Closed gregcaporaso closed 10 years ago
And the most common import from cogent in QIIME are (may be a little messy):
get_tmp_filename
(imported from cogent.app.util
) bumped this up in the list - notice that is is imported in qiime.util, and then a lot of things import it from thereMinimalFastaParser
(imported from cogent.parse.fasta
)create_dir
(imported from cogent.util.misc
)remove_files
(imported from cogent.util.misc
)DNA
(imported from cogent
)CommandLineApplication
(imported from cogent.app.util
)ValuedParameter
(imported from cogent.app.parameters
)LoadSeqs
(imported from cogent
)ApplicationNotFoundError
(imported from cogent.app.util
)app_path
(imported from cogent.util.misc
)FlagParameter
(imported from cogent.app.parameters
)get_random_directory_name
(imported from cogent.util.misc
)build_blast_db_from_fasta_path
(imported from cogent.app.formatdb
)PhyloNode
(imported from cogent.core.tree
)DndParser
(imported from cogent.parse.tree
)MinimalFastqParser
(imported from cogent.parse.fastq
)ResultPath
(imported from cogent.app.util
)ApplicationError
(imported from cogent.app.util
)FilePath
(imported from cogent.app.parameters
)subsample
(imported from cogent.maths.stats.rarefaction
)Blastall
(imported from cogent.app.blast
)Dict2D
(imported from cogent.util.dict2d
)lazy_parse_sff_handle
(imported from cogent.parse.flowgram_parser
)IUPAC_DNA_ambiguities
(imported from cogent.core.moltype
)blast_seqs
(imported from cogent.app.blast
)`(imported from`cogent.parse.binary_sff
)flatten
(imported from cogent.util.misc
)RecordError
(imported from cogent.parse.record
)DenseAlignment
(imported from cogent.core.alignment
)Sequence
(imported from cogent
)ResultPath,\
(imported from cogent.app.util
)Flowgram
(imported from cogent.parse.flowgram
)BlastResult
(imported from cogent.app.blast
)DnaSequence
(imported from cogent.core.sequence
)Parameters
(imported from cogent.app.parameters
)main
(imported from cogent.util.unit_test
)parse_otu_list
(imported from cogent.parse.mothur
)SequenceCollection
(imported from cogent.core.alignment
)CommandLineAppResult
(imported from cogent.app.util
)build_prefix_map
(imported from cogent.util.trie
)SeparatorFormatParser
(imported from cogent.parse.table
)unzip
(imported from cogent.util.misc
)procrustes
(imported from cogent.cluster.procrustes
)UPGMA_cluster
(imported from cogent.cluster.UPGMA
)IUPAC_DNA
(imported from cogent.seqsim.sequence_generators
)TestCase
(imported from cogent.util.unit_test
)Alignment
(imported from cogent.core.alignment
)subsample_multinomial
(imported from cogent.maths.stats.rarefaction
)safe_md5
(imported from cogent.util.misc
)SequenceGenerator
(imported from cogent.seqsim.sequence_generators
)eps
(imported from cogent.core.alignment
)lgam
(imported from cogent.maths.stats.special
)TreeNode
(imported from cogent.core.tree
)FormatDb
(imported from cogent.app.formatdb
)cdhit_clusters_from_seqs
(imported from cogent.app.cd_hit
)Gamma
(imported from cogent.maths.stats.special
)local_pairwise
(imported from cogent.align.align
)make_dna_scoring_dict
(imported from cogent.align.align
)dict
(imported from cogent.util.misc
)TEST_ON_TREE
(imported from cogent.maths.unifrac.fast_unifrac
)z_high
(imported from cogent.maths.stats.distribution
)ApplicationNotFoundError,ApplicationError
(imported from cogent.app.util
)chisqprob
(imported from cogent.maths.stats
)build_averaged_flowgram
(imported from cogent.parse.flowgram
)combinate
(imported from cogent.util.misc
)generate_box_plots
(imported from cogent.draw.distribution_plots
)chi_high
(imported from cogent.maths.stats.distribution
)hist
(imported from cogent.draw.util
)rtax
(imported from cogent.app
)MolType
(imported from cogent.core.moltype
)Numbers
(imported from cogent.maths.stats.util
)ChangedSequence
