bio-0.5.2: A bioinformatics library

Index

! | Bio.Sequence.SeqData, Bio.Sequence
? | Bio.Sequence.SeqData
AAProp | Bio.Sequence.AminoProperties
Ala | Bio.Sequence.SeqData, Bio.Sequence
Align |
1 (Type/Class) | Bio.Alignment.Bowtie
2 (Data Constructor) | Bio.Alignment.Bowtie
Alignment | Bio.Alignment.AlignData
aliphatic | Bio.Sequence.AminoProperties
Amino | Bio.Sequence.SeqData, Bio.Sequence
andSameSeq | Bio.Location.OnSeq
Ann | Bio.Sequence.GeneOntology, Bio.Sequence.GOA
Annotation | Bio.Sequence.GeneOntology, Bio.Sequence.GOA
appendHeader | Bio.Sequence.SeqData, Bio.Sequence
Arg | Bio.Sequence.SeqData, Bio.Sequence
aromatic | Bio.Sequence.AminoProperties
asksGFF | Bio.GFF3.FeatureHierSequences
Asm | Bio.Alignment.ACE
Asn | Bio.Sequence.SeqData, Bio.Sequence
Asp | Bio.Sequence.SeqData, Bio.Sequence
Assembly | Bio.Alignment.ACE
Asx | Bio.Sequence.SeqData, Bio.Sequence
attrByTag | Bio.GFF3.Feature
attributes | Bio.GFF3.Feature
attrTag | Bio.GFF3.Feature
attrValues | Bio.GFF3.Feature
Aux | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat
aux |
1 (Function) | Bio.Alignment.BlastData
2 (Function) | Bio.Alignment.BlastFlat
avg | Bio.Sequence.SFF_filters
b36 | Bio.Sequence.SFF_name
bases | Bio.Sequence.SFF
baseToFlowPos | Bio.Sequence.SFF
BED |
1 (Type/Class) | Bio.Alignment.BED
2 (Data Constructor) | Bio.Alignment.BED
bits |
1 (Function) | Bio.Alignment.BlastData
2 (Function) | Bio.Alignment.BlastFlat
blastdate | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat
BlastFlat |
1 (Type/Class) | Bio.Alignment.BlastFlat
2 (Data Constructor) | Bio.Alignment.BlastFlat
BlastHit |
1 (Type/Class) | Bio.Alignment.BlastData
2 (Data Constructor) | Bio.Alignment.BlastData
BlastMatch |
1 (Type/Class) | Bio.Alignment.BlastData
2 (Data Constructor) | Bio.Alignment.BlastData
blastn_default | Bio.Alignment.Matrices
blastprogram | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat
BlastRecord |
1 (Type/Class) | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat
2 (Data Constructor) | Bio.Alignment.BlastData
blastreferences | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat
BlastResult |
1 (Type/Class) | Bio.Alignment.BlastData
2 (Data Constructor) | Bio.Alignment.BlastData
blastversion | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat
blockcount | Bio.Alignment.PSL
blocksizes | Bio.Alignment.PSL
blockSizeStart | Bio.Alignment.BED
blosum45 | Bio.Alignment.Matrices
blosum62 | Bio.Alignment.Matrices
blosum80 | Bio.Alignment.Matrices
bounds |
1 (Function) | Bio.Location.ContigLocation
2 (Function) | Bio.Location.Location
Branch | Bio.Clustering
castSeq | Bio.Sequence.SeqData
castToAmino | Bio.Sequence.SeqData, Bio.Sequence
castToNuc | Bio.Sequence.SeqData, Bio.Sequence
charged | Bio.Sequence.AminoProperties
checkInvariants |
1 (Function) | Bio.Location.LocMap
2 (Function) | Bio.GFF3.FeatureHier
children |
1 (Function) | Bio.GFF3.FeatureHier
2 (Function) | Bio.GFF3.FeatureHierSequences
childrenM | Bio.GFF3.FeatureHier
Chr | Bio.Alignment.AlignData
chrom | Bio.Alignment.BED
chromEnd | Bio.Alignment.BED
chromosomes | Bio.GFF3.SGD
