Index

A

Adam_update() (sequencing_tools.stats_tools.regression.GradientDescent method)

after_cde (sequencing_tools.gene_tools.transcriptome.Exon attribute) after_cds (sequencing_tools.gene_tools.transcriptome.Exon attribute)

B

Bed12Record (class in sequencing_tools.gene_tools) binom_test() (in module sequencing_tools.stats_tools._stats_tools)

blocks() (sequencing_tools.gene_tools.transcriptome.Transcript method) Bootstrap (class in sequencing_tools.stats_tools._stats_tools), [1]

C

cde (sequencing_tools.gene_tools.transcriptome.Transcript attribute) cds (sequencing_tools.gene_tools.transcriptome.Transcript attribute) check_concordant() (in module sequencing_tools.bam_tools._bam_tools) check_degenerate() (sequencing_tools.fasta_tools.IUPAC method), [1] check_primary() (in module sequencing_tools.bam_tools._bam_tools) chrom (sequencing_tools.gene_tools.GTFRecord attribute) (sequencing_tools.gene_tools.transcriptome.Transcript attribute) cigar_to_str() (in module sequencing_tools.bam_tools._bam_tools) coding_bases (sequencing_tools.gene_tools.transcriptome.Exon attribute) coding_only (sequencing_tools.gene_tools.transcriptome.Transcriptome attribute) color_encoder (class in sequencing_tools.viz_tools)

colors (sequencing_tools.fasta_tools.MultiAlignments attribute) complement() (in module sequencing_tools.fastq_tools._fastq_tools) concensus() (sequencing_tools.fasta_tools.MultiAlignments method) concordant_alignment() (in module sequencing_tools.bam_tools._bam_tools) concordant_pairs() (in module sequencing_tools.bam_tools._bam_tools) ConsensusBuilder (class in sequencing_tools.fastq_tools.pe_align) contain_cde (sequencing_tools.gene_tools.transcriptome.Exon attribute) contain_cds (sequencing_tools.gene_tools.transcriptome.Exon attribute) cor_plot() (in module sequencing_tools.viz_tools) Correct() (sequencing_tools.consensus_tools._consensus_tools.ErrorCorrection method) Cost() (sequencing_tools.stats_tools.regression.GradientDescent method) cy_mean() (in module sequencing_tools.stats_tools._stats_tools)

D

decode() (sequencing_tools.fastq_tools._fastq_tools.onehot_sequence_encoder method)

douglas_palette() (in module sequencing_tools.viz_tools)

E

encoder (sequencing_tools.viz_tools.color_encoder attribute) end (sequencing_tools.gene_tools.GTFRecord attribute) (sequencing_tools.gene_tools.transcriptome.Exon attribute) ErrorCorrection (class in sequencing_tools.consensus_tools._consensus_tools) Exon (class in sequencing_tools.gene_tools.transcriptome) exon_count (sequencing_tools.gene_tools.transcriptome.Transcript attribute)

exon_ends (sequencing_tools.gene_tools.transcriptome.Transcript attribute) exon_num (sequencing_tools.gene_tools.transcriptome.Exon attribute) exon_starts (sequencing_tools.gene_tools.transcriptome.Transcript attribute) exons (sequencing_tools.gene_tools.transcriptome.Transcript attribute) expand() (sequencing_tools.fasta_tools.IUPAC method), [1] extract_kmer() (in module sequencing_tools.fastq_tools._fastq_tools)

F

fastqRecord (class in sequencing_tools.fastq_tools._fastq_tools), [1] feature_type (sequencing_tools.gene_tools.GTFRecord attribute) fit() (sequencing_tools.fastq_tools._fastq_tools.onehot_sequence_encoder method) (sequencing_tools.stats_tools.regression.GradientDescent method) (sequencing_tools.viz_tools.color_encoder method)

fit_transform() (sequencing_tools.fastq_tools._fastq_tools.onehot_sequence_encoder method) (sequencing_tools.viz_tools.color_encoder method) five_UTR_length (sequencing_tools.gene_tools.transcriptome.Transcript attribute) fragment_ends() (in module sequencing_tools.bam_tools._bam_tools)

G

GappedKmer (class in sequencing_tools.fastq_tools._fastq_tools) generate() (sequencing_tools.stats_tools._stats_tools.Bootstrap method), [1] genomic_position() (sequencing_tools.gene_tools.Bed12Record method) (sequencing_tools.gene_tools.transcriptome.Transcript method)

get_gene() (sequencing_tools.gene_tools.transcriptome.Transcriptome method) get_introns() (sequencing_tools.gene_tools.Bed12Record method) get_strand() (in module sequencing_tools.bam_tools._bam_tools) GradientDescent (class in sequencing_tools.stats_tools.regression) GTFRecord (class in sequencing_tools.gene_tools)

