Index

A

add_genome() (in module bioplus.genometools) analyze_sites() (in module bioplus.seqtools)

array_to_bedgraph() (in module bioplus.peaktools)

B

BAMFilenameParser (class in seriesoftubes.fnparsers) BarcodeFilenameParser (class in seriesoftubes.fnparsers) BedFile (class in bioplus.tabfile) BedRow (class in bioplus.tabfile) bioplus (module) bioplus.fasta (module) bioplus.genometools (module) bioplus.motif (module) bioplus.peaktools (module)

bioplus.seqtools (module) bioplus.sitefinder (module) bioplus.tabfile (module) bioplus.wrappers (module) blockCount() (bioplus.tabfile.BedRow method) blockSizes() (bioplus.tabfile.BedRow method) blockStart() (bioplus.tabfile.BedRow method) BowtieFilenameParser (class in seriesoftubes.fnparsers) Bzip2TabFile (class in bioplus.tabfile)

C

center_region() (in module bioplus.motif) CharDict (class in bioplus.motif) check_paired_end() (seriesoftubes.fnparsers.BowtieFilenameParser method) chr() (bioplus.tabfile.MacsRow method) chrom() (bioplus.tabfile.BedRow method) (bioplus.tabfile.MacsRow method) chrom_end() (bioplus.tabfile.BedRow method) (bioplus.tabfile.MacsRow method) chrom_start() (bioplus.tabfile.BedRow method) (bioplus.tabfile.MacsRow method) chromEnd() (bioplus.tabfile.BedRow method) (bioplus.tabfile.MacsRow method) chromStart() (bioplus.tabfile.BedRow method) (bioplus.tabfile.MacsRow method) close() (bioplus.tabfile.TabFile method)

column_dict() (bioplus.tabfile.TabFile method) comment_line_contents() (bioplus.tabfile.TabFile method) comment_line_numbers() (bioplus.tabfile.TabFile method) complement() (in module bioplus.seqtools) count() (in module bioplus.fasta) count_compare() (in module bioplus.seqtools) count_file() (bioplus.motif.PositionWeightMatrix method) count_letters() (in module bioplus.motif) count_seqs() (bioplus.motif.PositionWeightMatrix method) (in module bioplus.seqtools) count_spacers_from_info() (in module bioplus.motif)

D

DEFAULT_BED_COMMENTS (bioplus.tabfile.BedFile attribute) DetectCommentsError

discover_file_format() (in module seriesoftubes.converters.discover)

E

end() (bioplus.tabfile.MacsRow method)

F

FDR() (bioplus.tabfile.Macs2Row method) (bioplus.tabfile.MacsRow method) find_sites() (in module bioplus.sitefinder)

fold_enrichment() (bioplus.tabfile.MacsRow method)

G

genome() (in module bioplus.genometools) genome_from_bam() (in module bioplus.genometools) GenomeNotAvailableError get_column_names() (bioplus.tabfile.TabFile method) get_first() (in module bioplus.seqtools)

get_track_line() (bioplus.tabfile.BedFile method) guess_bam_genome() (in module bioplus.genometools) guess_genome() (in module bioplus.genometools) GzipTabFile (class in bioplus.tabfile)

I

import_db() (in module bioplus.genometools) import_from_MEME() (bioplus.motif.PositionWeightMatrix method) in_window_factory() (in module seriesoftubes.bedgraph)

in_windows_factory() (in module seriesoftubes.bedgraph) itemRgb() (bioplus.tabfile.BedRow method)

J

joint_matrix() (in module bioplus.motif)

K

KL() (in module bioplus.motif)

L

length() (bioplus.tabfile.MacsRow method)

log() (seriesoftubes.tubes.polledpipe.PolledPipe method)

M

Macs2Row (class in bioplus.tabfile) MACS_track_to_iter() (in module bioplus.peaktools) MacsFile (class in bioplus.tabfile) MacsRow (class in bioplus.tabfile) main() (in module seriesoftubes.converters.anytotab) (in module seriesoftubes.converters.bamtofastq) (in module seriesoftubes.converters.bamtofastq2) (in module seriesoftubes.converters.bamtotab) (in module seriesoftubes.converters.cat) (in module seriesoftubes.converters.fastqtotab) make_probs() (bioplus.motif.PositionWeightMatrix method)

make_Ri() (bioplus.motif.PositionWeightMatrix method) matches_genome() (in module bioplus.genometools) merge_files() (in module bioplus.tabfile) merge_tab_files() (in module bioplus.tabfile) mergesort() (bioplus.tabfile.TabFile method) MOODS_search() (in module bioplus.sitefinder)

