From f1d7e47a41a08c14b186d56ecce0c6cf734ecf71 Mon Sep 17 00:00:00 2001 From: Timothy Parnell Date: Thu, 22 Aug 2024 14:28:19 -0600 Subject: [PATCH] update docs add navigation bar, fix application headers, a few text changes --- docs/AdvancedInstallation.md | 36 +++++++++++++++--------- docs/Applications.md | 6 +++- docs/Examples.md | 6 +++- docs/FAQ.md | 6 +++- docs/Libraries.md | 6 +++- docs/MacOSNotes.md | 9 ++++-- docs/apps/bam2wig.md | 38 ++++++++++++++------------ docs/apps/correlate_position_data.md | 22 ++++++++------- docs/apps/data2bed.md | 22 ++++++++------- docs/apps/data2fasta.md | 26 ++++++++++-------- docs/apps/data2gff.md | 20 ++++++++------ docs/apps/data2wig.md | 26 ++++++++++-------- docs/apps/db_setup.md | 14 ++++++---- docs/apps/db_types.md | 14 ++++++---- docs/apps/get_binned_data.md | 28 ++++++++++--------- docs/apps/get_datasets.md | 28 ++++++++++--------- docs/apps/get_feature_info.md | 20 ++++++++------ docs/apps/get_features.md | 28 ++++++++++--------- docs/apps/get_gene_regions.md | 22 ++++++++------- docs/apps/get_intersecting_features.md | 22 ++++++++------- docs/apps/get_relative_data.md | 28 ++++++++++--------- docs/apps/join_data_file.md | 14 ++++++---- docs/apps/manipulate_datasets.md | 24 ++++++++-------- docs/apps/manipulate_wig.md | 24 ++++++++-------- docs/apps/merge_datasets.md | 18 ++++++------ docs/apps/pull_features.md | 22 ++++++++------- docs/apps/split_data_file.md | 20 ++++++++------ docs/apps/ucsc_table2gff3.md | 22 ++++++++------- 28 files changed, 323 insertions(+), 248 deletions(-) diff --git a/docs/AdvancedInstallation.md b/docs/AdvancedInstallation.md index e3b408d..255d9ee 100644 --- a/docs/AdvancedInstallation.md +++ b/docs/AdvancedInstallation.md @@ -1,4 +1,8 @@ -# ADVANCED INSTALLATION +# Bio::ToolBox + +|[Home](ReadMe.md)|[Install](AdvancedInstallation.md)|[Libraries](Libraries.md)|[Applications](Applications.md)|[Examples](Examples.md)|[FAQ](FAQ.md)| + +## Advanced Installation This is an advanced installation guide for getting a complete installation. @@ -20,9 +24,9 @@ accordingly for their system. If that doesn't describe you, skip ahead to the is officially recommended. It defaults to installing in `/usr/local` but doesn't have to be; see below. - curl -o htslib-1.9.tar.bz2 -L https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2 - tar -xf htslib-1.9.tar.bz2 - cd htslib-1.9 + curl -o htslib-1.19.tar.bz2 -L https://github.com/samtools/htslib/releases/download/1.19/htslib-1.19.tar.bz2 + tar -xf htslib-1.19.tar.bz2 + cd htslib-1.19 make && make install cd .. @@ -141,14 +145,18 @@ installed. - [HTSlib](https://github.com/samtools/htslib) - Follow the directions within for installation. - [Version 1.9](https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2) - is officially recommended by its authors; however, later versions appear to - work too and may be preferred. Versions of `htslib` up to 1.20 have been used - by this author. By default, it installs into `/usr/local`, or - it may be set to another directory (`$HOME` for example) by adding - `--prefix=$HOME` option to the `configure` step. This may also be available - via OS or other package managers. + Follow the directions within for installation. Version 1.9 is officially + recommended by the `Bio::DB::HTS` authors; however, later versions appear to work + just fine and should probably be preferred. + [Version 1.19](https://github.com/samtools/htslib/releases/download/1.19/htslib-1.19.tar.bz2) + have been used successfully by this author. By default, it installs into + `/usr/local`, or it may be set to another directory (`$HOME` for example) by + adding `--prefix=$HOME` option to the `configure` step. This may also be + available via OS or other package managers. + + Note that the `htslib` package is also included with the `samtools` and `bcftools` + packages and is compiled therein, but is not installed by default (although it + could be). - [libBigWig](https://github.com/dpryan79/libBigWig) @@ -158,7 +166,9 @@ installed. Note that the Perl module [Alien::LibBigWig](https://metacpan.org/pod/Alien::LibBigWig) is available - to install this library dependency for you automatically for Bio::DB::Big. + to install this library dependency for you automatically for `Bio::DB::Big`. + although by default it installs an older version and brings along a lot of + extra `Alien` Perl modules, if that concerns you. ## Perl modules diff --git a/docs/Applications.md b/docs/Applications.md index 14e9e23..51c57df 100644 --- a/docs/Applications.md +++ b/docs/Applications.md @@ -1,4 +1,8 @@ -# Included Applications +# Bio::ToolBox + +|[Home](ReadMe.md)|[Install](AdvancedInstallation.md)|[Libraries](Libraries.md)|[Applications](Applications.md)|[Examples](Examples.md)|[FAQ](FAQ.md)| + +## Included Applications There are 22 production-quality script applications included in the package. These are listed below, grouped by general function. Also see the diff --git a/docs/Examples.md b/docs/Examples.md index 5e83199..0c86861 100644 --- a/docs/Examples.md +++ b/docs/Examples.md @@ -1,4 +1,8 @@ -# Application Examples +# Bio::ToolBox + +|[Home](ReadMe.md)|[Install](AdvancedInstallation.md)|[Libraries](Libraries.md)|[Applications](Applications.md)|[Examples](Examples.md)|[FAQ](FAQ.md)| + +## Application Examples The BioToolBox package comes complete with a suite of high-quality, production-ready applications (Perl scripts) ready for a variety of analyses. A sampling of what diff --git a/docs/FAQ.md b/docs/FAQ.md index 7c503fe..7472ba7 100644 --- a/docs/FAQ.md +++ b/docs/FAQ.md @@ -1,4 +1,8 @@ -# Frequently Asked Questions +# Bio::ToolBox + +|[Home](ReadMe.md)|[Install](AdvancedInstallation.md)|[Libraries](Libraries.md)|[Applications](Applications.md)|[Examples](Examples.md)|[FAQ](FAQ.md)| + +## Frequently Asked Questions These may or may not have actually been asked, but it's a collection of hints that the programmer understands but a casual user might not, as well as rationale. diff --git a/docs/Libraries.md b/docs/Libraries.md index 9c8b239..000ecd1 100644 --- a/docs/Libraries.md +++ b/docs/Libraries.md @@ -1,4 +1,8 @@ -# LIBRARIES +# Bio::ToolBox + +|[Home](ReadMe.md)|[Install](AdvancedInstallation.md)|[Libraries](Libraries.md)|[Applications](Applications.md)|[Examples](Examples.md)|[FAQ](FAQ.md)| + +## Libraries Several library modules are included in this distribution. The following is a brief description of the primary user-oriented libraries that are available. Links will diff --git a/docs/MacOSNotes.md b/docs/MacOSNotes.md index 4480703..a2c9c78 100644 --- a/docs/MacOSNotes.md +++ b/docs/MacOSNotes.md @@ -1,4 +1,8 @@ -# MacOS Notes +# Bio::ToolBox + +|[Home](ReadMe.md)|[Install](AdvancedInstallation.md)|[Libraries](Libraries.md)|[Applications](Applications.md)|[Examples](Examples.md)|[FAQ](FAQ.md)| + +## MacOS Notes While Macs have a Unix-compatible command-line environment (Darwin), there are a few issues and solutions that I have encountered that may be useful to someone. Some of @@ -97,7 +101,8 @@ dependencies, it attempts to compile a small test program and runs the command `mktemp --suffix=.c`. While that `--suffix` option is available to versions on Linux platforms, it is not available to the version on macOS, thus breaking the detection of libCurl. To work around this, we just have to tell it that, yes, we have libCurl. -Comment out the five lines after `# Create a simple test-program...` and add a new line +Edit the `Makefile` and comment out the five lines after +`# Create a simple test-program...` and add a new line HAVE_CURL=YES diff --git a/docs/apps/bam2wig.md b/docs/apps/bam2wig.md index 17b14bd..7ae5fb5 100644 --- a/docs/apps/bam2wig.md +++ b/docs/apps/bam2wig.md @@ -1,10 +1,12 @@ -# NAME +# Bio::ToolBox -bam2wig.pl +|[Home](ReadMe.md)|[Install](AdvancedInstallation.md)|[Libraries](Libraries.md)|[Applications](Applications.md)|[Examples](Examples.md)|[FAQ](FAQ.md)| + +## bam2wig.pl A program to convert Bam alignments into a wig representation file. -# SYNOPSIS +## SYNOPSIS bam2wig.pl \[--options...