H

hamming_distance() (in module sequencing_tools.stats_tools._stats_tools)

I

id (sequencing_tools.gene_tools.transcriptome.Transcript attribute)

info (sequencing_tools.gene_tools.GTFRecord attribute) IUPAC (class in sequencing_tools.fasta_tools), [1]

K

kmer_bag() (in module sequencing_tools.fastq_tools._fastq_tools)

L

length (sequencing_tools.gene_tools.transcriptome.Exon attribute)

levenshtein_distance() (in module sequencing_tools.stats_tools._stats_tools)

M

make_cigar_seq() (in module sequencing_tools.bam_tools._bam_tools) make_regions() (in module sequencing_tools.bam_tools._bam_tools) maximum_palette() (in module sequencing_tools.viz_tools) mixed_sort() (in module sequencing_tools.viz_tools) module sequencing_tools.bam_tools._bam_tools sequencing_tools.fasta_tools sequencing_tools.fastq_tools._fastq_tools sequencing_tools.stats_tools._stats_tools sequencing_tools.utils sequencing_tools.viz_tools

mul_df (sequencing_tools.fasta_tools.MultiAlignments attribute) MultiAlignments (class in sequencing_tools.fasta_tools)

N

normalize_count() (in module sequencing_tools.stats_tools._stats_tools)

O

okabeito_palette() (in module sequencing_tools.viz_tools)

onehot_sequence_encoder (class in sequencing_tools.fastq_tools._fastq_tools)

P

p_adjust() (in module sequencing_tools.stats_tools._stats_tools) paired_bam() (in module sequencing_tools.bam_tools._bam_tools) PairMatrix() (sequencing_tools.fasta_tools.MultiAlignments method)

pairwise (sequencing_tools.fasta_tools.MultiAlignments attribute) plot() (sequencing_tools.fasta_tools.MultiAlignments method) plot_upset() (in module sequencing_tools.viz_tools)

R

read_ends() (in module sequencing_tools.bam_tools._bam_tools) read_interleaved() (in module sequencing_tools.fastq_tools._fastq_tools) readfa() (in module sequencing_tools.fasta_tools) readfq() (in module sequencing_tools.fastq_tools._fastq_tools)

ReadTrimmer (class in sequencing_tools.fastq_tools.function_clip) remove_insert() (in module sequencing_tools.bam_tools._bam_tools) reverse_complement() (in module sequencing_tools.fastq_tools._fastq_tools) run() (sequencing_tools.fastq_tools.pe_align.ConsensusBuilder method)

S

sequencing_tools.bam_tools._bam_tools module sequencing_tools.fasta_tools module sequencing_tools.fastq_tools._fastq_tools module sequencing_tools.stats_tools._stats_tools module sequencing_tools.utils module sequencing_tools.viz_tools module

SeqUtilsError show_legend() (sequencing_tools.viz_tools.color_encoder method) simpsons_palette() (in module sequencing_tools.viz_tools) split_cigar() (in module sequencing_tools.bam_tools._bam_tools) start (sequencing_tools.gene_tools.GTFRecord attribute) (sequencing_tools.gene_tools.transcriptome.Exon attribute) strand (sequencing_tools.gene_tools.GTFRecord attribute) (sequencing_tools.gene_tools.transcriptome.Exon attribute) (sequencing_tools.gene_tools.transcriptome.Transcript attribute) subseq() (sequencing_tools.fastq_tools._fastq_tools.fastqRecord method), [1]

T

Transcript (class in sequencing_tools.gene_tools.transcriptome) transcript_count (sequencing_tools.gene_tools.transcriptome.Transcriptome attribute) transcript_dict (sequencing_tools.gene_tools.transcriptome.Transcriptome attribute) transcript_end (sequencing_tools.gene_tools.transcriptome.Exon attribute) transcript_length (sequencing_tools.gene_tools.transcriptome.Transcript attribute) transcript_start (sequencing_tools.gene_tools.transcriptome.Exon attribute)

Transcriptome (class in sequencing_tools.gene_tools.transcriptome) transform() (sequencing_tools.fastq_tools._fastq_tools.onehot_sequence_encoder method) (sequencing_tools.viz_tools.color_encoder method) trim_reads() (sequencing_tools.fastq_tools.function_clip.ReadTrimmer method) tx_end (sequencing_tools.gene_tools.transcriptome.Transcript attribute) tx_start (sequencing_tools.gene_tools.transcriptome.Transcript attribute)