.\" Automatically generated by Pod::Man 4.11 (Pod::Simple 3.35) .\" .\" Standard preamble: .\" ======================================================================== .de Sp \" Vertical space (when we can't use .PP) .if t .sp .5v .if n .sp .. .de Vb \" Begin verbatim text .ft CW .nf .ne \\$1 .. .de Ve \" End verbatim text .ft R .fi .. .\" Set up some character translations and predefined strings. \*(-- will .\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left .\" double quote, and \*(R" will give a right double quote. \*(C+ will .\" give a nicer C++. Capital omega is used to do unbreakable dashes and .\" therefore won't be available. \*(C` and \*(C' expand to `' in nroff, .\" nothing in troff, for use with C<>. .tr \(*W- .ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p' .ie n \{\ . ds -- \(*W- . ds PI pi . if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch . if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\" diablo 12 pitch . ds L" "" . ds R" "" . ds C` "" . ds C' "" 'br\} .el\{\ . ds -- \|\(em\| . ds PI \(*p . ds L" `` . ds R" '' . ds C` . ds C' 'br\} .\" .\" Escape single quotes in literal strings from groff's Unicode transform. .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" .\" If the F register is >0, we'll generate index entries on stderr for .\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index .\" entries marked with X<> in POD. Of course, you'll have to process the .\" output yourself in some meaningful fashion. .\" .\" Avoid warning from groff about undefined register 'F'. .de IX .. .nr rF 0 .if \n(.g .if rF .nr rF 1 .if (\n(rF:(\n(.g==0)) \{\ . if \nF \{\ . de IX . tm Index:\\$1\t\\n%\t"\\$2" .. . if !\nF==2 \{\ . nr % 0 . nr F 2 . \} . \} .\} .rr rF .\" ======================================================================== .\" .IX Title "BP_FAST_LOAD_GFF 1p" .TH BP_FAST_LOAD_GFF 1p "2020-01-13" "perl v5.30.0" "User Contributed Perl Documentation" .\" For nroff, turn off justification. Always turn off hyphenation; it makes .\" way too many mistakes in technical documents. .if n .ad l .nh .SH "NAME" bp_fast_load_gff.pl \- Fast\-load a Bio::DB::GFF database from GFF files. .SH "SYNOPSIS" .IX Header "SYNOPSIS" .Vb 1 \& % bp_fast_load_gff.pl \-d testdb dna1.fa dna2.fa features1.gff features2.gff ... .Ve .SH "DESCRIPTION" .IX Header "DESCRIPTION" This script loads a Bio::DB::GFF database with the features contained in a list of \s-1GFF\s0 files and/or \s-1FASTA\s0 sequence files. You must use the exact variant of \s-1GFF\s0 described in Bio::DB::GFF. Various command-line options allow you to control which database to load and whether to allow an existing database to be overwritten. .PP This script is similar to load_gff.pl, but is much faster. However, it is hard-coded to use MySQL and probably only works on Unix platforms due to its reliance on pipes. See bp_load_gff.pl for an incremental loader that works with all databases supported by Bio::DB::GFF, and bp_bulk_load_gff.pl for a fast MySQL loader that supports all platforms. .SS "\s-1NOTES\s0" .IX Subsection "NOTES" If the filename is given as \*(L"\-\*(R" then the input is taken from standard input. Compressed files (.gz, .Z, .bz2) are automatically uncompressed. .PP \&\s-1FASTA\s0 format files are distinguished from \s-1GFF\s0 files by their filename extensions. Files ending in .fa, .fasta, .fast, .seq, .dna and their uppercase variants are treated as \s-1FASTA\s0 files. Everything else is treated as a \s-1GFF\s0 file. If you wish to load \-fasta files from \s-1STDIN,\s0 then use the \-f command-line swith with an argument of '\-', as in .PP .Vb 1 \& gunzip my_data.fa.gz | bp_fast_load_gff.pl \-d test \-f \- .Ve .PP The nature of the load requires that the database be on the local machine and that the indicated user have the \*(L"file\*(R" privilege to load the tables and have enough room in /usr/tmp (or whatever is specified by the \e$TMPDIR environment variable), to hold the tables transiently. If your MySQL is version 3.22.6 and was compiled using the \*(L"load local file\*(R" option, then you may be able to load remote databases with local data using the \-\-local option. .PP About maxfeature: the default value is 100,000,000 bases. If you have features that are close to or greater that 100Mb in length, then the value of maxfeature should be increased to 1,000,000,000. This value must be a power of 10. .PP If the list of \s-1GFF\s0 or fasta files exceeds the kernel limit for the maximum number of command-line arguments, use the \&\-\-long_list /path/to/files option. .PP The adaptor used is dbi::mysqlopt. There is currently no way to change this. .SH "COMMAND-LINE OPTIONS" .IX Header "COMMAND-LINE OPTIONS" Command-line options can be abbreviated to single-letter options. e.g. \-d instead of \-\-database. .PP .Vb 10 \& \-\-database Mysql database name \& \-\-create Reinitialize/create data tables without asking \& \-\-local Try to load a remote database using local data. \& \-\-user Username to log in as \& \-\-fasta File or directory containing fasta files to load \& \-\-password Password to use for authentication \& \-\-long_list Directory containing a very large number of \& GFF and/or FASTA files \& \-\-maxfeature Set the value of the maximum feature size (default 100Mb; must be a power of 10) \& \-\-group A list of one or more tag names (comma or space separated) \& to be used for grouping in the 9th column. \& \-\-gff3_munge Activate GFF3 name munging (see Bio::DB::GFF) \& \-\-summary Generate summary statistics for drawing coverage histograms. \& This can be run on a previously loaded database or during \& the load. \& \-\-Temporary Location of a writable scratch directory .Ve .SH "SEE ALSO" .IX Header "SEE ALSO" Bio::DB::GFF, bulk_load_gff.pl, load_gff.pl .SH "AUTHOR" .IX Header "AUTHOR" Lincoln Stein, lstein@cshl.org .PP Copyright (c) 2002 Cold Spring Harbor Laboratory .PP This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See \s-1DISCLAIMER\s0.txt for disclaimers of warranty.