\] <file.bam> @@ -85,11 +87,11 @@ bam2wig.pl --extend --rpm --mean --out file --bw file1.bam file2.bam -v --version print version information -h --help show full documentation -# OPTIONS +## OPTIONS The command line flags and descriptions: -## Input +### Input - --in <filename> @@ -98,7 +100,7 @@ The command line flags and descriptions: or simply appended to the command. Bam files will be automatically indexed if necessary. -## Reporting Options +### Reporting Options - --start @@ -152,7 +154,7 @@ The command line flags and descriptions: Legacy option for supporting previous versions of bam2wig. -## Alignment reporting options +### Alignment reporting options - --splice @@ -175,7 +177,7 @@ The command line flags and descriptions: Do this when RNA-Seq alignments map to the opposite strand of the coding sequence, depending on the library preparation method. -## Paired-end alignments +### Paired-end alignments - --pe @@ -215,7 +217,7 @@ The command line flags and descriptions: a single-end alignment. No test of insert size or proper pair status is made. -## Alignment filtering options: +### Alignment filtering options: - --qual <integer> @@ -269,7 +271,7 @@ The command line flags and descriptions: when splitting on splices. If an N operation in the CIGAR string exceeds this limit, the alignment is skipped. Default is 0 (no filtering). -## Shift options +### Shift options - --shift @@ -331,7 +333,7 @@ The command line flags and descriptions: using the output base name. The default is to not write the model shift data. -## Score Options +### Score Options - --rpm @@ -389,7 +391,7 @@ The command line flags and descriptions: apply the specific normalization factor. For example, 'chrX$' to specify the X chromosome only. -## Wig format +### Wig format - --bin <integer> @@ -418,7 +420,7 @@ The command line flags and descriptions: When writing bedGraph format, skip (do not write) intervals with a value of zero. Does not apply to fixedStep or variableStep formats. -## Output Options +### Output Options - --out <filename> @@ -443,7 +445,7 @@ The command line flags and descriptions: Specify whether (or not) the output text file should be compressed with gzip. Disable with `--nogz`. Does not apply to bigWig format. -## General options +### General options - --cpu <integer> @@ -470,7 +472,7 @@ The command line flags and descriptions: Display this POD documentation. -# DESCRIPTION +## DESCRIPTION This program will enumerate aligned sequence tags and generate a wig, or optionally BigWig, file. Alignments may be counted and recorded @@ -502,7 +504,7 @@ bedGraph format. The wig file may be further converted into a compressed, indexed, binary bigWig format, dependent on the availability of the appropriate conversion utilities. -# RECOMMENDED SETTINGS +## RECOMMENDED SETTINGS The type of wig file to generate for your Bam sequencing file can vary depending on your particular experimental application. Here are a few @@ -605,7 +607,7 @@ the wig or bigWig file. bam2wig --smartcov --strand --rpm --in -# TEXT REPRESENTATION OF RECORDING ALIGNMENTS +## TEXT REPRESENTATION OF RECORDING ALIGNMENTS To help users visualize how this program records alignments in a wig file, drawn below are 10 alignments, five forward and five reverse. @@ -672,7 +674,7 @@ are drawn for visualization purposes only. Values of X represent 10. ....12224455555555555555555555555555555555555555555443333332211111 -# AUTHOR +## AUTHOR Timothy J. Parnell, PhD Huntsman Cancer Institute diff --git a/docs/apps/correlate_position_data.md b/docs/apps/correlate_position_data.md index bcd9fef..3ac33ba 100644 --- a/docs/apps/correlate_position_data.md +++ b/docs/apps/correlate_position_data.md @@ -1,10 +1,12 @@ -# NAME +# Bio::ToolBox -correlate\_position\_data.pl +|[Home](ReadMe.md)|[Install](AdvancedInstallation.md)|[Libraries](Libraries.md)|[Applications](Applications.md)|[Examples](Examples.md)|[FAQ](FAQ.md)| + +## correlate\_position\_data.pl