Provided by: libbio-eutilities-perl_1.75-3_all 
NAME
bp_genbank_ref_extractor - Retrieves all related sequences for a list of searches on Entrez gene
VERSION
version 1.75
SYNOPSIS
bp_genbank_ref_extractor [options] [Entrez Gene Queries]
DESCRIPTION
This script searches on Entrez Gene database and retrieves not only the gene sequence but also the
related transcript and protein sequences.
The gene UIDs of multiple searches are collected before attempting to retrieve them so each gene will
only be analyzed once even if appearing as result on more than one search.
Note that by default no sequences are saved (see options and examples).
OPTIONS
Several options can be used to fine tune the script behaviour. It is possible to obtain extra base pairs
upstream and downstream of the gene, control the naming of files and genome assembly to use.
See the section bugs for problems when using default values of options.
--assembly
When retrieving the sequence, a specific assemly can be defined. The value expected is a regex that
will be case-insensitive. If it matches more than one assembly, it will use the first match. It
defauls to "(primary|reference) assembly".
--debug
If set, even more output will be printed that may help on debugging. Unlike the messages from
--verbose and --very-verbose, these will not appear on the log file unless this option is selected.
This option also sets --very-verbose.
--downstream, --down
Specifies the number of extra base pairs to be retrieved downstream of the gene. This extra base
pairs will only affect the gene sequence, not the transcript or proteins.
--email
A valid email used to connect to the NCBI servers. This may be used by NCBI to contact users in case
of problems and before blocking access in case of heavy usage.
--format
Specifies the format that the sequences will be saved. Defaults to genbank format. Valid formats are
'genbank' or 'fasta'.
--genes
Specifies the name for gene file. By default, they are not saved. If no value is given defaults to
its UID. Possible values are 'uid', 'name', 'symbol' (the official symbol or nomenclature).
--help
Display the documentation (this text).
--limit
When making a query, limit the result to these first specific results. This is to prevent the use of
specially unspecific queries and a warning will be given if a query returns more results than the
limit. The default value is 200. Note that this limit is for each search.
--non-coding, --nonon-coding
Some protein coding genes have transcripts that are non-coding. By default, these sequences are saved
as well. --nonon-coding can be used to ignore those transcripts.
--proteins
Specifies the name for proteins file. By default, they are not saved. If no value is given defaults
to its accession. Possible values are 'accession', 'description', 'gene' (the corresponding gene ID)
and 'transcript' (the corresponding transcript accesion).
Note that if not using 'accession' is possible for files to be overwritten. It is possible for the
same gene to encode more than one protein or different proteins to have the same description.
--pseudo, --nopseudo
By default, sequences of pseudo genes will be saved. --nopseudo can be used to ignore those genes.
--save
Specifies the path for the directory where the sequence and log files will be saved. If the directory
does not exist it will be created altough the path to it must exist. Files on the directory may be
rewritten if necessary. If unspecified, a directory named extracted sequences on the current
directory will be used.
--save-data
This options saves the data (gene UIDs, description, product accessions, etc) to a file. As an
optional value, the file format can be specified. Defaults to CSV.
Currently only CSV is supported.
Saving the data structure as a CSV file, requires the installation of the Text::CSV module.
--transcripts, --mrna
Specifies the name for transcripts file. By default, they are not saved. If no value is given
defaults to its accession. Possible values are 'accession', 'description', 'gene' (the corresponding
gene ID) and 'protein' (the protein the transcript encodes).
Note that if not using 'accession' is possible for files to be overwritten. It is possible for the
same gene to have more than one transcript or different transcripts to have the same description.
Also, non-coding transcripts will create problems if using 'protein'.
--upstream, --up
Specifies the number of extra base pairs to be extracted upstream of the gene. This extra base pairs
will only affect the gene sequence, not the transcript or proteins.
--verbose, --v
If set, program becomes verbose. For an extremely verbose program, use --very-verbose instead.
--very-verbose, --vv
If set, program becomes extremely verbose. Setting this option, automatically sets --verbose as well.
For help in debugging, consider using --debug
EXAMPLES
"bp_genbank_ref_extractor --transcripts=accession '"homo sapiens"[organism] AND H2B'"
Search Entrez gene with the query '"homo sapiens"[organism] AND H2B', and save their transcripts
sequences. Note that default value of --limit may only extract some of the hits.