chromStart | Bio.Alignment.BED
clipFlows | Bio.Sequence.SFF_filters
clipSeq | Bio.Sequence.SFF_filters
clip_adapter_left | Bio.Sequence.SFF
clip_adapter_right | Bio.Sequence.SFF
clip_qual_left | Bio.Sequence.SFF
clip_qual_right | Bio.Sequence.SFF
Clustered | Bio.Clustering
cluster_sl | Bio.Clustering
columns | Bio.Alignment.AlignData
CommonHeader |
1 (Type/Class) | Bio.Sequence.SFF
2 (Data Constructor) | Bio.Sequence.SFF
Comp | Bio.Sequence.GeneOntology, Bio.Sequence.GOA
compact | Bio.Sequence.HashWord
compl | Bio.Sequence.SeqData, Bio.Sequence
complement | Bio.Sequence.HashWord
contig | Bio.Alignment.ACE
ContigLoc |
1 (Type/Class) | Bio.Location.ContigLocation
2 (Data Constructor) | Bio.Location.ContigLocation
contigLoc | Bio.GFF3.Feature
contigous | Bio.Sequence.HashWord, Bio.Sequence
ContigSeqLoc | Bio.Location.SeqLocation
convert | Bio.Sequence.SFF
countIO | Bio.Util
countSeqs | Bio.Sequence.Fasta
cumulative_index | Bio.Sequence.SFF
Cys | Bio.Sequence.SeqData, Bio.Sequence
database | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat
date | Bio.Sequence.SFF_name, Bio.Sequence.SFF
dbchars | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat
dbsequences | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat
decCh | Bio.Sequence.SFF_name
decode2Bit | Bio.Sequence.TwoBit, Bio.Sequence
decode36 | Bio.Sequence.SFF_name
decodeDate | Bio.Sequence.SFF_name
decodeKO | Bio.Sequence.KEGG
decodeLocation | Bio.Sequence.SFF_name
decodeReadName | Bio.Sequence.SFF_name, Bio.Sequence.SFF
decodeUP | Bio.Sequence.KEGG
decomment | Bio.Sequence.GeneOntology, Bio.Sequence.GOA
defragSeq | Bio.Sequence.SeqData, Bio.Sequence
Del | Bio.Alignment.AlignData
delete |
1 (Function) | Bio.Location.LocMap
2 (Function) | Bio.GFF3.FeatureHier
deleteBy | Bio.Location.LocMap
Dir |
1 (Type/Class) | Bio.Alignment.AlignData
2 (Type/Class) | Bio.Alignment.BED
DiscardFilter | Bio.Sequence.SFF_filters
discard_dots | Bio.Sequence.SFF_filters
discard_empty | Bio.Sequence.SFF_filters
discard_key | Bio.Sequence.SFF_filters
discard_length | Bio.Sequence.SFF_filters
discard_mixed | Bio.Sequence.SFF_filters
display |
1 (Function) | Bio.Location.Position
2 (Function) | Bio.Location.ContigLocation
3 (Function) | Bio.Location.Location
4 (Function) | Bio.Location.SeqLocation
displayContigSeqLoc | Bio.Location.SeqLocation
displaySeqPos | Bio.Location.SeqLocation
divMods | Bio.Sequence.SFF_name
dlength | Bio.Sequence.SFF_filters
Edit | Bio.Alignment.AlignData
EditList | Bio.Alignment.AlignData
empty | Bio.Location.SeqLocMap
encode2Bit | Bio.Sequence.TwoBit
encode36 | Bio.Sequence.SFF_name
encodeDate | Bio.Sequence.SFF_name
encodeLocation | Bio.Sequence.SFF_name
encodeReadName | Bio.Sequence.SFF_name, Bio.Sequence.SFF
encodeRegion | Bio.Sequence.SFF_name
end | Bio.GFF3.Feature
endPos |
1 (Function) | Bio.Location.ContigLocation
2 (Function) | Bio.Location.Location
entropy | Bio.Sequence.Entropy, Bio.Sequence
escapeAllBut | Bio.GFF3.Escape
escapeAllOf | Bio.GFF3.Escape
escapeByteString | Bio.GFF3.Escape
eval | Bio.Alignment.AlignData
EvidenceCode | Bio.Sequence.GeneOntology, Bio.Sequence.GOA
extend |
