Index

A | B | C | D | E | F | G | I | L | M | N | O | P | Q | R | S | T | V | W

A

abc() (in module g2gtools.chain)
ALT (g2gtools.vcf.VCFRecord attribute)
app_exit() (in module g2gtools.g2g_utils)
attributes (g2gtools.gtf.GTFRecord attribute)

B

BED (class in g2gtools.bed)
BEDRecord (class in g2gtools.bed)
bin_info() (in module g2gtools.bins)
bins() (in module g2gtools.bins)

C

ChainEntry (class in g2gtools.chain)
ChainFile (class in g2gtools)
(class in g2gtools.chain)
ChainIter (class in g2gtools.chain)
chrom (g2gtools.bed.BEDRecord attribute)
CHROM (g2gtools.vcf.VCFRecord attribute)
Cigar (class in g2gtools.bamsam)
cigar_to_string() (in module g2gtools.bamsam)
cigarlist_to_cigarstring() (in module g2gtools.bamsam)
code (g2gtools.bamsam.Cigar attribute)
collapse_entries() (in module g2gtools.chain)
command_convert() (in module g2gtools)
(in module g2gtools.g2g_commands)
command_db2chain() (in module g2gtools)
(in module g2gtools.g2g_commands)
command_dbfetch() (in module g2gtools.g2g_commands)
command_fasta_extract() (in module g2gtools)
(in module g2gtools.g2g_commands)
command_fasta_patch() (in module g2gtools)
(in module g2gtools.g2g_commands)
command_fasta_transform() (in module g2gtools)
(in module g2gtools.g2g_commands)
command_gtf2chain() (in module g2gtools)
(in module g2gtools.g2g_commands)
command_gtf2db() (in module g2gtools)
(in module g2gtools.g2g_commands)
command_offset2chain() (in module g2gtools)
(in module g2gtools.g2g_commands)
command_parse_location() (in module g2gtools)
(in module g2gtools.g2g_commands)
command_vcf2chain() (in module g2gtools)
(in module g2gtools.g2g_commands)
compare_files() (in module g2gtools.fasta)
complement_sequence() (in module g2gtools)
(in module g2gtools.g2g_utils)
(in module g2gtools.sequence)
configure_logging() (in module g2gtools.g2g_utils)
convert_bam_file() (in module g2gtools.bamsam)
convert_bed_file() (in module g2gtools.bed)
convert_cigar() (in module g2gtools.bamsam)
convert_gene_transcripts() (in module g2gtools.g2g)
convert_gtf_file() (in module g2gtools.gtf)

D

db2chain() (in module g2gtools)
(in module g2gtools.g2g)
dbfetch() (in module g2gtools.g2g)
dbg_fmt (g2gtools.g2g_utils.G2GFormatter attribute)
diff() (in module g2gtools.fasta)

E

end (g2gtools.bamsam.Cigar attribute)
(g2gtools.bed.BEDRecord attribute)
(g2gtools.g2g_utils.Location attribute)
(g2gtools.gtf.GTFRecord attribute)
err_fmt (g2gtools.g2g_utils.G2GFormatter attribute)
extra (g2gtools.bed.BEDRecord attribute)
extract() (in module g2gtools.fasta)
extract_id() (in module g2gtools.fasta)

F

FAI (class in g2gtools.fasta)
FAIEntry (class in g2gtools.fasta)
fasta_extract() (in module g2gtools)
fasta_extract_exons() (in module g2gtools.g2g)
fasta_extract_transcripts() (in module g2gtools.g2g)
fasta_patch() (in module g2gtools)
fasta_transform() (in module g2gtools)
(in module g2gtools.g2g)
fi (g2gtools.vcf.GTData attribute)
file_convert() (in module g2gtools)
(in module g2gtools.g2g)
FILTER (g2gtools.vcf.VCFRecord attribute)
find_mappings() (g2gtools.chain.ChainFile method)
(g2gtools.ChainFile method)
FORMAT (g2gtools.vcf.VCFRecord attribute)
format() (g2gtools.g2g_utils.G2GFormatter method)
format_time() (in module g2gtools.g2g_utils)
frame (g2gtools.gtf.GTFRecord attribute)
from_chr (g2gtools.chain.IntervalMapping attribute)
from_end (g2gtools.chain.IntervalMapping attribute)
from_seq (g2gtools.chain.IntervalMapping attribute)
from_start (g2gtools.chain.IntervalMapping attribute)