A script to calculate correlations between two datasets along the length of a feature. -# SYNOPSIS +## SYNOPSIS correlate\_position\_data.pl \[--options\] <filename> @@ -32,11 +34,11 @@ correlate\_position\_data.pl \[--options\] <filename> -v --version print version and exit -h --help show extended documentation -# OPTIONS +## OPTIONS The command line flags and descriptions: -## Options for data files +### Options for data files - --in <filename> @@ -59,7 +61,7 @@ The command line flags and descriptions: file), or when using an existing input file with the database indicated in the metadata. -## Options for data sources +### Options for data sources - --ddb <name | filename> @@ -76,7 +78,7 @@ The command line flags and descriptions: they may be a BigWig or even Bam file. Both options are required. If not provided, they may be interactively chosen from the database. -## Options for correlating data +### Options for correlating data - --pval @@ -130,7 +132,7 @@ The command line flags and descriptions: data column in the input file with strand information. The default is no enforcement of strand. -## General options +### General options - --gz @@ -144,7 +146,7 @@ The command line flags and descriptions: Display this POD documentation. -# DESCRIPTION +## DESCRIPTION This program will calculate statistics between the positioned scores of two different datasets over a window from an annotated feature or @@ -184,7 +186,7 @@ test data look like the reference data? The window is shifted from -2 radius to +2 radius relative to the reference point, and the highest correlation is reported along with the shift value that generated it. -# AUTHOR +## AUTHOR Timothy J. Parnell, PhD Dept of Oncological Sciences diff --git a/docs/apps/data2bed.md b/docs/apps/data2bed.md index 74c1227..7610568 100644 --- a/docs/apps/data2bed.md +++ b/docs/apps/data2bed.md @@ -1,10 +1,12 @@ -# NAME +# Bio::ToolBox -data2bed.pl +|[Home](ReadMe.md)|[Install](AdvancedInstallation.md)|[Libraries](Libraries.md)|[Applications](Applications.md)|[Examples](Examples.md)|[FAQ](FAQ.md)| + +## data2bed.pl A program to convert a data file to a bed file. -# SYNOPSIS +## SYNOPSIS data2bed.pl \[--options...\] <filename> @@ -37,11 +39,11 @@ data2bed.pl \[--options...\] <filename> -v --version print version and exit -h --help show extended documentation -# OPTIONS +## OPTIONS The command line flags and descriptions: -## File Options +### File Options - --in <filename> @@ -70,7 +72,7 @@ The command line flags and descriptions: BioPerl (and, by extension, all biotoolbox) scripts are base (1-based) coordinates. Default behavior is to convert. -## Column indices +### Column indices - --bed \[3|4|5|6\] @@ -122,7 +124,7 @@ The command line flags and descriptions: for strand information. Accepted values might include any of the following: +, -, 1, -1, 0, . -## BigBed options +### BigBed options - --bigbed - --bb @@ -153,7 +155,7 @@ The command line flags and descriptions: search the default environment path for the utility. If found, it will automatically execute the utility to convert the bed file. -## General options +### General options - --sort @@ -177,7 +179,7 @@ The command line flags and descriptions: Display this POD documentation. -# DESCRIPTION +## DESCRIPTION This program will convert a tab-delimited data file into a BED file, according to the specifications here @@ -207,7 +209,7 @@ An option exists to further convert the BED file to an indexed, binary BigBed format. Jim Kent's bedToBigBed conversion utility must be available, and either a chromosome definition file or access to a Bio::DB database is required. -# AUTHOR +## AUTHOR Timothy J. Parnell, PhD Howard Hughes Medical Institute diff --git a/docs/apps/data2fasta.md b/docs/apps/data2fasta.md index 204f8fb..4ee8d9c 100644 --- a/docs/apps/data2fasta.md +++ b/docs/apps/data2fasta.md @@ -1,10 +1,12 @@ -# NAME +# Bio::ToolBox -data2fasta.pl +|[Home](ReadMe.md)|[Install](AdvancedInstallation.md)|[Libraries](Libraries.md)|[Applications](Applications.md)|[Examples](Examples.md)|[FAQ](FAQ.md)| + +## data2fasta.pl A program to retrieve sequences from a list of features -# SYNOPSIS +## SYNOPSIS data2fasta.pl \[--options...