1 (Function) | Bio.Location.ContigLocation
2 (Function) | Bio.Location.Location
extractGaps | Bio.Alignment.AlignData
e_val |
1 (Function) | Bio.Alignment.BlastData
2 (Function) | Bio.Alignment.BlastFlat
Feature |
1 (Type/Class) | Bio.GFF3.Feature
2 (Data Constructor) | Bio.GFF3.Feature
FeatureHier | Bio.GFF3.FeatureHier
FeatureHierSequences | Bio.GFF3.FeatureHierSequences
features |
1 (Function) | Bio.GFF3.FeatureHier
2 (Function) | Bio.GFF3.FeatureHierSequences
featureSequence | Bio.GFF3.FeatureHierSequences
find_primer | Bio.Sequence.SFF_filters
flatten | Bio.Alignment.BlastFlat
Flow | Bio.Sequence.SFF
flow | Bio.Sequence.SFF
flowgram | Bio.Sequence.SFF
flowgram_fmt | Bio.Sequence.SFF
flowToBasePos | Bio.Sequence.SFF
flow_data | Bio.Sequence.SFF
flow_index | Bio.Sequence.SFF
flow_length | Bio.Sequence.SFF
flx_linker | Bio.Sequence.SFF_filters
fragments | Bio.Alignment.ACE
Frame | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat
fromIUPAC | Bio.Sequence.SeqData, Bio.Sequence
fromList |
1 (Function) | Bio.Location.LocMap
2 (Function) | Bio.Location.SeqLocMap
3 (Function) | Bio.GFF3.FeatureHier
fromLists | Bio.GFF3.FeatureHierSequences
fromPosLen | Bio.Location.ContigLocation
fromStartEnd | Bio.Location.ContigLocation
fromStr | Bio.Sequence.SeqData, Bio.Sequence
ftype | Bio.GFF3.Feature
Func | Bio.Sequence.GeneOntology, Bio.Sequence.GOA
Fwd |
1 (Data Constructor) | Bio.Alignment.AlignData
2 (Data Constructor) | Bio.Location.Strand
3 (Data Constructor) | Bio.Alignment.BED
gapped | Bio.Sequence.HashWord
Gaps | Bio.Alignment.AlignData
geneCDSes | Bio.GFF3.SGD
geneCDS_SLM | Bio.GFF3.SGD
genes | Bio.GFF3.SGD
geneSeqLoc | Bio.GFF3.SGD
geneSequence | Bio.GFF3.SGD
genkeys | Bio.Sequence.HashWord
genReadKegg | Bio.Sequence.KEGG
getSequence | Bio.GFF3.FeatureHierSequences
GFFAttr |
1 (Type/Class) | Bio.GFF3.Feature
2 (Data Constructor) | Bio.GFF3.Feature
Gln | Bio.Sequence.SeqData, Bio.Sequence
global_align |
1 (Function) | Bio.Alignment.SAlign
2 (Function) | Bio.Alignment.AAlign
3 (Function) | Bio.Alignment.QAlign
global_score |
1 (Function) | Bio.Alignment.SAlign
2 (Function) | Bio.Alignment.AAlign
3 (Function) | Bio.Alignment.QAlign
Glu | Bio.Sequence.SeqData, Bio.Sequence
Glx | Bio.Sequence.SeqData, Bio.Sequence
Gly | Bio.Sequence.SeqData, Bio.Sequence
GO | Bio.Sequence.GeneOntology, Bio.Sequence.GOA
GoClass | Bio.Sequence.GeneOntology, Bio.Sequence.GOA
GoDef |
1 (Type/Class) | Bio.Sequence.GeneOntology, Bio.Sequence.GOA
2 (Data Constructor) | Bio.Sequence.GeneOntology, Bio.Sequence.GOA
GoHierarchy | Bio.Sequence.GeneOntology, Bio.Sequence.GOA
GoTerm | Bio.Sequence.GeneOntology, Bio.Sequence.GOA
group | Bio.Alignment.Soap
hash | Bio.Sequence.HashWord, Bio.Sequence
hashes | Bio.Sequence.HashWord, Bio.Sequence
HashF | Bio.Sequence.HashWord, Bio.Sequence
hasqual | Bio.Sequence.SeqData
helixP | Bio.Sequence.AminoProperties
HF | Bio.Sequence.HashWord, Bio.Sequence
His | Bio.Sequence.SeqData, Bio.Sequence
hits | Bio.Alignment.BlastData
hRead2Bit | Bio.Sequence.TwoBit, Bio.Sequence
hReadFasta | Bio.Sequence.Fasta, Bio.Sequence
hReadFastQ | Bio.Sequence.FastQ, Bio.Sequence
