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 0xb6fb1...
|
Group |
accession_block = <Martel.Expression.Group instance at 0...
|
Group |
authors_block = <Martel.Expression.Group instance at 0xb...
|
Group |
base_count = <Martel.Expression.Group instance at 0xb6f4...
|
Group |
base_count_line = <Martel.Expression.Group instance at 0...
|
Group |
base_number = <Martel.Expression.Group instance at 0xb6f...
|
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 0xb...
|
Group |
consrtm_block = <Martel.Expression.Group instance at 0xb...
|
Group |
contig_block = <Martel.Expression.Group instance at 0xb6...
|
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 0xb6facb2c>
|
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 0xb6facb...
|
Group |
feature = <Martel.Expression.Group instance at 0xb6f45e0...
|
Group |
feature_block = <Martel.Expression.Group instance at 0xb...
|
Group |
feature_key = <Martel.Expression.Group instance at 0xb6f...
|
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 0xb...
|
ParseRecords |
format = <Martel.Expression.ParseRecords instance at 0xb...
|
Group |
gi = <Martel.Expression.Group instance at 0xb6fb1a6c>
|
Seq |
header = <Martel.Expression.Seq instance at 0xb6f4cacc>
|
int |
INDENT = 12 |
Group |
journal_block = <Martel.Expression.Group instance at 0xb...
|
Group |
keywords_block = <Martel.Expression.Group instance at 0x...
|
Group |
location = <Martel.Expression.Group instance at 0xb6f455...
|
Group |
locus = <Martel.Expression.Group instance at 0xb6fac64c>
|
Group |
locus_line = <Martel.Expression.Group instance at 0xb6fa...
|
Group |
medline_line = <Martel.Expression.Group instance at 0xb6...
|
HeaderFooter |
ncbi_format = <Martel.Expression.HeaderFooter instance a...
|
Group |
nid = <Martel.Expression.Group instance at 0xb6fb17ac>
|
Group |
nid_line = <Martel.Expression.Group instance at 0xb6fb18...
|
Group |
organism = <Martel.Expression.Group instance at 0xb6fb77...
|
Group |
organism_block = <Martel.Expression.Group instance at 0x...
|
Group |
origin_line = <Martel.Expression.Group instance at 0xb6f...
|
Group |
pid = <Martel.Expression.Group instance at 0xb6fb18cc>
|
Group |
pid_line = <Martel.Expression.Group instance at 0xb6fb19...
|
Group |
primary = <Martel.Expression.Group instance at 0xb6f4546...
|
Group |
primary_line = <Martel.Expression.Group instance at 0xb6...
|
Group |
primary_ref_line = <Martel.Expression.Group instance at ...
|
Group |
pubmed_line = <Martel.Expression.Group instance at 0xb6f...
|
Group |
qualifier = <Martel.Expression.Group instance at 0xb6f45...
|
Alt |
qualifier_space = <Martel.Expression.Alt instance at 0xb...
|
Str |
quote = <Martel.Expression.Str instance at 0xb6f458ac>
|
Group |
quoted_chars = <Martel.Expression.Group instance at 0xb6...
|
Seq |
quoted_string = <Martel.Expression.Seq instance at 0xb6f...
|
Group |
record = <Martel.Expression.Group instance at 0xb6f4ca6c...
|
Group |
record_end = <Martel.Expression.Group instance at 0xb6f4...
|
Group |
reference = <Martel.Expression.Group instance at 0xb6fbe...
|
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 0xb...
|
Group |
region = <Martel.Expression.Group instance at 0xb6fb144c...
|
Group |
remark_block = <Martel.Expression.Group instance at 0xb6...
|
list |
residue_prefixes = [<Martel.Expression.Str instance at 0...
|
Group |
residue_type = <Martel.Expression.Group instance at 0xb6...
|
list |
residue_types = [<Martel.Expression.Str instance at 0xb6...
|
Group |
segment = <Martel.Expression.Group instance at 0xb6fb71e...
|
Group |
segment_line = <Martel.Expression.Group instance at 0xb6...
|
Group |
sequence = <Martel.Expression.Group instance at 0xb6f4c1...
|
Group |
sequence_entry = <Martel.Expression.Group instance at 0x...
|
Group |
sequence_line = <Martel.Expression.Group instance at 0xb...
|
Group |
sequence_plus_spaces = <Martel.Expression.Group instance...
|
Group |
size = <Martel.Expression.Group instance at 0xb6fac70c>
|
Str |
small_indent_space = <Martel.Expression.Str instance at ...
|
Group |
source_block = <Martel.Expression.Group instance at 0xb6...
|
Group |
taxonomy = <Martel.Expression.Group instance at 0xb6fb75...
|
Group |
title_block = <Martel.Expression.Group instance at 0xb6f...
|
Seq |
unquoted_string = <Martel.Expression.Seq instance at 0xb...
|
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 0xb6fb19a...
|
Group |
version_line = <Martel.Expression.Group instance at 0xb6...
|