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QIIME - Static variable in class biolockj.Constants

QIIME application: "qiime"

QIIME_ALPHA_DIVERSITY_METRICS - Static variable in class biolockj.Constants

Config list property to calculate alpha diversity metrics.
For complete list of skbio.diversity.alpha options, see http://scikit-bio.org/docs/latest/generated/skbio.diversity.alpha.html
"qiime.alphaMetrics"

QIIME_AMBIGUOUS_TAXA - Static variable in class biolockj.Constants

Qiime may find ambiguous taxa identified in various formats in different databases.

QIIME_BARCODE_SEQ_COL - Static variable in class biolockj.Constants

QIIME mapping file required 2nd column name

QIIME_COMMENT - Static variable in class biolockj.module.implicit.qiime.BuildQiimeMapping

Comment used to populate "Description" column

QIIME_DEMUX_COL - Static variable in class biolockj.Constants

QIIME mapping column created by BuildQiimeMapping that stores the name of the original fasta file associated with the sample: "BioLockJFileName"

QIIME_DESC_COL - Static variable in class biolockj.Constants

QIIME mapping file required name of last column

QIIME_DOMAIN_DELIM - Static variable in class biolockj.node.r16s.QiimeNode

QIIME domain taxonomy level delimiter: "k__"

QIIME_ID - Static variable in class biolockj.module.implicit.qiime.BuildQiimeMapping

QIIME mapping file required 1st column name, containing the sample ID

QIIME_LINKER_PRIMER_SEQ_COL - Static variable in class biolockj.Constants

QIIME mapping file required 3rd column name

QIIME_PARAMS - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier

Config List property used to obtain the QIIME executable params

QIIME_PYNAST_ALIGN_DB - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier

Config File property to define ~/.qiime_config pynast_template_alignment_fp: "qiime.pynastAlignDB"

QIIME_REF_SEQ_DB - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier

Config File property to define ~/.qiime_config pick_otus_reference_seqs_fp and assign_taxonomy_reference_seqs_fp: "qiime.refSeqDB"

QIIME_REMOVE_CHIMERAS - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier

Config boolean property to indicate if "exe.vsearch" is needed for chimera removal: "qiime.removeChimeras"

QIIME_TAXA_DB - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier

Config File property to define ~/.qiime_config assign_taxonomy_id_to_taxonomy_fp: "qiime.taxaDB"

QiimeClassifier - Class in biolockj.module.implicit.qiime

This BioModule generates the bash script used to create QIIME summary scripts, taxonomy-level reports, and add alpha diversity metrics (if configured) to the metadata file.
For a complete list of available metrics, see: http://scikit-bio.org/docs/latest/generated/skbio.diversity.alpha.html

QiimeClassifier() - Constructor for class biolockj.module.implicit.qiime.QiimeClassifier

QiimeClosedRefClassifier - Class in biolockj.module.classifier.r16s

This BioModule executes the QIIME script pick_closed_reference_otus.py on a FastA sequence files.

QiimeClosedRefClassifier() - Constructor for class biolockj.module.classifier.r16s.QiimeClosedRefClassifier

QiimeDeNovoClassifier - Class in biolockj.module.classifier.r16s

This module runs the QIIME pick_de_novo_otus.py script on FastA sequence files in a single script so it is important to allocate sufficient job resources if running in a clustered environment.

QiimeDeNovoClassifier() - Constructor for class biolockj.module.classifier.r16s.QiimeDeNovoClassifier

qiimeIdToSampleIdMap - Static variable in class biolockj.module.implicit.parser.r16s.QiimeParser

Convenience map, to convert Qiime ID to Sample ID

QiimeNode - Class in biolockj.node.r16s

This class holds the OTU assignments from one line of QiimeClassifier output.

QiimeNode(String, String, int) - Constructor for class biolockj.node.r16s.QiimeNode

Build the OtuNode by extracting the OTU names for each level from the line.

QiimeOpenRefClassifier - Class in biolockj.module.classifier.r16s

This module runs the QIIME pick_open_reference_otus.py script on FastA sequence files in a single script so it is important to allocate sufficient job resources if running in a clustered environment.

QiimeOpenRefClassifier() - Constructor for class biolockj.module.classifier.r16s.QiimeOpenRefClassifier

QiimeParser - Class in biolockj.module.implicit.parser.r16s

This BioModules parses QiimeClassifier output reports to build standard OTU abundance tables.

QiimeParser() - Constructor for class biolockj.module.implicit.parser.r16s.QiimeParser

QUANTILE - Static variable in class biolockj.module.report.otu.RarefyOtuCounts

Config Positive Double property "rarefyOtuCounts.quantile" defines quantile for rarefication.

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