Martel based parser to read GenBank formatted files.
This is a huge regular regular expression for GenBank, built using the
'regular expressions on steroids' capabilities of Martel.
o GenBank/EMBL feature tables are described at:
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
o There are also descriptions of different GenBank lines at:
http://www.ibc.wustl.edu/standards/gbrel.txt
Variable Summary |
Group |
accession = <Martel.Expression.Group instance at 0x2aaaa...
|
Group |
accession_block = <Martel.Expression.Group instance at 0...
|
Group |
authors_block = <Martel.Expression.Group instance at 0x2...
|
Group |
base_count = <Martel.Expression.Group instance at 0x2aaa...
|
Group |
base_count_line = <Martel.Expression.Group instance at 0...
|
Group |
base_number = <Martel.Expression.Group instance at 0x2aa...
|
Str |
big_indent_space = <Martel.Expression.Str instance at 0x...
|
MaxRepeat |
blank_space = <Martel.Expression.MaxRepeat instance at 0...
|
Group |
comment_block = <Martel.Expression.Group instance at 0x2...
|
Group |
consrtm_block = <Martel.Expression.Group instance at 0x2...
|
Group |
contig_block = <Martel.Expression.Group instance at 0x2a...
|
Group |
contig_location = <Martel.Expression.Group instance at 0...
|
Group |
data_file_division = <Martel.Expression.Group instance a...
|
Group |
date = <Martel.Expression.Group instance at 0x2aaaae674e...
|
Group |
db_source_block = <Martel.Expression.Group instance at 0...
|
Group |
definition_block = <Martel.Expression.Group instance at ...
|
list |
divisions = [<Martel.Expression.Str instance at 0x2aaaae...
|
Group |
feature = <Martel.Expression.Group instance at 0x2aaaae6...
|
Group |
feature_block = <Martel.Expression.Group instance at 0x2...
|
Group |
feature_key = <Martel.Expression.Group instance at 0x2aa...
|
int |
FEATURE_KEY_INDENT = 5 |
Group |
feature_key_line = <Martel.Expression.Group instance at ...
|
int |
FEATURE_QUALIFIER_INDENT = 21 |
Group |
features_line = <Martel.Expression.Group instance at 0x2...
|
ParseRecords |
format = <Martel.Expression.ParseRecords instance at 0x2...
|
Group |
gi = <Martel.Expression.Group instance at 0x2aaaae67ecb0...
|
Seq |
header = <Martel.Expression.Seq instance at 0x2aaaae6a5f...
|
int |
INDENT = 12 |
Group |
journal_block = <Martel.Expression.Group instance at 0x2...
|
Group |
keywords_block = <Martel.Expression.Group instance at 0x...
|
Group |
location = <Martel.Expression.Group instance at 0x2aaaae...
|
Group |
locus = <Martel.Expression.Group instance at 0x2aaaae674...
|
Group |
locus_line = <Martel.Expression.Group instance at 0x2aaa...
|
Group |
medline_line = <Martel.Expression.Group instance at 0x2a...
|
HeaderFooter |
ncbi_format = <Martel.Expression.HeaderFooter instance a...
|
Group |
nid = <Martel.Expression.Group instance at 0x2aaaae67e68...
|
Group |
nid_line = <Martel.Expression.Group instance at 0x2aaaae...
|
Group |
organism = <Martel.Expression.Group instance at 0x2aaaae...
|
Group |
organism_block = <Martel.Expression.Group instance at 0x...
|
Group |
origin_line = <Martel.Expression.Group instance at 0x2aa...
|
Group |
pid = <Martel.Expression.Group instance at 0x2aaaae67e90...
|
Group |
pid_line = <Martel.Expression.Group instance at 0x2aaaae...
|
Group |
primary = <Martel.Expression.Group instance at 0x2aaaae6...
|
Group |
primary_line = <Martel.Expression.Group instance at 0x2a...
|
Group |
primary_ref_line = <Martel.Expression.Group instance at ...
|
Group |
pubmed_line = <Martel.Expression.Group instance at 0x2aa...
|
Group |
qualifier = <Martel.Expression.Group instance at 0x2aaaa...
|
Alt |
qualifier_space = <Martel.Expression.Alt instance at 0x2...
|
Str |
quote = <Martel.Expression.Str instance at 0x2aaaae6a051...
|
Group |
quoted_chars = <Martel.Expression.Group instance at 0x2a...
|
Seq |
quoted_string = <Martel.Expression.Seq instance at 0x2aa...
|
Group |
record = <Martel.Expression.Group instance at 0x2aaaae6a...
|
Group |
record_end = <Martel.Expression.Group instance at 0x2aaa...
|
Group |
reference = <Martel.Expression.Group instance at 0x2aaaa...
|
Group |
reference_bases = <Martel.Expression.Group instance at 0...
|
Group |
reference_line = <Martel.Expression.Group instance at 0x...
|
Group |
reference_num = <Martel.Expression.Group instance at 0x2...
|
Group |
remark_block = <Martel.Expression.Group instance at 0x2a...
|
list |
residue_prefixes = [<Martel.Expression.Str instance at 0...
|
Group |
residue_type = <Martel.Expression.Group instance at 0x2a...
|
list |
residue_types = [<Martel.Expression.Str instance at 0x2a...
|
Group |
segment = <Martel.Expression.Group instance at 0x2aaaae6...
|
Group |
segment_line = <Martel.Expression.Group instance at 0x2a...
|
Group |
sequence = <Martel.Expression.Group instance at 0x2aaaae...
|
Group |
sequence_entry = <Martel.Expression.Group instance at 0x...
|
Group |
sequence_line = <Martel.Expression.Group instance at 0x2...
|
Group |
sequence_plus_spaces = <Martel.Expression.Group instance...
|
Group |
size = <Martel.Expression.Group instance at 0x2aaaae6745...
|
Str |
small_indent_space = <Martel.Expression.Str instance at ...
|
Group |
source_block = <Martel.Expression.Group instance at 0x2a...
|
Group |
taxonomy = <Martel.Expression.Group instance at 0x2aaaae...
|
Group |
title_block = <Martel.Expression.Group instance at 0x2aa...
|
Seq |
unquoted_string = <Martel.Expression.Seq instance at 0x2...
|
list |
valid_divisions = ['PRI', 'ROD', 'MAM', 'VRT', 'INV', 'P...
|
list |
valid_residue_prefixes = ['ss-', 'ds-', 'ms-']
|
list |
valid_residue_types = ['DNA', 'RNA', 'mRNA', 'tRNA', 'rR...
|
Group |
version = <Martel.Expression.Group instance at 0x2aaaae6...
|
Group |
version_line = <Martel.Expression.Group instance at 0x2a...
|