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gtftk 0.9.6 documentation
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A
add_attr() (pygtftk.Line.Feature method)
add_attr_and_write() (pygtftk.Line.Feature method)
add_attr_column() (pygtftk.gtf_interface.GTF method)
add_attr_from_dict() (pygtftk.gtf_interface.GTF method)
add_attr_from_file() (pygtftk.gtf_interface.GTF method)
add_attr_from_list() (pygtftk.gtf_interface.GTF method)
add_attr_from_matrix_file() (pygtftk.gtf_interface.GTF method)
add_attr_to_pos() (pygtftk.gtf_interface.GTF method)
add_exon_number() (pygtftk.gtf_interface.GTF method)
add_prefix() (pygtftk.gtf_interface.GTF method)
add_prefix_to_file() (in module pygtftk.utils)
add_r_lib() (in module pygtftk.utils)
as_data_frame() (pygtftk.tab_interface.TAB method)
as_dict() (pygtftk.fasta_interface.FASTA method)
as_simple_list() (pygtftk.tab_interface.TAB method)
B
bw_cov_mp() (in module pygtftk.bwig.bw_coverage)
bw_profile_mp() (in module pygtftk.bwig.bw_coverage)
C
check_file_or_dir_exists() (in module pygtftk.utils)
check_r_installed() (in module pygtftk.utils)
check_r_packages() (in module pygtftk.utils)
chomp() (in module pygtftk.utils)
chrom_info_as_dict() (in module pygtftk.utils)
chrom_info_to_bed_file() (in module pygtftk.utils)
close_properly() (in module pygtftk.utils)
convert_to_ensembl() (pygtftk.gtf_interface.GTF method)
D
del_attr() (pygtftk.gtf_interface.GTF method)
E
enumerate() (pygtftk.fasta_interface.FASTA method)
extract_data() (pygtftk.gtf_interface.GTF method)
extract_data_iter_list() (pygtftk.gtf_interface.GTF method)
F
FASTA (class in pygtftk.fasta_interface)
FastaSequence (class in pygtftk.Line)
Feature (class in pygtftk.Line)
FieldSet (class in pygtftk.Line)
flatten_list() (in module pygtftk.utils)
flatten_list_recur() (in module pygtftk.utils)
format() (pygtftk.Line.FastaSequence method)
(pygtftk.Line.Feature method)
(pygtftk.Line.FieldSet method)
format_tab() (pygtftk.Line.Feature method)
from_list() (pygtftk.Line.Feature class method)
G
get_3p_end() (pygtftk.gtf_interface.GTF method)
(pygtftk.Line.Feature method)
get_5p_end() (pygtftk.gtf_interface.GTF method)
(pygtftk.Line.Feature method)
get_attr_list() (pygtftk.gtf_interface.GTF method)
get_attr_names() (pygtftk.Line.Feature method)
get_attr_value() (pygtftk.Line.Feature method)
get_attr_value_list() (pygtftk.gtf_interface.GTF method)
get_chroms() (pygtftk.gtf_interface.GTF method)
get_example_feature() (in module pygtftk.utils)
get_example_file() (in module pygtftk.utils)
get_feature_list() (pygtftk.gtf_interface.GTF method)
get_feature_size() (pygtftk.gtf_interface.GTF method)
get_gn_id() (pygtftk.Line.Feature method)
get_gn_ids() (pygtftk.gtf_interface.GTF method)
get_gn_strand() (pygtftk.gtf_interface.GTF method)
get_gn_to_tx() (pygtftk.gtf_interface.GTF method)
get_gname_to_tx() (pygtftk.gtf_interface.GTF method)
get_intergenic() (pygtftk.gtf_interface.GTF method)
get_introns() (pygtftk.gtf_interface.GTF method)
get_midpoints() (pygtftk.gtf_interface.GTF method)
get_sequences() (pygtftk.gtf_interface.GTF method)
get_transcript_size() (pygtftk.gtf_interface.GTF method)