hReadIllumina | Bio.Sequence.FastQ, Bio.Sequence
hReadPhd | Bio.Sequence.Phd, Bio.Sequence
hReadSangerQ | Bio.Sequence.FastQ, Bio.Sequence
hWrite2Bit | Bio.Sequence.TwoBit
hWriteFasta | Bio.Sequence.Fasta, Bio.Sequence
hWriteFastaQual | Bio.Sequence.Fasta, Bio.Sequence
hWriteFastQ | Bio.Sequence.FastQ, Bio.Sequence
hWriteIllumina | Bio.Sequence.FastQ, Bio.Sequence
hWriteQual | Bio.Sequence.Fasta, Bio.Sequence
hWriteSangerQ | Bio.Sequence.FastQ, Bio.Sequence
hydropathy | Bio.Sequence.AminoProperties
hydrophobic | Bio.Sequence.AminoProperties
h_from |
1 (Function) | Bio.Alignment.BlastData
2 (Function) | Bio.Alignment.BlastFlat
h_to |
1 (Function) | Bio.Alignment.BlastData
2 (Function) | Bio.Alignment.BlastFlat
IC | Bio.Sequence.GeneOntology, Bio.Sequence.GOA
IDA | Bio.Sequence.GeneOntology, Bio.Sequence.GOA
identity |
1 (Function) | Bio.Alignment.BlastData
2 (Function) | Bio.Alignment.BlastFlat
ids | Bio.GFF3.Feature
IEA | Bio.Sequence.GeneOntology, Bio.Sequence.GOA
IEP | Bio.Sequence.GeneOntology, Bio.Sequence.GOA
IGC | Bio.Sequence.GeneOntology, Bio.Sequence.GOA
IGI | Bio.Sequence.GeneOntology, Bio.Sequence.GOA
Ile | Bio.Sequence.SeqData, Bio.Sequence
IMP | Bio.Sequence.GeneOntology, Bio.Sequence.GOA
Index | Bio.Sequence.SFF
index_length | Bio.Sequence.SFF
index_offset | Bio.Sequence.SFF
indirect | Bio.Alignment.Multiple
Ins | Bio.Alignment.AlignData
insert |
1 (Function) | Bio.Location.LocMap
2 (Function) | Bio.Location.SeqLocMap
3 (Function) | Bio.GFF3.FeatureHier
insertGaps | Bio.Alignment.AlignData
IPI | Bio.Sequence.GeneOntology, Bio.Sequence.GOA
isCurated | Bio.Sequence.GeneOntology, Bio.Sequence.GOA
isN | Bio.Sequence.HashWord
isRepl | Bio.Alignment.AlignData
ISS | Bio.Sequence.GeneOntology, Bio.Sequence.GOA
isWithin |
1 (Function) | Bio.Location.ContigLocation
2 (Function) | Bio.Location.Location
3 (Function) | Bio.Location.SeqLocation
itemRGB | Bio.Alignment.BED
k2n | Bio.Sequence.HashWord
k2n' | Bio.Sequence.HashWord
key | Bio.Sequence.SFF
key_length | Bio.Sequence.SFF
KO |
1 (Type/Class) | Bio.Sequence.KEGG
2 (Data Constructor) | Bio.Sequence.KEGG
ksort | Bio.Sequence.HashWord, Bio.Sequence
KWords | Bio.Sequence.Entropy, Bio.Sequence
kwords | Bio.Sequence.Entropy, Bio.Sequence
lazyMany | Bio.Util.Parsex
Leaf | Bio.Clustering
leftoffset | Bio.Alignment.Bowtie
length |
1 (Function) | Bio.Location.ContigLocation
2 (Function) | Bio.Location.Location
3 (Function) | Bio.Alignment.Bowtie
4 (Function) | Bio.Alignment.Soap
5 (Function) | Bio.GFF3.Feature
Leu | Bio.Sequence.SeqData, Bio.Sequence
lines | Bio.Util
Loc |
1 (Type/Class) | Bio.Location.Location
2 (Data Constructor) | Bio.Location.Location
loc | Bio.GFF3.Feature
local_align |
1 (Function) | Bio.Alignment.SAlign
2 (Function) | Bio.Alignment.AAlign
3 (Function) | Bio.Alignment.QAlign
local_score |
1 (Function) | Bio.Alignment.SAlign
2 (Function) | Bio.Alignment.AAlign
3 (Function) | Bio.Alignment.QAlign
LocMap | Bio.Location.LocMap
lookupId |
1 (Function) | Bio.GFF3.FeatureHier
2 (Function) | Bio.GFF3.FeatureHierSequences
lookupIdChildren | Bio.GFF3.FeatureHier