N

name() (bioplus.tabfile.BedRow method) (bioplus.tabfile.Macs2Row method)

NoMatchFoundError

O

open() (bioplus.tabfile.TabFile method) output_filename() (seriesoftubes.fnparsers.BarcodeFilenameParser method)

output_filename2() (seriesoftubes.fnparsers.BarcodeFilenameParser method)

P

pad() (in module bioplus.fasta) PairedBAMToFastqConverter (class in seriesoftubes.converters.bamtofastq2) PeaksFilenameParser (class in seriesoftubes.fnparsers) permute_fasta() (in module bioplus.fasta) PolledPipe (class in seriesoftubes.tubes.polledpipe)

PositionWeightMatrix (class in bioplus.motif) previous_line() (bioplus.tabfile.TabFile method) process_table() (bioplus.tabfile.TabFile method) pvalue() (bioplus.tabfile.MacsRow method)

Q

qvalue() (bioplus.tabfile.Macs2Row method)

R

random_files() (in module bioplus.fasta) random_seq() (in module bioplus.fasta) (in module bioplus.wrappers) random_seq_generator() (in module bioplus.wrappers) rc() (bioplus.motif.PositionWeightMatrix method) (in module bioplus.seqtools) read_col() (bioplus.tabfile.TabFile method) read_cols() (bioplus.tabfile.TabFile method) read_files() (in module seriesoftubes.converters.bamtofastq) (in module seriesoftubes.converters.fastqtotab) read_first_col() (bioplus.tabfile.TabFile method)

read_last_col() (bioplus.tabfile.TabFile method) read_row() (bioplus.tabfile.TabFile method) read_table() (bioplus.tabfile.TabFile method) reader() (in module bioplus.fasta) readline() (bioplus.tabfile.TabFile method) reversecomplement() (in module bioplus.seqtools) Rs() (bioplus.motif.PositionWeightMatrix method)

S

score() (bioplus.tabfile.BedRow method) search_peak() (in module bioplus.sitefinder) seq_Ri() (bioplus.motif.PositionWeightMatrix method) seriesoftubes.bedgraph (module) seriesoftubes.converters (module) seriesoftubes.converters.anytotab (module) seriesoftubes.converters.bamtofastq (module) seriesoftubes.converters.bamtofastq2 (module) seriesoftubes.converters.bamtotab (module) seriesoftubes.converters.cat (module)

seriesoftubes.converters.discover (module) seriesoftubes.converters.fastqtotab (module) seriesoftubes.fnparsers (module) seriesoftubes.tubes (module) set_column_names() (bioplus.tabfile.TabFile method) shift_peaks() (in module bioplus.tabfile) spacerGC() (in module bioplus.motif) start() (bioplus.tabfile.MacsRow method) strand() (bioplus.tabfile.BedRow method) summit() (bioplus.tabfile.MacsRow method)

T

TabFile (class in bioplus.tabfile) TabFileError tags() (bioplus.tabfile.MacsRow method) tagsv1() (bioplus.tabfile.MacsRow method) tagsv2() (bioplus.tabfile.MacsRow method) TemporaryGenomeFile() (in module bioplus.genometools)

thickEnd() (bioplus.tabfile.BedRow method) thickStart() (bioplus.tabfile.BedRow method) tmp_filename() (seriesoftubes.fnparsers.BowtieFilenameParser method) truncate_lines() (in module bioplus.fasta) truncate_seqs() (in module bioplus.fasta)

U

uncertainty() (bioplus.motif.CharDict method) (bioplus.motif.PositionWeightMatrix method)

UnpairedBAMToFastqConverter (class in seriesoftubes.converters.bamtofastq)

W

wait_for_job() (in module seriesoftubes.tubes) window_to_iter() (in module seriesoftubes.bedgraph) write() (bioplus.tabfile.TabFile method) write_column_names() (bioplus.tabfile.TabFile method)

write_row() (bioplus.tabfile.TabFile method) write_rows() (bioplus.tabfile.TabFile method) write_table() (bioplus.tabfile.TabFile method) writer() (in module bioplus.fasta)

Z

zap() (bioplus.tabfile.TabFile method)