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bioconvert
Index
Edit on GitHub
Index
_
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A
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B
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C
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D
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E
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F
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G
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I
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J
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
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X
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Y
_
_default_method (ABI2FASTA attribute)
(ABI2FASTQ attribute)
(ABI2QUAL attribute)
(BAM2BEDGRAPH attribute)
(BAM2BIGWIG attribute)
(BAM2CRAM attribute)
(BAM2FASTA attribute)
(BAM2FASTQ attribute)
(BAM2JSON attribute)
(BAM2SAM attribute)
(BAM2TSV attribute)
(BCF2WIGGLE attribute)
(BEDGRAPH2BIGWIG attribute)
(BEDGRAPH2COV attribute)
(BEDGRAPH2WIGGLE attribute)
(BIGBED2BED attribute)
(BIGBED2WIGGLE attribute)
(BIGWIG2BEDGRAPH attribute)
(BIGWIG2WIGGLE attribute)
(BPLINK2PLINK attribute)
(BZ22GZ attribute)
(CLUSTAL2FASTA attribute)
(CLUSTAL2PHYLIP attribute)
(CLUSTAL2STOCKHOLM attribute)
(CRAM2BAM attribute)
(CRAM2FASTA attribute)
(CRAM2FASTQ attribute)
(CRAM2SAM attribute)
(CSV2TSV attribute)
(CSV2XLS attribute)
(DSRC2GZ attribute)
(EMBL2FASTA attribute)
(EMBL2GENBANK attribute)
(FASTA2CLUSTAL attribute)
(FASTA2FAA attribute)
(FASTA2FASTQ attribute)
(FASTA2GENBANK attribute)
(FASTA2NEXUS attribute)
(FASTA2PHYLIP attribute)
(FASTA2TWOBIT attribute)
(FASTA_QUAL2FASTQ attribute)
(FASTQ2FASTA attribute)
(GENBANK2EMBL attribute)
(GENBANK2FASTA attribute)
(GENBANK2GFF3 attribute)
(GFA2FASTA attribute)
(GFF22GFF3 attribute)
(GFF32GFF2 attribute)
(GZ2BZ2 attribute)
(GZ2DSRC attribute)
(JSON2YAML attribute)
(MAF2SAM attribute)
(NEWICK2NEXUS attribute)
(NEWICK2PHYLOXML attribute)
(NEXUS2FASTA attribute)
(NEXUS2NEWICK attribute)
(NEXUS2PHYLIP attribute)
(NEXUS2PHYLOXML attribute)
(ODS2CSV attribute)
(PHYLIP2CLUSTAL attribute)
(PHYLIP2FASTA attribute)
(PHYLIP2NEXUS attribute)
(PHYLIP2STOCKHOLM attribute)
(PHYLIP2XMFA attribute)
(PHYLOXML2NEWICK attribute)
(PHYLOXML2NEXUS attribute)
(PLINK2BPLINK attribute)
(SAM2BAM attribute)
(SAM2CRAM attribute)
(SAM2PAF attribute)
(SCF2FASTA attribute)
(SCF2FASTQ attribute)
(SRA2FASTQ attribute)
(STOCKHOLM2CLUSTAL attribute)
(STOCKHOLM2PHYLIP attribute)
(TSV2CSV attribute)
(TWOBIT2FASTA attribute)
(VCF2BCF attribute)
(VCF2BED attribute)
(VCF2WIGGLE attribute)
(XLSX2CSV attribute)
(XMFA2PHYLIP attribute)
(YAML2JSON attribute)
_method_awk() (FASTQ2FASTA method)
(GFA2FASTA method)
(VCF2BED method)
_method_bamCoverage() (BAM2BIGWIG method)
_method_bamtools() (BAM2JSON method)
_method_bcftools() (BCF2VCF method)
(VCF2BCF method)
_method_bedtools() (BAM2BEDGRAPH method)