lookupOverlaps |
1 (Function) | Bio.Location.LocMap
2 (Function) | Bio.Location.SeqLocMap
lookupWithin |
1 (Function) | Bio.Location.LocMap
2 (Function) | Bio.Location.SeqLocMap
Lys | Bio.Sequence.SeqData, Bio.Sequence
masked_bases | Bio.Sequence.SFF
mass | Bio.Sequence.AminoProperties
match | Bio.Alignment.PSL
matches | Bio.Alignment.BlastData
Met | Bio.Sequence.SeqData, Bio.Sequence
Minus | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat
Mismatch |
1 (Type/Class) | Bio.Alignment.Bowtie
2 (Data Constructor) | Bio.Alignment.Bowtie
mismatch | Bio.Alignment.PSL
mismatches |
1 (Function) | Bio.Alignment.Bowtie
2 (Function) | Bio.Alignment.Soap
mismatchSeqPos |
1 (Function) | Bio.Alignment.Bowtie
2 (Function) | Bio.Alignment.Soap
mkSeqs | Bio.Sequence.Fasta
mmoffset | Bio.Alignment.Bowtie
mylines | Bio.Util
n2i' | Bio.Sequence.HashWord
n2k | Bio.Sequence.HashWord
name |
1 (Function) | Bio.Alignment.Bowtie
2 (Function) | Bio.Alignment.Soap
3 (Function) | Bio.Alignment.BED
4 (Function) | Bio.GFF3.Feature
namedSLM | Bio.GFF3.SGD
name_length | Bio.Sequence.SFF
NAS | Bio.Sequence.GeneOntology, Bio.Sequence.GOA
ncount | Bio.Alignment.PSL
ND | Bio.Sequence.GeneOntology, Bio.Sequence.GOA
negative | Bio.Sequence.AminoProperties
nhit | Bio.Alignment.Soap
nmismatch |
1 (Function) | Bio.Alignment.Bowtie
2 (Function) | Bio.Alignment.Soap
noncodingExons | Bio.GFF3.SGD
noncodingSeqLoc | Bio.GFF3.SGD
noncodingSequence | Bio.GFF3.SGD
NR | Bio.Sequence.GeneOntology, Bio.Sequence.GOA
Nuc | Bio.Sequence.SeqData, Bio.Sequence
num_bases | Bio.Sequence.SFF
num_reads | Bio.Sequence.SFF
Offset | Bio.Sequence.SeqData, Bio.Sequence
offset |
1 (Function) | Bio.Location.Position
2 (Function) | Bio.Alignment.Soap
offset5 | Bio.Location.ContigLocation
on | Bio.Alignment.AlignData
oneOf | Bio.Sequence.AminoProperties
onSameSeq | Bio.Location.OnSeq
OnSeq |
1 (Type/Class) | Bio.Location.OnSeq
2 (Data Constructor) | Bio.Location.OnSeq
onSeqName | Bio.Location.OnSeq
onSeqObj | Bio.Location.OnSeq
OnSeqs | Bio.Location.OnSeq
or | Bio.Sequence.AminoProperties
overlaps |
1 (Function) | Bio.Location.ContigLocation
2 (Function) | Bio.Location.Location
3 (Function) | Bio.Location.SeqLocation
overlap_align | Bio.Alignment.QAlign
overlap_score | Bio.Alignment.QAlign
packFlows | Bio.Sequence.SFF
pairend | Bio.Alignment.Soap
pam30 | Bio.Alignment.Matrices
pam70 | Bio.Alignment.Matrices
parentIds | Bio.GFF3.Feature
parents |
1 (Function) | Bio.GFF3.FeatureHier
2 (Function) | Bio.GFF3.FeatureHierSequences
parentsM | Bio.GFF3.FeatureHier
parse |
1 (Function) | Bio.Alignment.Blast
2 (Function) | Bio.Sequence.FastQ
3 (Function) | Bio.Alignment.Bowtie
4 (Function) | Bio.Alignment.Soap
5 (Function) | Bio.GFF3.Feature
6 (Function) | Bio.GFF3.FeatureHierSequences
parseMismatch | Bio.Alignment.Soap
parsePSL | Bio.Alignment.PSL
parseWithFasta | Bio.GFF3.Feature
perSeq | Bio.Location.OnSeq
perSeqUpdate | Bio.Location.OnSeq
phase | Bio.GFF3.Feature
Phe | Bio.Sequence.SeqData, Bio.Sequence
Plus | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat
polar | Bio.Sequence.AminoProperties
Pos |