"bp_genbank_ref_extractor --transcripts=accession --proteins=accession --format=fasta '"homo
sapiens"[organism] AND H2B' '"homo sapiens"[organism] AND MCPH1'"
Same as first example but also searches for '"homo sapiens"[organism] AND MCPH1', proteins sequences,
and saves them in the fasta format.
"bp_genbank_ref_extractor --genes --up=100 --down=500 '"homo sapiens"[organism] AND H2B'"
Same search as first example but saves the genomic sequences instead including 100 and 500 bp
upstream and downstream.
"bp_genbank_ref_extractor --genes --asembly='Alternate HuRef' '"homo sapiens"[organism] AND H2B'"
Same search as first example but saves genomic sequences and from the Alternate HuRef genome assembly
instead.
"bp_genbank_ref_extractor --save-data=CSV '"homo sapiens"[organism] AND H2B'"
Same search as first example but does not save any sequence but saves all the results in a CSV file.
"bp_genbank_ref_extractor --save='search results' --genes=name --upstream=200 downstream=500 --nopseudo
--nonnon-coding --transcripts --proteins --format=fasta --save-data=CSV '"homo sapiens"[organism] AND
H2B' '"homo sapiens"[organism] AND MCPH1'"
Searches on Entrez gene for both '"homo sapiens"[organism] AND H2B' and '"homo sapiens"[organism] AND
MCPH1' and saves the gene sequences of all hits (not passing the default limit and ignoring
pseudogenes) plus 200 and 500bp upstream and downstream of them. It will also save the sequences of
all transcripts and proteins of each gene (but ignoring non-coding transcripts). It will save the
sequences in the fasta format, inside a directory "search results", and save the results in a CSV
file
KNOWN BUGS
• When supplying options, it's possible to not supply a value and use their default. However, when the
expected value is a string, the next argument may be confused as value for the option. For example,
when using the following command:
"bp_genbank_ref_extractor --transcripts 'H2A AND homo sapiens'"
we mean to search for 'H2A AND homo sapiens' saving only the transcripts and using the default as
base for the filename. However, the search terms will be interpreted as the base for the filenames
(but since it's not a valid identifier, it will return an error). To prevent this, you can either
specify the values:
"bp_genbank_ref_extractor --transcripts 'accession' 'H2A AND homo sapiens'"
"bp_genbank_ref_extractor --transcripts='accession' 'H2A AND homo sapiens'"
or you can use the double hash to stop processing options. Note that this should only be used after
the last option. All arguments supplied after the double dash will be interpreted as search terms
"bp_genbank_ref_extractor --transcripts -- 'H2A AND homo sapiens'"
NOTES ON USAGE
• Genes that are marked as 'live' and 'protein-coding' should have at least one transcript. However,
This is not always true due to mistakes on annotation. Such cases will throw a warning. When faced
with this, be nice and write to the entrez RefSeq maintainers
<http://www.ncbi.nlm.nih.gov/RefSeq/update.cgi>.
• When creating the directories to save the files, if the directory already exists it will be used and
no error or warning will be issued unless --debug as been set. If a non-directory file already exists
with that name bp_genbank_ref_extractor exits with an error.
• On the subject of verbosity, all messages are saved on the log file. The options --verbose and
--very-verbose only affect their printing to standard output. Debug messages are different as they
will only show up (and be logged) if requested with --debug.
• When saving a file, to avoid problems with limited filesystems such as NTFS or FAT, only some
characters are allowed. All other characters will be replaced by an underscore. Allowed characters
are:
a-z 0-9 - + . , () {} []'
• bp_genbank_ref_extractor tries to use the same file extensions that bioperl would expect when saving
the file. If unable it will use the '.seq' extension.
FEEDBACK
Mailing lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments
and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list: bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look
at the problem and quickly address it. Please include a thorough description of the problem with code and
data examples if at all possible.
Reporting bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution.
Bug reports can be submitted via the web:
https://github.com/bioperl/%%7Bdist%7D
AUTHOR
Carnë Draug <carandraug+dev@gmail.com>
COPYRIGHT
This software is copyright (c) 2011-2015 by Carnë Draug.
This software is available under the GNU General Public License, Version 3, June 2007.
perl v5.24.1 2017-04-07 BP_GENBANK_REF_EXTRACTOR(1p)