VAMP
Introduction
Installation
Install Prequisites
Install VAMP
Non-root users
Usage
Align Contigs to Reference
Stitch Together Scaffold
Genome Annotation and Comparison
Commands
compare_genomes.py
fastq_to_fasta.py
find_contig_deletions.py
gff2gtf_simple.py
maf_net.py
makePairedOutput2EQUALfiles_vamp.pl
makePairedOutput2UNEQUALfiles_vamp.pl
TQSfastq_vamp.py
translate_cds.py
Modules
vamp.utils
seq_utils.convert_coordinates
seq_utils.fasta_from_gff
seq_utils.summarize_alignments
seq_utils.utils
VAMP
Docs
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Index
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E
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C
contig (vamp.utils.ContigComposition attribute)
contig_end (vamp.utils.ContigComposition attribute)
contig_size (vamp.utils.ContigComposition attribute)
contig_start (vamp.utils.ContigComposition attribute)
ContigComposition (class in vamp.utils)
convert_interval_gapped_to_nongapped() (in module seq_utils.utils)
convert_interval_nongapped_to_gapped() (in module seq_utils.utils)
E
end (vamp.utils.ContigComposition attribute)
F
find_aligned_position() (in module seq_utils.convert_coordinates)
find_deletions() (in module vamp.utils)
G
get_block_by_label() (in module vamp.utils)
get_sequence_length_from_maf() (in module vamp.utils)
get_sequence_net_alignment() (in module vamp.utils)
get_vamp_home() (in module vamp.utils)
M
main() (in module seq_utils.summarize_alignments)
mismatch_string() (in module seq_utils.summarize_alignments)
P
parse_event() (in module seq_utils.summarize_alignments)
R
read_contig_composition_summary() (in module vamp.utils)
replace_alignment_with_block() (in module vamp.utils)
S
seq (vamp.utils.ContigComposition attribute)
seq_utils.convert_coordinates (module)
seq_utils.fasta_from_gff (module)
seq_utils.summarize_alignments (module)
seq_utils.utils (module)
start (vamp.utils.ContigComposition attribute)
strand (vamp.utils.ContigComposition attribute)
subtract_intervals() (in module vamp.utils)
summarize_contig_composition() (in module vamp.utils)
summary_of_alignment() (in module seq_utils.summarize_alignments)
T
tab_headings() (vamp.utils.ContigComposition static method)
to_tab() (vamp.utils.ContigComposition method)
U
update_contig_composition_summary() (in module vamp.utils)
update_sequence_with_replacements() (in module vamp.utils)
V
vamp.utils (module)
verify_maf_fasta() (in module vamp.utils)
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