1 (Type/Class) | Bio.Location.Position
2 (Data Constructor) | Bio.Location.Position
posInto |
1 (Function) | Bio.Location.ContigLocation
2 (Function) | Bio.Location.Location
positive | Bio.Sequence.AminoProperties
posOutof |
1 (Function) | Bio.Location.ContigLocation
2 (Function) | Bio.Location.Location
Pro | Bio.Sequence.SeqData, Bio.Sequence
Proc | Bio.Sequence.GeneOntology, Bio.Sequence.GOA
progressive | Bio.Alignment.Multiple
PSL |
1 (Type/Class) | Bio.Alignment.PSL
2 (Data Constructor) | Bio.Alignment.PSL
pslHeader | Bio.Alignment.PSL
ptest | Bio.Alignment.ACE
putSeqLn | Bio.Sequence.SeqData
qend | Bio.Alignment.PSL
qgapcount | Bio.Alignment.PSL
qgaplength | Bio.Alignment.PSL
qlength |
1 (Function) | Bio.Alignment.BlastData
2 (Function) | Bio.Alignment.BlastFlat
qname | Bio.Alignment.PSL
qsize | Bio.Alignment.PSL
qstart | Bio.Alignment.PSL
qstarts | Bio.Alignment.PSL
Qual | Bio.Sequence.SeqData, Bio.Sequence.Fasta, Bio.Sequence.SFF, Bio.Sequence
qual |
1 (Function) | Bio.Alignment.Bowtie
2 (Function) | Bio.Alignment.Soap
qual20 | Bio.Sequence.SFF_filters
QualData | Bio.Sequence.SeqData, Bio.Sequence.SFF, Bio.Sequence
quality | Bio.Sequence.SFF
qualMx | Bio.Alignment.QAlign
qualnt | Bio.Alignment.Soap
query |
1 (Function) | Bio.Alignment.BlastData
2 (Function) | Bio.Alignment.BlastFlat
queryQual | Bio.Alignment.Bowtie
querySequ | Bio.Alignment.Bowtie
q_from |
1 (Function) | Bio.Alignment.BlastData
2 (Function) | Bio.Alignment.BlastFlat
q_to |
1 (Function) | Bio.Alignment.BlastData
2 (Function) | Bio.Alignment.BlastFlat
rapid_adapter | Bio.Sequence.SFF_filters
rbToSequence | Bio.Sequence.SFF
RCA | Bio.Sequence.GeneOntology, Bio.Sequence.GOA
rcontig | Bio.Sequence.HashWord, Bio.Sequence
rcpacked | Bio.Sequence.HashWord, Bio.Sequence
read2Bit | Bio.Sequence.TwoBit, Bio.Sequence
readACE | Bio.Alignment.ACE
readbase | Bio.Alignment.Bowtie
readBED | Bio.Alignment.BED
ReadBlock |
1 (Type/Class) | Bio.Sequence.SFF
2 (Data Constructor) | Bio.Sequence.SFF
readFasta | Bio.Sequence.Fasta, Bio.Sequence
readFastaQual | Bio.Sequence.Fasta, Bio.Sequence
readFastQ | Bio.Sequence.FastQ, Bio.Sequence
readGO | Bio.Sequence.GOA
readGOA | Bio.Sequence.GeneOntology, Bio.Sequence.GOA
ReadHeader |
1 (Type/Class) | Bio.Sequence.SFF
2 (Data Constructor) | Bio.Sequence.SFF
readIllumina | Bio.Sequence.FastQ, Bio.Sequence
ReadName |
1 (Type/Class) | Bio.Sequence.SFF_name, Bio.Sequence.SFF
2 (Data Constructor) | Bio.Sequence.SFF_name, Bio.Sequence.SFF
readnt | Bio.Alignment.Soap
readNuc | Bio.Sequence
readObo | Bio.Sequence.GeneOntology, Bio.Sequence.GOA
readPhd | Bio.Sequence.Phd, Bio.Sequence
readProt | Bio.Sequence
readPSL | Bio.Alignment.PSL
readQual | Bio.Sequence.Fasta, Bio.Sequence
reads | Bio.Alignment.ACE
readSangerQ | Bio.Sequence.FastQ, Bio.Sequence
readSFF | Bio.Sequence.SFF
readTerms | Bio.Sequence.GeneOntology, Bio.Sequence.GOA
readXML |
1 (Function) | Bio.Alignment.BlastXML
2 (Function) | Bio.Alignment.BlastFlat
read_header | Bio.Sequence.SFF
read_name | Bio.Sequence.SFF
recoverSFF | Bio.Sequence.SFF
refbase | Bio.Alignment.Bowtie
refCLoc | Bio.Alignment.Bowtie