(BAM2COV method)
(BAM2FASTQ method)
_method_biocode() (GENBANK2GFF3 method)
_method_bioconvert() (FASTA2FAA method)
(FASTA2GENBANK method)
(FASTQ2FASTA method)
(GFF22GFF3 method)
(GFF32GFF2 method)
_method_biopython() (ABI2FASTA method)
(ABI2FASTQ method)
(ABI2QUAL method)
(CLUSTAL2FASTA method)
(CLUSTAL2PHYLIP method)
(CLUSTAL2STOCKHOLM method)
(EMBL2FASTA method)
(EMBL2GENBANK method)
(FASTA2CLUSTAL method)
(FASTA2GENBANK method)
(FASTA2PHYLIP method)
(GENBANK2EMBL method)
(GENBANK2FASTA method)
(NEXUS2FASTA method)
(NEXUS2NEWICK method)
(PHYLIP2CLUSTAL method)
(PHYLIP2FASTA method)
(PHYLIP2STOCKHOLM method)
(PHYLIP2XMFA method)
(STOCKHOLM2CLUSTAL method)
(STOCKHOLM2PHYLIP method)
(XMFA2PHYLIP method)
_method_bz2_gz() (BZ22GZ method)
_method_dsrcpigz() (DSRC2GZ method)
_method_fastq_dump() (SRA2FASTQ method)
_method_goalign() (CLUSTAL2FASTA method)
(FASTA2CLUSTAL method)
(FASTA2NEXUS method)
(FASTA2PHYLIP method)
(NEXUS2FASTA method)
(NEXUS2PHYLIP method)
(PHYLIP2FASTA method)
(PHYLIP2NEXUS method)
_method_gotree() (NEWICK2NEXUS method)
(NEWICK2PHYLOXML method)
(NEXUS2NEWICK method)
(NEXUS2PHYLOXML method)
(PHYLOXML2NEWICK method)
(PHYLOXML2NEXUS method)
_method_gunzip_bzip2() (GZ2BZ2 method)
_method_mappy() (FASTQ2FASTA method)
_method_mawk() (FASTQ2FASTA method)
_method_mosdepth() (BAM2BEDGRAPH method)
_method_pandas() (CSV2TSV method)
(CSV2XLS method)
(TSV2CSV method)
(XLS2CSV method)
(XLSX2CSV method)
_method_perl() (FASTQ2FASTA method)
_method_pigz_pbzip2() (GZ2BZ2 method)
_method_pigzdsrc() (GZ2DSRC method)
_method_plink() (BPLINK2PLINK method)
(PLINK2BPLINK method)
_method_py2bit() (TWOBIT2FASTA method)
_method_pybigwig() (BIGBED2BED method)
(BIGWIG2BEDGRAPH method)
_method_pyexcel() (CSV2XLS method)
(ODS2CSV method)
(XLS2CSV method)
(XLSX2CSV method)
_method_pysam() (BAM2SAM method)
(BAM2TSV method)
(FASTA2FASTQ method)
(FASTA_QUAL2FASTQ method)
_method_python() (BEDGRAPH2COV method)
(BZ22GZ method)
(CSV2TSV method)
(GENBANK2FASTA method)
(GFA2FASTA method)
(GZ2BZ2 method)
(MAF2SAM method)
(SAM2PAF method)
(SCF2FASTA method)
(SCF2FASTQ method)
(TSV2CSV method)
(YAML2JSON method)
_method_python_v2() (CSV2TSV method)
(TSV2CSV method)
_method_readfq() (FASTQ2FASTA method)
_method_sambamba() (BAM2SAM method)
_method_samtools() (BAM2COV method)
(BAM2CRAM method)
(BAM2FASTA method)
(BAM2FASTQ method)
(BAM2SAM method)
(BAM2TSV method)
(CRAM2BAM method)
(CRAM2FASTA method)
(CRAM2FASTQ method)
(CRAM2SAM method)
(SAM2BAM method)
(SAM2CRAM method)
_method_sed() (FASTQ2FASTA method)
_method_seqkit() (FASTQ2FASTA method)
_method_seqtk() (FASTQ2FASTA method)
_method_squizz() (CLUSTAL2FASTA method)
(CLUSTAL2PHYLIP method)
(CLUSTAL2STOCKHOLM method)
(EMBL2FASTA method)
(EMBL2GENBANK method)
(FASTA2CLUSTAL method)
(FASTA2GENBANK method)
(FASTA2PHYLIP method)
(GENBANK2EMBL method)
(GENBANK2FASTA method)
(NEXUS2FASTA method)
(PHYLIP2CLUSTAL method)
(PHYLIP2FASTA method)
(PHYLIP2STOCKHOLM method)
(STOCKHOLM2CLUSTAL method)
