Aerial.bio.utils 2.0.0
Various bioinformatic general utility tools
Topics
Namespaces
aerial.bio.utils.aligners
Various sequence aligners by means of low level hackery...
Public variables and functions:
aerial.bio.utils.extools
Intended to include/contain various utilities for operating with and on sequence data. Originally this was all about working with (NCBI) Blast+, CMFINDER (and associated utils) and Infernal tools, but now may branch out to many others.
Public variables and functions:
- assert-tools-exist
- blast
- blastn
- blastpgm
- canda
- candf
- cands
- cd-hit-est
- cmalign
- cmbuild
- cmcalibrate
- cmf-post-process-combine
- cmf-post-process-filter
- cmfinder
- cmfinder*
- cmsearch
- correct-dir-stos
- correct-sto-coordinates
- embl-sto->nc-sto
- embl-to-nc
- entry-aln-sqs
- entry-file->blastdb
- entry-file-difference
- entry-file-difference-with-seqs
- entry-file-intersect
- entry-file-intersect-with-seqs
- entry-file-setop
- entry-file-union
- entry-file-union-with-seqs
- entry-range->fasta-file
- filter-base-hits-to-most-likely
- fuzzy-entry-file-difference
- fuzzy-entry-file-intersect
- fuzzy-entry-file-union
- genome-seq-dup?
- get-blast-id-info-new
- get-cd-hit-infile
- get-cmfsto-glob
- get-embl-blast-candidates
- get-entry-set
- get-tool-path
- infernal-2+?
- mk-infernal-cmd
- parse-blast
- process-blast-for-cmfinder
- rank-em
- refseq-entry?
- summary-map
- tblastn
aerial.bio.utils.files
Various bio sequence file format readers, writers, verifiers, and manipulators.
Public variables and functions:
- canonical-csv-entry-info
- check-sto
- chunk-genome-fnas
- collapse-group
- collapse-one
- entry-file->fasta-file
- entry-parts
- fastq->fna
- fastqs->fnas
- fna->fastq
- fnas->fastqs
- gaisr-seq-set?
- gbank->fna
- gbank-loci-sane-loci
- gbanks->fnas
- gen-entry-file
- gen-entry-nv-file
- gen-name-seq
- gen-name-seq-pairs
- gen-nc-genome-fnas
- genbank-recs
- genbk2gtf
- get-csv-entry-info
- get-ent-as-csv-info
- get-entries
- get-gaisr-csv-info
- get-legacy-csv-info
- get-selection-fna
- get-sto-as-csv-info
- has-loc?
- join-sto-fasta-file
- join-sto-fasta-lines
- make-entry
- map-aln-seqs
- map-seqs
- nms-sqs->fasta-file
- print-sto
- read-aln-seqs
- read-dirs-aln-seqs
- read-farec
- read-farecs
- read-fqrec
- read-fqrecs
- read-seqs
- reduce-aln-seqs
- reduce-seqs
- sample-fna
- sample-fq
- seqline-info-mapper
- split-join-fasta-file
- split-join-ncbi-fasta-file
- sto->aln
- sto->aln-blocked
- sto->fna
- sto-GC-and-seq-lines
- write-farec
- write-farecs
- write-fqrec
- write-fqrecs
- write-sto
aerial.bio.utils.filters
Various scoring, filtering, of sequence data.
Public variables and functions:
aerial.bio.utils.infoth
Various information theory computations, calculations and results as applied to bio sequences and alignments thereof. Includes entropy, joint entropy, conditional entropy, mutual information, conditional mi, et. al.
aerial.bio.utils.seqxform
Various sequence transformation and generation functions.
Public variables and functions:
- +AMINO-ACID-MAP+
- +DNA-CONDON-MAP+
- +IUPAC+
- +NONSTD-RNA+
- +REVERSE-AMINO-ACID-MAP+
- +REVERSE-DNA-CODON-MAP+
- +REVERSE-RNA-CODON-MAP+
- +RNA-CONDON-MAP+
- +RY-XLATE+
- +START-CODON+
- +STOP-CODONS+
- alphabet
- check-limit
- cut-cols
- degap-seqs
- dint-seq-shuffle
- dint-shuffle
- filter-pgap
- gap-count
- gap-percent
- gaps?
- gen-random-bioseq
- legal-ends
- limit-counter
- monte-carlo-subseq-cnts
- monte-carlo-subseq-cnts-body
- monte-carlo-subseq-freq
- norm-elements
- nt-cntn
- nts-map
- ntseq->aaseq
- pmonte-carlo-subseq-cnts
- print-limit-info
- reduce-seqcnt-results
- reverse-compliment
- seqXlate
- shuffles
- test-nts