refCSeqLoc |
1 (Function) | Bio.Alignment.Bowtie
2 (Function) | Bio.Alignment.Soap
refname |
1 (Function) | Bio.Alignment.Bowtie
2 (Function) | Bio.Alignment.Soap
refnt | Bio.Alignment.Soap
refSeqLoc |
1 (Function) | Bio.Alignment.Bowtie
2 (Function) | Bio.Alignment.Soap
refSeqPos |
1 (Function) | Bio.Alignment.Bowtie
2 (Function) | Bio.Alignment.Soap
refstart | Bio.Alignment.Soap
region | Bio.Sequence.SFF_name, Bio.Sequence.SFF
removePrefix | Bio.Sequence.KEGG
Repl | Bio.Alignment.AlignData
repmatch | Bio.Alignment.PSL
results | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat
Rev |
1 (Data Constructor) | Bio.Alignment.AlignData
2 (Data Constructor) | Bio.Alignment.BED
RevCompl | Bio.Location.Strand
revCompl | Bio.Location.Strand
revcompl | Bio.Sequence.SeqData, Bio.Sequence
revcompl' | Bio.Sequence.SeqData, Bio.Sequence
rna_adapter | Bio.Sequence.SFF_filters
rna_adapter2 | Bio.Sequence.SFF_filters
rna_adapter3 | Bio.Sequence.SFF_filters
rRNAs | Bio.GFF3.SGD
runGFF | Bio.GFF3.FeatureHierSequences
runGFFIO | Bio.GFF3.FeatureHierSequences
SA | Bio.Alignment.Soap
SAM | Bio.Alignment.Soap
sameRead | Bio.Alignment.Bowtie
score |
1 (Function) | Bio.Alignment.BED
2 (Function) | Bio.GFF3.Feature
Selector | Bio.Alignment.AlignData
Seq | Bio.Sequence.SeqData, Bio.Sequence
SeqData | Bio.Sequence.SeqData, Bio.Sequence.SFF, Bio.Sequence
seqData |
1 (Function) | Bio.Location.ContigLocation
2 (Function) | Bio.Location.Location
3 (Function) | Bio.Location.SeqLocation
4 (Function) | Bio.GFF3.FeatureHierSequences
seqdata | Bio.Sequence.SeqData, Bio.Sequence
seqDataPadded |
1 (Function) | Bio.Location.ContigLocation
2 (Function) | Bio.Location.Location
seqheader | Bio.Sequence.SeqData, Bio.Sequence
SeqId | Bio.Alignment.BlastData
seqid | Bio.GFF3.Feature
seqlabel | Bio.Sequence.SeqData, Bio.Sequence
seqlength | Bio.Sequence.SeqData, Bio.Sequence
SeqLoc | Bio.Location.SeqLocation
seqLoc | Bio.GFF3.Feature
SeqLocMap | Bio.Location.SeqLocMap
seqmap | Bio.Sequence.SeqData, Bio.Sequence
SeqName | Bio.Location.OnSeq
seqNt | Bio.Location.Position
seqNtPadded | Bio.Location.Position
SeqPos | Bio.Location.SeqLocation
seqqual | Bio.Sequence.SeqData, Bio.Sequence
seqToStr | Bio.Sequence.SeqData
sequ |
1 (Function) | Bio.Alignment.Bowtie
2 (Function) | Bio.Alignment.Soap
Sequence | Bio.Sequence.SeqData, Bio.Sequence
sequence' | Bio.Util
sequences | Bio.GFF3.FeatureHierSequences
Ser | Bio.Sequence.SeqData, Bio.Sequence
setHeader | Bio.Sequence.SeqData, Bio.Sequence
SFF |
1 (Type/Class) | Bio.Sequence.SFF
2 (Data Constructor) | Bio.Sequence.SFF
sffToSequence | Bio.Sequence.SFF
Shape | Bio.Sequence.HashWord
showalign | Bio.Alignment.AlignData
sigint | Bio.Sequence.SFF_filters
simpleMx | Bio.Alignment.Matrices
slength |
1 (Function) | Bio.Alignment.BlastData
2 (Function) | Bio.Alignment.BlastFlat
slide |
1 (Function) | Bio.Location.Position
2 (Function) | Bio.Location.ContigLocation
small | Bio.Sequence.AminoProperties
SoapAlign | Bio.Alignment.Soap
SoapAlignMismatch | Bio.Alignment.Soap
sortExons | Bio.GFF3.SGD
source | Bio.GFF3.Feature
splitWhen | Bio.Util
start | Bio.GFF3.Feature