(STOCKHOLM2PHYLIP method)
_method_ucsc() (BAM2BIGWIG method)
(BEDGRAPH2BIGWIG method)
(BIGWIG2BEDGRAPH method)
(FASTA2TWOBIT method)
(TWOBIT2FASTA method)
_method_wiggletools() (BAM2WIGGLE method)
(BCF2WIGGLE method)
(BED2WIGGLE method)
(BEDGRAPH2WIGGLE method)
(BIGBED2WIGGLE method)
(BIGWIG2WIGGLE method)
(VCF2WIGGLE method)
_method_yaml() (JSON2YAML method)
A
ABI
ABI2FASTA (class in bioconvert.abi2fasta)
ABI2FASTQ (class in bioconvert.abi2fastq)
ABI2QUAL (class in bioconvert.abi2qual)
ASQG
AttrDict (class in bioconvert.core.extensions)
B
BAI
BAM
BAM2BEDGRAPH (class in bioconvert.bam2bedgraph)
BAM2BIGWIG (class in bioconvert.bam2bigwig)
BAM2COV (class in bioconvert.bam2cov)
BAM2CRAM (class in bioconvert.bam2cram)
BAM2FASTA (class in bioconvert.bam2fasta)
BAM2FASTQ (class in bioconvert.bam2fastq)
BAM2JSON (class in bioconvert.bam2json)
BAM2SAM (class in bioconvert.bam2sam)
BAM2TSV (class in bioconvert.bam2tsv)
BAM2WIGGLE (class in bioconvert.bam2wiggle)
BCF
BCF2VCF (class in bioconvert.bcf2vcf)
BCF2WIGGLE (class in bioconvert.bcf2wiggle)
BCL
BED
BED2WIGGLE (class in bioconvert.bed2wiggle)
BED3
BED4
BEDGRAPH
BEDGRAPH2BIGWIG (class in bioconvert.bedgraph2bigwig)
BEDGRAPH2COV (class in bioconvert.bedgraph2cov)
BEDGRAPH2WIGGLE (class in bioconvert.bedgraph2wiggle)
Benchmark (class in bioconvert.core.benchmark)
BIGBED
BIGBED2BED (class in bioconvert.bigbed2bed)
BIGBED2WIGGLE (class in bioconvert.bigbed2wiggle)
BIGWIG
BIGWIG2BEDGRAPH (class in bioconvert.bigwig2bedgraph)
BIGWIG2WIGGLE (class in bioconvert.bigwig2wiggle)
Bioconvert (class in bioconvert.core.converter)
bioconvert.abi2fasta
module
bioconvert.abi2fastq
module
bioconvert.abi2qual
module
bioconvert.bam2bedgraph
module
bioconvert.bam2bigwig
module
bioconvert.bam2cov
module
bioconvert.bam2cram
module
bioconvert.bam2fasta
module
bioconvert.bam2fastq
module
bioconvert.bam2json
module
bioconvert.bam2sam
module
bioconvert.bam2tsv
module
bioconvert.bam2wiggle
module
bioconvert.bcf2vcf
module
bioconvert.bcf2wiggle
module
bioconvert.bed2wiggle
module
bioconvert.bedgraph2bigwig
module
bioconvert.bedgraph2cov
module
bioconvert.bedgraph2wiggle
module
bioconvert.bigbed2bed
module
bioconvert.bigbed2wiggle
module
bioconvert.bigwig2bedgraph
module
bioconvert.bigwig2wiggle
module
bioconvert.bplink2plink
module
bioconvert.bz22gz
module
bioconvert.clustal2fasta
module
bioconvert.clustal2phylip
module
bioconvert.clustal2stockholm
module
bioconvert.core.base
module
bioconvert.core.benchmark
module
bioconvert.core.converter
module
bioconvert.core.decorators
module
bioconvert.core.downloader
module
bioconvert.core.extensions
module
bioconvert.core.graph
module
bioconvert.core.registry
module
bioconvert.core.utils
module
bioconvert.cram2bam
module
bioconvert.cram2fasta
module
bioconvert.cram2fastq
module
bioconvert.cram2sam
module
bioconvert.csv2tsv
module
bioconvert.csv2xls
module
bioconvert.dsrc2gz
module
bioconvert.embl2fasta
module
bioconvert.embl2genbank
module
