Provided by: libbio-eutilities-perl_1.76-1_all bug

NAME

       bp_genbank_ref_extractor - Retrieves all related sequences for a list of searches on
       Entrez gene

VERSION

       version 1.76

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.

       B <--api_key> NCBI requires an API key for requests over 10/sec as of December 2018. You
       may generate one in the "My NCBI" area
       --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 although 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 only.  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'

       Save both transcript and protein sequences in the fasta format, for two queries, '"homo
       sapiens"[organism] AND H2B' and '"homo sapiens"[organism] AND MCPH1'.

        bp_genbank_ref_extractor \
          --genes --down=500 --up=100 \
          '"homo sapiens"[organism] AND H2B'

       Download genomic sequences, including 500 bp downstream and 100 bp upstream of each gene.

        bp_genbank_ref_extractor \
          --genes --asembly='Alternate HuRef' \
          '"homo sapiens"[organism] AND H2B'

       Download genomic sequences from the Alternate HuRef genome assembly.

        bp_genbank_ref_extractor --save-data=CSV \
          '"homo sapiens"[organism] AND H2B'

       Do not save any sequence, only save the results in a CSV file.

        bp_genbank_ref_extractor --save='search-results' \
          --genes=name  downstream=500 --upstream=200 \
          --nopseudo --nonnon-coding --transcripts --proteins \
          --format=fasta --save-data=CSV \
          '"homo sapiens"[organism] AND H2B' \
          '"homo sapiens"[organism] AND MCPH1'

       Ignoring non-coding and pseudo genes, downloads: genomic sequences with 500 and 200 bp
       downstream and upstream respectively, using the gene name as filename; transcript and
       proteins sequences using their accession number as filename; everything in fasta format
       plus a CSV file with search results; saved in a directory named search-results

NON-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'

           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
         https://bioperl.org/Support.html    - 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/bio-eutilities/issues

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.