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aerial.bio.utils.aligners
Various sequence aligners by means of low level hackery...
Various sequence aligners by means of low level hackery...
aerial.bio.utils.files
Various bio sequence file format readers, writers, verifiers, and manipulators.
Various bio sequence file format readers, writers, verifiers, and manipulators.
- 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-full-comma-sep-stg
- 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
- rxy
- sample-fna
- sample-fq
- sample-paired-fqs
- sampR2fq
- 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.
Various scoring, filtering, of sequence data.
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.
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.
Various sequence transformation and generation 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
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