bioconvert.fasta2clustal
module
bioconvert.fasta2faa
module
bioconvert.fasta2fastq
module
bioconvert.fasta2genbank
module
bioconvert.fasta2nexus
module
bioconvert.fasta2phylip
module
bioconvert.fasta2twobit
module
bioconvert.fasta_qual2fastq
module
bioconvert.fastq2fasta
module
bioconvert.genbank2embl
module
bioconvert.genbank2fasta
module
bioconvert.genbank2gff3
module
bioconvert.gfa2fasta
module
bioconvert.gff22gff3
module
bioconvert.gff32gff2
module
bioconvert.gz2bz2
module
bioconvert.gz2dsrc
module
bioconvert.io.maf
module
bioconvert.io.scf
module
bioconvert.json2yaml
module
bioconvert.maf2sam
module
bioconvert.newick2nexus
module
bioconvert.newick2phyloxml
module
bioconvert.nexus2fasta
module
bioconvert.nexus2newick
module
bioconvert.nexus2phylip
module
bioconvert.nexus2phyloxml
module
bioconvert.ods2csv
module
bioconvert.phylip2clustal
module
bioconvert.phylip2fasta
module
bioconvert.phylip2nexus
module
bioconvert.phylip2stockholm
module
bioconvert.phylip2xmfa
module
bioconvert.phyloxml2newick
module
bioconvert.phyloxml2nexus
module
bioconvert.plink2bplink
module
bioconvert.sam2bam
module
bioconvert.sam2cram
module
bioconvert.sam2paf
module
bioconvert.scf2fasta
module
bioconvert.scf2fastq
module
bioconvert.sra2fastq
module
bioconvert.stockholm2clustal
module
bioconvert.stockholm2phylip
module
bioconvert.tsv2csv
module
bioconvert.twobit2fasta
module
bioconvert.vcf2bcf
module
bioconvert.vcf2bed
module
bioconvert.vcf2wiggle
module
bioconvert.xls2csv
module
bioconvert.xlsx2csv
module
bioconvert.xmfa2phylip
module
bioconvert.yaml2json
module
boxplot_benchmark() (ConvBase method)
BPLINK
BPLINK2PLINK (class in bioconvert.bplink2plink)
BZ2
BZ22GZ (class in bioconvert.bz22gz)
C
CLUSTAL
CLUSTAL2FASTA (class in bioconvert.clustal2fasta)
CLUSTAL2PHYLIP (class in bioconvert.clustal2phylip)
CLUSTAL2STOCKHOLM (class in bioconvert.clustal2stockholm)
compressor() (in module bioconvert.core.decorators)
compute_benchmark() (ConvBase method)
ConvArg (class in bioconvert.core.base)
ConvBase (class in bioconvert.core.base)
conversion_exists() (Registry method)
conversion_path() (Registry method)
ConvMeta (class in bioconvert.core.base)
count_insertions() (MAF method)
COV
CRAM
CRAM2BAM (class in bioconvert.cram2bam)
CRAM2FASTA (class in bioconvert.cram2fasta)
CRAM2FASTQ (class in bioconvert.cram2fastq)
CRAM2SAM (class in bioconvert.cram2sam)
create_graph() (in module bioconvert.core.graph)
create_graph_for_cytoscape() (in module bioconvert.core.graph)
CSV
CSV2TSV (class in bioconvert.csv2tsv)
CSV2XLS (class in bioconvert.csv2xls)
D
DSRC
DSRC2GZ (class in bioconvert.dsrc2gz)
E
EMBL
EMBL2FASTA (class in bioconvert.embl2fasta)
EMBL2GENBANK (class in bioconvert.embl2genbank)
extensions (in module bioconvert.core.extensions)
F
FAA
FASTA
FASTA2CLUSTAL (class in bioconvert.fasta2clustal)
FASTA2FAA (class in bioconvert.fasta2faa)
FASTA2FASTQ (class in bioconvert.fasta2fastq)
FASTA2GENBANK (class in bioconvert.fasta2genbank)
FASTA2NEXUS (class in bioconvert.fasta2nexus)