get_tss() (pygtftk.gtf_interface.GTF method)
get_tts() (pygtftk.gtf_interface.GTF method)
get_tx_id() (pygtftk.Line.Feature method)
get_tx_ids() (pygtftk.gtf_interface.GTF method)
get_tx_strand() (pygtftk.gtf_interface.GTF method)
get_tx_to_gn() (pygtftk.gtf_interface.GTF method)
get_tx_to_gname() (pygtftk.gtf_interface.GTF method)
GTF (class in pygtftk.gtf_interface)
GTFtkError
GTFtkInteractiveError
H
head() (pygtftk.gtf_interface.GTF method)
head_file() (in module pygtftk.utils)
I
intervals() (in module pygtftk.utils)
is_comment() (in module pygtftk.utils)
is_empty() (in module pygtftk.utils)
is_exon() (in module pygtftk.utils)
is_fasta_header() (in module pygtftk.utils)
iter_as_list() (pygtftk.tab_interface.TAB method)
iter_features() (pygtftk.fasta_interface.FASTA method)
iterate_with_header() (pygtftk.tab_interface.TAB method)
M
make_outdir_and_file() (in module pygtftk.utils)
make_tmp_file() (in module pygtftk.utils)
median_comp() (in module pygtftk.utils)
merge_attr() (pygtftk.gtf_interface.GTF method)
message() (in module pygtftk.utils)
mkdir_p() (in module pygtftk.utils)
N
nb_exons() (pygtftk.gtf_interface.GTF method)
nrow() (pygtftk.gtf_interface.GTF method)
P
pygtftk.bwig.bw_coverage (module)
pygtftk.fasta_interface (module)
pygtftk.gtf_interface (module)
pygtftk.Line (module)
pygtftk.tab_interface (module)
pygtftk.utils (module)
R
random_string() (in module pygtftk.utils)
S
select_5p_transcript() (pygtftk.gtf_interface.GTF method)
select_by_key() (pygtftk.gtf_interface.GTF method)
select_by_loc() (pygtftk.gtf_interface.GTF method)
select_by_max_exon_nb() (pygtftk.gtf_interface.GTF method)
select_by_number_of_exons() (pygtftk.gtf_interface.GTF method)
select_by_numeric_value() (pygtftk.gtf_interface.GTF method)
select_by_positions() (pygtftk.gtf_interface.GTF method)
select_by_regexp() (pygtftk.gtf_interface.GTF method)
select_by_transcript_size() (pygtftk.gtf_interface.GTF method)
select_longuest_transcripts() (pygtftk.gtf_interface.GTF method)
select_shortest_transcripts() (pygtftk.gtf_interface.GTF method)
set_attr() (pygtftk.Line.Feature method)
silentremove() (in module pygtftk.utils)
simple_line_count() (in module pygtftk.utils)
simple_nb_column() (in module pygtftk.utils)
sort_2_lists() (in module pygtftk.utils)
T
TAB (class in pygtftk.tab_interface)
tab_line() (in module pygtftk.utils)
tail() (pygtftk.gtf_interface.GTF method)
to_alphanum() (in module pygtftk.utils)
to_bed() (pygtftk.gtf_interface.GTF method)
transcript_as_bioseq_records() (pygtftk.fasta_interface.FASTA method)
W
write() (pygtftk.fasta_interface.FASTA method)
(pygtftk.Line.FastaSequence method)
(pygtftk.Line.Feature method)
(pygtftk.Line.FieldSet method)
(pygtftk.gtf_interface.GTF method)
(pygtftk.tab_interface.TAB method)
write_bed() (pygtftk.Line.Feature method)
write_bed_3p_end() (pygtftk.Line.Feature method)
write_bed_5p_end() (pygtftk.Line.Feature method)
write_gtf_to_bed6() (pygtftk.Line.Feature method)
write_properly() (in module pygtftk.utils)
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gtftk 0.9.6 documentation
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