(imported from cogent.parse.rfam
)DnaMW
(imported from cogent.data.molecular_weight
)Parameter
(imported from cogent.app.parameters
)log_one_minus
(imported from cogent.maths.stats.special
)one_minus_exp
(imported from cogent.maths.stats.special
)DNA
(imported from cogent.core.moltype
)majorityRule
(imported from cogent.phylo.consensus
)fit_function
(imported from cogent.maths.fit_function
)Mothur
(imported from cogent.app.mothur
)Dna
(imported from cogent.core.sequence
)IUPAC_DNA_ambiguities,\
(imported from cogent.core.moltype
)fast_p_test_file
(imported from cogent.maths.unifrac.fast_unifrac
)zprob
(imported from cogent.maths.stats.distribution
)TEST_ON_ENVS
(imported from cogent.maths.unifrac.fast_unifrac
)InverseDict
(imported from cogent.util.misc
)InverseDictMulti
(imported from cogent.util.misc
)ndtri
(imported from cogent.maths.stats.distribution
)build_blast_db_from_fasta_path,\
(imported from cogent.app.formatdb
)psmirnov2x
(imported from cogent.maths.stats.ks
)nj
(imported from cogent.phylo.nj
)Alignment
(imported from cogent
)MinimalRfamParser
(imported from cogent.parse.rfam
)cmalign_from_alignment
(imported from cogent.app.infernal
)FastaFinder
(imported from cogent.parse.fasta
)z_low
(imported from cogent.maths.stats.distribution
)fast_unifrac_one_sample
(imported from cogent.maths.unifrac.fast_unifrac
)__version__
(imported from cogent
)seq_to_flow
(imported from cogent.parse.flowgram
)minimise
(imported from cogent.maths.optimisers
)BlastResult
(imported from cogent.parse.blast
)fast_unifrac
(imported from cogent.maths.unifrac.fast_unifrac
)t_one_sample
(imported from cogent.maths.stats.test
)MinimalFastqParserCogent
(imported from cogent.parse.fastq
)FlowgramCollection
(imported from cogent.parse.flowgram_collection
)ModelDnaSequence
(imported from cogent.core.sequence
)Profile
(imported from cogent.core.profile
)GeneticCodes
(imported from cogent.core.genetic_code
)TEST_ON_PAIRWISE
(imported from cogent.maths.unifrac.fast_unifrac
)pycogent_lib_version
(imported from cogent
)SquareDendrogram
(imported from cogent.draw.dendrogram
)fmin_powell
(imported from cogent.maths.scipy_optimize
)IUPAC_DNA_chars
(imported from cogent.core.moltype
)pkstwo
(imported from cogent.maths.stats.ks
)mothur_parse
(imported from cogent.parse.mothur
)LabeledRecordFinder
(imported from cogent.parse.record_finder
)MinimalBlatParser9
(imported from cogent.parse.blast
)PROTEIN
(imported from cogent
)fast_unifrac_permutations_file
(imported from cogent.maths.unifrac.fast_unifrac
)When MinimalFastqParser
is shifted to this repo, I believe we should update it to handle casava to ensure that fastq data yielded are sane as early as possible. The current yielding of the ascii encoding means you have to think a bit more about how to get the data into a format you can actually use leading to different handling of qual from fastq already. MinimalFastqParser
also differs from the datatype yielded by MinimalQualParser
which is a numpy array
. This adds a trivial amount of overhead but will likely not impact performance noticeably. The conceptual benefits I think outweigh any performance concerns here, and if there are concerns, we can push the parser to cython.
This discussion has shifted to the Boulder sprint spreadsheet.
Is there still an interest to have upgma
?
No, SciPy already implements it as scipy.cluster.hierarchy.average
. Additionally QIIME's PyCogent's UPGMA is actually subtly incorrect, we explored this early on in the beginning of skbio: https://github.com/biocore/qiime/issues/1541.
Ahhh, I did not see TreeNode.from_linkage_matrix
. Thanks!!!
@rob-knight put these notes together. We should use this document to prioritize porting functionality. Please request write access to the doc if you'd like to add notes, etc.