FASTA2PHYLIP (class in bioconvert.fasta2phylip)
FASTA2TWOBIT (class in bioconvert.fasta2twobit)
FASTA_QUAL2FASTQ (class in bioconvert.fasta_qual2fastq)
FASTQ
FASTQ2FASTA (class in bioconvert.fastq2fasta)
G
GENBANK
GENBANK2EMBL (class in bioconvert.genbank2embl)
GENBANK2FASTA (class in bioconvert.genbank2fasta)
GENBANK2GFF3 (class in bioconvert.genbank2gff3)
generate_outfile_name() (in module bioconvert.core.utils)
get_all_conversions() (Registry method)
get_conversions() (Registry method)
get_conversions_from_ext() (Registry method)
get_converters_names() (Registry method)
get_ext() (Registry method)
get_extension() (in module bioconvert.core.utils)
get_format_from_extension() (in module bioconvert.core.utils)
get_json() (YAML2JSON method)
GFA
GFA2FASTA (class in bioconvert.gfa2fasta)
GFF2
GFF22GFF3 (class in bioconvert.gff22gff3)
GFF3
GFF32GFF2 (class in bioconvert.gff32gff2)
GZ
GZ2BZ2 (class in bioconvert.gz2bz2)
GZ2DSRC (class in bioconvert.gz2dsrc)
I
in_gz() (in module bioconvert.core.decorators)
install_tool() (ConvBase method)
iter_converters() (Registry method)
J
JSON
JSON2YAML (class in bioconvert.json2yaml)
just_name() (FASTQ2FASTA static method)
M
MAF
(class in bioconvert.io.maf)
MAF2SAM (class in bioconvert.maf2sam)
MAFLine (class in bioconvert.io.maf)
make_chain() (in module bioconvert.core.base)
make_in_gz_tester() (in module bioconvert.core.decorators)
md5() (in module bioconvert.core.utils)
module
bioconvert.abi2fasta
bioconvert.abi2fastq
bioconvert.abi2qual
bioconvert.bam2bedgraph
bioconvert.bam2bigwig
bioconvert.bam2cov
bioconvert.bam2cram
bioconvert.bam2fasta
bioconvert.bam2fastq
bioconvert.bam2json
bioconvert.bam2sam
bioconvert.bam2tsv
bioconvert.bam2wiggle
bioconvert.bcf2vcf
bioconvert.bcf2wiggle
bioconvert.bed2wiggle
bioconvert.bedgraph2bigwig
bioconvert.bedgraph2cov
bioconvert.bedgraph2wiggle
bioconvert.bigbed2bed
bioconvert.bigbed2wiggle
bioconvert.bigwig2bedgraph
bioconvert.bigwig2wiggle
bioconvert.bplink2plink
bioconvert.bz22gz
bioconvert.clustal2fasta
bioconvert.clustal2phylip
bioconvert.clustal2stockholm
bioconvert.core.base
bioconvert.core.benchmark
bioconvert.core.converter
bioconvert.core.decorators
bioconvert.core.downloader
bioconvert.core.extensions
bioconvert.core.graph
bioconvert.core.registry
bioconvert.core.utils
bioconvert.cram2bam
bioconvert.cram2fasta
bioconvert.cram2fastq
bioconvert.cram2sam
bioconvert.csv2tsv
bioconvert.csv2xls
bioconvert.dsrc2gz
bioconvert.embl2fasta
bioconvert.embl2genbank
bioconvert.fasta2clustal
bioconvert.fasta2faa
bioconvert.fasta2fastq
bioconvert.fasta2genbank
bioconvert.fasta2nexus
bioconvert.fasta2phylip
bioconvert.fasta2twobit
bioconvert.fasta_qual2fastq
bioconvert.fastq2fasta
bioconvert.genbank2embl
bioconvert.genbank2fasta
bioconvert.genbank2gff3
bioconvert.gfa2fasta
bioconvert.gff22gff3
bioconvert.gff32gff2
bioconvert.gz2bz2
bioconvert.gz2dsrc
bioconvert.io.maf
bioconvert.io.scf
bioconvert.json2yaml
bioconvert.maf2sam