G

G2GBAMError, [1]
G2GBedError, [1]
G2GChainFileError, [1]
G2GCigarFormatError, [1]
G2GError, [1]
G2GFastaError, [1]
G2GFetchError, [1]
G2GFormatter (class in g2gtools.g2g_utils)
G2GGTFError, [1]
G2GLocationError, [1]
g2gtools (module)
g2gtools.bamsam (module)
g2gtools.bed (module)
g2gtools.bins (module)
g2gtools.chain (module)
g2gtools.exceptions (module)
g2gtools.fasta (module)
g2gtools.g2g (module)
g2gtools.g2g_commands (module)
g2gtools.g2g_utils (module)
g2gtools.gtf (module)
g2gtools.seq_offsets (module)
g2gtools.sequence (module)
g2gtools.vcf (module)
G2GValueError, [1]
G2GVCFError, [1]
get() (in module g2gtools.fasta)
get_logger() (in module g2gtools.g2g_utils)
get_multiplier() (in module g2gtools.g2g_utils)
get_sample_index() (g2gtools.vcf.VCF method)
get_seqids() (g2gtools.chain.ChainFile method)
(g2gtools.ChainFile method)
gt (g2gtools.vcf.GTData attribute)
GTData (class in g2gtools.vcf)
GTF (class in g2gtools.gtf)
gtf2chain() (in module g2gtools)
(in module g2gtools.g2g)
gtf2db() (in module g2gtools), [1]
GTFRecord (class in g2gtools.gtf)

I

ID (g2gtools.vcf.VCFRecord attribute)
info (g2gtools.sequence.Sequence attribute)
INFO (g2gtools.vcf.VCFRecord attribute)
info_fmt (g2gtools.g2g_utils.G2GFormatter attribute)
intersect_regions() (in module g2gtools.g2g_utils)
IntervalMapping (class in g2gtools.chain)

L

left (g2gtools.vcf.GTData attribute)
length (g2gtools.bamsam.Cigar attribute)
Location (class in g2gtools.g2g_utils)

M

merge_dicts() (in module g2gtools.g2g_utils)

N

name (g2gtools.bed.BEDRecord attribute)
next() (g2gtools.bed.BED method)
(g2gtools.chain.ChainIter method)
(g2gtools.gtf.GTF method)
(g2gtools.vcf.VCF method)

O

offset2chain() (in module g2gtools)
(in module g2gtools.g2g)
offset_chromosome_to_chain() (in module g2gtools.g2g)
offset_parse_chromosomes() (in module g2gtools.seq_offsets)

P

parse() (g2gtools.chain.ChainFile method)
(g2gtools.ChainFile method)
parse_attributes() (in module g2gtools.gtf)
parse_chromosome() (in module g2gtools.g2g_utils)
parse_gt() (g2gtools.vcf.VCF method)
(in module g2gtools.vcf)
parse_gt_new() (in module g2gtools.vcf)
parse_gtf_line() (in module g2gtools.gtf)
parse_line() (g2gtools.chain.ChainIter method)
parse_location() (in module g2gtools)
(in module g2gtools.g2g_utils)
parse_vcf_line() (in module g2gtools.vcf)
phase (g2gtools.vcf.GTData attribute)
POS (g2gtools.vcf.VCFRecord attribute)

Q

QUAL (g2gtools.vcf.VCFRecord attribute)

R

read() (g2gtools.fasta.FAI method)
ref (g2gtools.vcf.GTData attribute)
REF (g2gtools.vcf.VCFRecord attribute)
reset() (g2gtools.chain.ChainIter method)
reverse_complement_sequence() (in module g2gtools)
(in module g2gtools.g2g_utils)
(in module g2gtools.sequence)
reverse_sequence() (in module g2gtools)
(in module g2gtools.g2g_utils)
(in module g2gtools.sequence)
right (g2gtools.vcf.GTData attribute)

S

same_bases (g2gtools.chain.IntervalMapping attribute)
SAMPLES (g2gtools.vcf.VCFRecord attribute)
score (g2gtools.bed.BEDRecord attribute)
(g2gtools.gtf.GTFRecord attribute)
seqid (g2gtools.gtf.GTFRecord attribute)
Sequence (class in g2gtools.sequence)
source (g2gtools.gtf.GTFRecord attribute)
start (g2gtools.bamsam.Cigar attribute)
(g2gtools.bed.BEDRecord attribute)
(g2gtools.g2g_utils.Location attribute)
(g2gtools.gtf.GTFRecord attribute)
strand (g2gtools.bed.BEDRecord attribute)
(g2gtools.g2g_utils.Location attribute)
(g2gtools.gtf.GTFRecord attribute)

T

to_chr (g2gtools.chain.IntervalMapping attribute)
to_end (g2gtools.chain.IntervalMapping attribute)
to_seq (g2gtools.chain.IntervalMapping attribute)
to_start (g2gtools.chain.IntervalMapping attribute)
type (g2gtools.gtf.GTFRecord attribute)

V

VCF (class in g2gtools.vcf)
vcf_pos (g2gtools.chain.IntervalMapping attribute)
VCFRecord (class in g2gtools.vcf)

W

wrap_sequence() (in module g2gtools.g2g_utils)