = 'Fq to Fa'
short = 'FQA'
command = [
config['scripts']['fasta_to_fastq'], '--input', fastq_fp, '--output',
fasta_fp, '--extract_label'
]
return program_module.ProgramCommand(description, short, command)
def get_create_barplot_data_command(config, taxa_otu_rank, otu_sample_table,
tax_count_table, tax_abund_table):
"""Extracts data from the otu-taxa-table and outputs taxa barplot data"""
description = 'Create bar-data'
short = 'cbd'
command = [
config['scripts']['create_barplot_table'], '--taxa_table',
taxa_otu_rank, '--otu_sample_table', otu_sample_table,
'--barplot_cluster', tax_count_table, '--barplot_abund',
tax_abund_table
]
return program_module.ProgramCommand(description, short, command)
def get_generate_alpha_plots_command(config, plot_rar, plot_chao, otu_mapping_table):
"""Runs the preliminary chao1/rarefaction calculating script"""
description = 'Chao1'
short = 'PC'
command = [config['scripts']['alpha_plots'],
'--plot_rarefaction', plot_rar,
'--plot_chao', plot_chao,
'--samplepoints', SAMPLE_STEPS,
'--replicates', SAMPLE_REPLICATES,
'--otu_mapping_table', otu_mapping_table]
return program_module.ProgramCommand(description, short, command)
def get_filter_otu_command(config, complete_otu_fp, otu_abundancy_fp,
output_fp, abund_filt_fp, filter_threshold):
"""
Filters the otus based on mapped read count
"""
description = 'Abund. filtering'
short = 'af'
command = [
config['scripts']['filter_otus'], '-i', complete_otu_fp, '-m',
otu_abundancy_fp, '-o', output_fp, '-t', filter_threshold, '-O',
abund_filt_fp
]
return program_module.ProgramCommand(description, short, command)
def get_create_otu_table_command(config, cluster_mapping, derep_mapping, name_mapping_table, otu_table):
"""
Creates OTU table where counts in separate samples are mapped to the different OTUs
"""
description = 'OTU-table'
short = 'OT'
command = [config['scripts']['create_otu_table'],
'--cluster_mapping', cluster_mapping,
'--derep_mapping', derep_mapping,
'--name_mapping', name_mapping_table,
'--output', otu_table]
return program_module.ProgramCommand(description, short, command)
def get_ete_command(config, input_tree_fp, output_tree_pic_fp,
otu_abund_fp, color_strap_fp, labels_fp):
"""Uses the Python ETE module to create and render a tree"""
description = 'ETE'
short = 'ete'
command = ['xvfb-run', config['scripts']['ete'],
'--input', input_tree_fp,
'--output', output_tree_pic_fp,
'--labels', labels_fp,
'--abundancies', otu_abund_fp,
'--color_taxa', color_strap_fp]
return program_module.ProgramCommand(description, short, command)
def get_chimera_checking_command(config, unchecked_fp, non_chimeric_fp):
"""
Runs chimeric checking
Identifies chimeric reads, and outputs non-chimeric reads to target file path
"""
description = 'Chim. checking'
short = 'cc'
command = [
config['programs']['vsearch'], '-uchime_ref', unchecked_fp, '-db',
config['databases']['vsearch_16S_ref'], '-uchimeout',
str(non_chimeric_fp + '.OUTPUT'), '-nonchimeras', non_chimeric_fp
]
return program_module.ProgramCommand(description, short, command)
def get_cdhit_parser_command(config, input_mapping_matrix_fp,
output_mapping_table_fp, cluster_mapping_fp):
"""
Extracts OTU counts from CDHIT mapping table and outputs them
as an abundancy matrix
"""
description = 'Extract otu table'
short = 'eOt'
command = [
config['scripts']['cdhit_output_parser'], '-i',
input_mapping_matrix_fp, '-o', output_mapping_table_fp,
'--count_dereplicated', '--seq_matrix', cluster_mapping_fp
]
return program_module.ProgramCommand(description, short, command)
def get_rename_otus_command(config, input_otus, input_table, renamed_fasta,
renamed_table, name_mapping):
"""
Renames OTUs in fasta-file and abundancy matrix
Outputs then as 'output.fasta' and 'output.table'
"""
description = 'Rename otus'
short = 'rO'
command = [
config['scripts']['rename_otus'], '--fasta', input_otus, '--table',
input_table, '--output_fasta', renamed_fasta, '--output_table',
renamed_table, '--name_mapping', name_mapping
]
return program_module.ProgramCommand(description, short, command)
def get_label_fasta_header_command(config, raw_reads_fp, labelled_fp):
"""
Adds labels to fasta headers
Is used to add ';size=1;' if the derep command isn't used
"""
description = 'Label reads'
short = 'lr'
label = ';size=1;'
command = [
config['scripts']['label_fasta_headers'], '-i', raw_reads_fp, '-o',
labelled_fp, '-l', label
]
return program_module.ProgramCommand(description, short, command)
def get_script_dereplicator_command(config, raw_reads_fp, dereplicated_fp,
mapping_fp):
"""
Home-made dereplication script
"""
description = 'Dereplicate script'
short = 'dr'
# command = [config['programs']['dereplicate'], raw_reads_fp, dereplicated_fp]
command = [
config['scripts']['script_dereplicator'], '--input', raw_reads_fp,
'--output', dereplicated_fp, '--mapping_file', mapping_fp
]
return program_module.ProgramCommand(description, short, command)
def get_annotate_otus_command(config, raw_otus, raw_abundance, annotated_otus,
annotated_abundance, taxa_otu_rank,
fixed_rank_annotation):
"""
Annotates an OTU-fasta file and an OTU-abundancy matrix
"""
description = 'Annotate otu'
short = 'ao'
command = [
config['scripts']['annotate_otu'], '--input_fasta', raw_otus,
'--input_abundancy', raw_abundance, '--input_taxa', taxa_otu_rank,
'--annotated_fasta', annotated_otus, '--annotated_abundancy',
annotated_abundance, '--fixed_rank_annotation', fixed_rank_annotation
]
return program_module.ProgramCommand(description, short, command)
def get_filter_bad_taxa_command(config, raw_otus, abundancy_matrix,
otu_taxa_table, output_dir):
"""
Filters out OTUs whose taxa is determined with low confidence
by RDP classifier.