bioconvert.newick2nexus
bioconvert.newick2phyloxml
bioconvert.nexus2fasta
bioconvert.nexus2newick
bioconvert.nexus2phylip
bioconvert.nexus2phyloxml
bioconvert.ods2csv
bioconvert.phylip2clustal
bioconvert.phylip2fasta
bioconvert.phylip2nexus
bioconvert.phylip2stockholm
bioconvert.phylip2xmfa
bioconvert.phyloxml2newick
bioconvert.phyloxml2nexus
bioconvert.plink2bplink
bioconvert.sam2bam
bioconvert.sam2cram
bioconvert.sam2paf
bioconvert.scf2fasta
bioconvert.scf2fastq
bioconvert.sra2fastq
bioconvert.stockholm2clustal
bioconvert.stockholm2phylip
bioconvert.tsv2csv
bioconvert.twobit2fasta
bioconvert.vcf2bcf
bioconvert.vcf2bed
bioconvert.vcf2wiggle
bioconvert.xls2csv
bioconvert.xlsx2csv
bioconvert.xmfa2phylip
bioconvert.yaml2json
N
name (ConvBase property)
NEWICK
NEWICK2NEXUS (class in bioconvert.newick2nexus)
NEWICK2PHYLOXML (class in bioconvert.newick2phyloxml)
NEXUS
NEXUS2FASTA (class in bioconvert.nexus2fasta)
NEXUS2NEWICK (class in bioconvert.nexus2newick)
NEXUS2PHYLIP (class in bioconvert.nexus2phylip)
NEXUS2PHYLOXML (class in bioconvert.nexus2phyloxml)
O
ODS2CSV (class in bioconvert.ods2csv)
out_compressor() (in module bioconvert.core.decorators)
P
PAF
PHYLIP
PHYLIP2CLUSTAL (class in bioconvert.phylip2clustal)
PHYLIP2FASTA (class in bioconvert.phylip2fasta)
PHYLIP2NEXUS (class in bioconvert.phylip2nexus)
PHYLIP2STOCKHOLM (class in bioconvert.phylip2stockholm)
PHYLIP2XMFA (class in bioconvert.phylip2xmfa)
PHYLOXML
PHYLOXML2NEWICK (class in bioconvert.phyloxml2newick)
PHYLOXML2NEXUS (class in bioconvert.phyloxml2nexus)
PLINK
PLINK2BPLINK (class in bioconvert.plink2bplink)
plot() (Benchmark method)
plot_multi_benchmark_max() (in module bioconvert.core.benchmark)
Q
QUAL
R
read_from_buffer() (in module bioconvert.io.scf)
Registry (class in bioconvert.core.registry)
requires() (in module bioconvert.core.decorators)
requires_nothing() (in module bioconvert.core.decorators)
run_methods() (Benchmark method)
S
SAM
SAM2BAM (class in bioconvert.sam2bam)
SAM2CRAM (class in bioconvert.sam2cram)
SAM2PAF (class in bioconvert.sam2paf)
SCF
SCF2FASTA (class in bioconvert.scf2fasta)
SCF2FASTQ (class in bioconvert.scf2fastq)
set_ext() (Registry method)
SRA
SRA2FASTQ (class in bioconvert.sra2fastq)
STOCKHOLM
STOCKHOLM2CLUSTAL (class in bioconvert.stockholm2clustal)
STOCKHOLM2PHYLIP (class in bioconvert.stockholm2phylip)
T
TempFile (class in bioconvert.core.utils)
Timer (class in bioconvert.core.utils)
TSV
TSV2CSV (class in bioconvert.tsv2csv)
TWOBIT
TWOBIT2FASTA (class in bioconvert.twobit2fasta)
U
unwrap_fasta() (FASTQ2FASTA static method)
update() (AttrDict method)
V
VCF
VCF2BCF (class in bioconvert.vcf2bcf)
VCF2BED (class in bioconvert.vcf2bed)
VCF2WIGGLE (class in bioconvert.vcf2wiggle)
W
WIG
WIGGLE
X
XLS
XLS2CSV (class in bioconvert.xls2csv)
XLSX
XLSX2CSV (class in bioconvert.xlsx2csv)
XMFA
XMFA2PHYLIP (class in bioconvert.xmfa2phylip)
Y
YAML
YAML2JSON (class in bioconvert.yaml2json)
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