startPos |
1 (Function) | Bio.Location.ContigLocation
2 (Function) | Bio.Location.Location
STP | Bio.Sequence.SeqData, Bio.Sequence
Strand |
1 (Type/Class) | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat
2 (Type/Class) | Bio.Location.Strand
strand |
1 (Function) | Bio.Alignment.PSL
2 (Function) | Bio.Location.Position
3 (Function) | Bio.Location.ContigLocation
4 (Function) | Bio.Alignment.Bowtie
5 (Function) | Bio.Alignment.Soap
6 (Function) | Bio.Alignment.BED
7 (Function) | Bio.GFF3.Feature
Stranded | Bio.Location.Strand
stranded | Bio.Location.Strand
strandP | Bio.Sequence.AminoProperties
Strands | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat
subject |
1 (Function) | Bio.Alignment.BlastData
2 (Function) | Bio.Alignment.BlastFlat
SubstMx | Bio.Alignment.AlignData
TAS | Bio.Sequence.GeneOntology, Bio.Sequence.GOA
tend | Bio.Alignment.PSL
test |
1 (Function) | Bio.Sequence.SFF
2 (Function) | Bio.Alignment.QAlign
tgapcount | Bio.Alignment.PSL
tgaplength | Bio.Alignment.PSL
thickEnd | Bio.Alignment.BED
thickStart | Bio.Alignment.BED
Thr | Bio.Sequence.SeqData, Bio.Sequence
time | Bio.Sequence.SFF_name, Bio.Sequence.SFF
tiny | Bio.Sequence.AminoProperties
ti_adapter_b | Bio.Sequence.SFF_filters
ti_linker | Bio.Sequence.SFF_filters
tname | Bio.Alignment.PSL
toIUPAC | Bio.Sequence.SeqData, Bio.Sequence
toStr | Bio.Sequence.SeqData, Bio.Sequence
toStrings | Bio.Alignment.AlignData
translate | Bio.Sequence.SeqData, Bio.Sequence
trim | Bio.Sequence.SFF
TrimFilter | Bio.Sequence.SFF_filters
trimFlows | Bio.Sequence.SFF
trimFromTo | Bio.Sequence.SFF
trimKey | Bio.Sequence.SFF
trim_primer | Bio.Sequence.SFF_filters
trim_qual20 | Bio.Sequence.SFF_filters
trim_sigint | Bio.Sequence.SFF_filters
Trp | Bio.Sequence.SeqData, Bio.Sequence
tsize | Bio.Alignment.PSL
tstart | Bio.Alignment.PSL
tstarts | Bio.Alignment.PSL
Tyr | Bio.Sequence.SeqData, Bio.Sequence
unEscapeByteString | Bio.GFF3.Escape
UniProtAcc | Bio.Sequence.GeneOntology, Bio.Sequence.GOA
Unknown | Bio.Sequence.SeqData, Bio.Sequence
unpackFlows | Bio.Sequence.SFF
unparse |
1 (Function) | Bio.Sequence.FastQ
2 (Function) | Bio.Alignment.Soap
3 (Function) | Bio.GFF3.Feature
unparseMismatch | Bio.Alignment.Soap
unparsePSL | Bio.Alignment.PSL
unval | Bio.Sequence.HashWord
Val | Bio.Sequence.SeqData, Bio.Sequence
val | Bio.Sequence.HashWord
withinContigSeqLoc | Bio.Location.SeqLocation
withNameAndSeq | Bio.Location.OnSeq
withSeqData | Bio.Location.OnSeq
write2Bit | Bio.Sequence.TwoBit
writeACE | Bio.Alignment.ACE
writeBED | Bio.Alignment.BED
writeFasta | Bio.Sequence.Fasta, Bio.Sequence
writeFastaQual | Bio.Sequence.Fasta, Bio.Sequence
writeFastQ | Bio.Sequence.FastQ, Bio.Sequence
writeIllumina | Bio.Sequence.FastQ, Bio.Sequence
writePSL | Bio.Alignment.PSL
writeQual | Bio.Sequence.Fasta, Bio.Sequence
writeSangerQ | Bio.Sequence.FastQ, Bio.Sequence
writeSFF | Bio.Sequence.SFF
writeSFF' | Bio.Sequence.SFF
Xaa | Bio.Sequence.SeqData, Bio.Sequence
Xle | Bio.Sequence.SeqData, Bio.Sequence
x_loc | Bio.Sequence.SFF_name, Bio.Sequence.SFF
y_loc | Bio.Sequence.SFF_name, Bio.Sequence.SFF