Filtering effects both OTU fasta file, and abundancy table
"""
description = 'Filter taxa'
short = 'ft'
command = [
config['scripts']['filter_poor_taxa'], '--input', raw_otus,
'--taxa_table', otu_taxa_table, '--suffix', TAX_FILTER_SUFFIX,
'--abund_matrix', abundancy_matrix, '--output_dir', output_dir
]
return program_module.ProgramCommand(description, short, command)
def get_raxml_command(config, input_alignment_fp, output_dir):
"""Produces a tree file from a PyNAST alignment using Fast Tree"""
description = 'RAxML'
short = 'Rx'
seed = 12345
model_of_substitution = 'GTRGAMMA'
raxml_out_name = 'raxml_tree.tre'
command = [config['programs']['raxml'],
'-p', seed,
'-m', model_of_substitution,
'-s', input_alignment_fp,
'-n', raxml_out_name,
'-w', output_dir]
return program_module.ProgramCommand(description, short, command)
def get_taxa_barplot_command(config,
tax_count_table_fp,
matlibplot_out_fp,
taxa_color_table,
plot_relative_abundance=False,
title='MODTITL',
ylabel='MODYLABL'):
"""Create a taxa barplot using matplotlib"""
description = 'Taxa-barplot'
short = 'tb'
command = [
config['scripts']['make_barplot'], '--input', tax_count_table_fp,
'--output', matlibplot_out_fp, '--title', title, '--ylabel', ylabel,
'--color_table', taxa_color_table
]
if plot_relative_abundance:
command.append('--relative_abundance')
return program_module.ProgramCommand(description, short, command)
def get_rdp_command(config, input_fp, fixed_rank_fp, significant_taxa_fp, significance_threshold, chosen_database):
"""Run the RDP classification program"""
description = 'RDP Classifier'
short = 'RDP'
if chosen_database == '18S':
train_option = ['-t', config['databases']['rdpclassifier_18S']]
else:
train_option = []
command = ['java', '-Xmx' + str(MEMORY_SIZE_GB) + 'g',
'-jar', config['programs']['rdpclassifier'],
'classify', '-c', significance_threshold,
'-f', 'fixrank',
'-o', fixed_rank_fp,
'-h', significant_taxa_fp]
command += train_option
command += [input_fp]
return program_module.ProgramCommand(description, short, command)
def get_run_cdhit_command(config, input_reads_fp, output_otus_fp,
clustering_identity):
"""
Runs CD-HIT, clustering sequences into OTUs
"""
description = 'CD-HIT'
short = 'CH'
output_description_length_option = 0
command = [
config['programs']['cdhit'], '-i', input_reads_fp, '-o',
output_otus_fp, '-c', clustering_identity, '-n', CDHIT_WORD_SIZE, '-T',
CDHIT_THREADS, '-M', CDHIT_MEMORY, '-d',
output_description_length_option
]
if ACCURATE_CLUSTERING:
command.append('-g')
command.append(1)
print('CD-HIT command: {}'.format(command))
return program_module.ProgramCommand(description, short, command)
def get_pynast_command(config, filtered_otus, pynast_alignment_fasta,
pynast_log, pynast_failed,
min_alignment_similarity_percentage, rdp_database):
"""Run PyNAST"""
description = 'PyNAST'
short = 'PN'
if rdp_database == '16S':
pynast_database = config['databases']['pynast_16S']
elif rdp_database == '18S':
pynast_database = config['databases']['pynast_16S']
else:
raise AttributeError(
'Chosen RDP database: {} doesn\'t exist!'.format(rdp_database))
command = [
config['programs']['pynast'], '-i', filtered_otus, '-t',
pynast_database, '-l', MIN_INPUT_TO_ALIGNMENT_LENGTH, '-p',
min_alignment_similarity_percentage, '-a', pynast_alignment_fasta,
'-g', pynast_log, '-f', pynast_failed
]
return program_module.ProgramCommand(description, short, command)