\] <filename> @@ -39,11 +41,11 @@ data2fasta.pl \[--options...\] <filename> -v --version print version and exit -h --help show extended documentation -# OPTIONS +## OPTIONS The command line flags and descriptions: -## File options +### File options - --in <filename> @@ -61,7 +63,7 @@ The command line flags and descriptions: Specify the output filename. By default it uses the input file basename. -## Database +### Database - --db <name|fasta> @@ -77,7 +79,7 @@ The command line flags and descriptions: The database name may be obtained from the input file metadata. Required only if collecting sequence from genomic coordinates. -## Feature selection +### Feature selection - --feature <text> @@ -90,7 +92,7 @@ The command line flags and descriptions: list available. No merging of overlapping or redundant subfeatures is performed here. See [get\_features.pl](https://metacpan.org/pod/get_features.pl). -## Column indices +### Column indices - --name --id <column\_index> @@ -136,7 +138,7 @@ The command line flags and descriptions: Optionally specify the index of the description column. It may be automatically determined from the column header. -## Fasta output options +### Fasta output options - --cat @@ -150,7 +152,7 @@ The command line flags and descriptions: indicate the number of 'N' bases to insert between the individual sequences. The default is zero. -## General options +### General options - --gz @@ -164,7 +166,7 @@ The command line flags and descriptions: Display this POD documentation. -# DESCRIPTION +## DESCRIPTION This program will take a tab-delimited text file (BED file, for example) and generate either a multi-sequence fasta file containing the @@ -184,7 +186,7 @@ databases such as [Bio::DB::SeqFeature::Store](https://metacpan.org/pod/Bio%3A%3 If strand information is provided, then the sequence reverse complement is returned for reverse strand coordinates. -# AUTHOR +## AUTHOR Timothy J. Parnell, PhD Dept of Oncological Sciences diff --git a/docs/apps/data2gff.md b/docs/apps/data2gff.md index df36e34..2f4302c 100644 --- a/docs/apps/data2gff.md +++ b/docs/apps/data2gff.md @@ -1,10 +1,12 @@ -# NAME +# Bio::ToolBox -data2gff.pl +|[Home](ReadMe.md)|[Install](AdvancedInstallation.md)|[Libraries](Libraries.md)|[Applications](Applications.md)|[Examples](Examples.md)|[FAQ](FAQ.md)| + +## data2gff.pl A program to convert a generic data file to GFF format. -# SYNOPSIS +## SYNOPSIS data2gff.pl \[--options...\] <filename> @@ -35,11 +37,11 @@ data2gff.pl \[--options...\] <filename> -v --version print version and exit -h --help show extended documentation -# OPTIONS +## OPTIONS The command line flags and descriptions: -## File options +### File options - --in <filename> @@ -65,7 +67,7 @@ The command line flags and descriptions: Input file is in interbase or 0-based coordinates. This should be automatically detected for most known file formats, e.g. BED. -## Column indices +### Column indices - --ask @@ -137,7 +139,7 @@ The command line flags and descriptions: the 'score' or 'name' column, if defined. As a last resort, it will use the most creative method of 'Experiment'. -## General options +### General options - --unique @@ -168,14 +170,14 @@ The command line flags and descriptions: Display the POD documentation -# DESCRIPTION +## DESCRIPTION This program will convert a data file into a GFF version 3 formatted text file. Only simple conversions are performed, where each data line is converted to a single feature. Complex features with parent-child relationships (such as genes) should be converted with something more advanced. -# AUTHOR +## AUTHOR Timothy J. Parnell, PhD Howard Hughes Medical Institute diff --git a/docs/apps/data2wig.md b/docs/apps/data2wig.md index 31e4eef..7a1b822 100644 --- a/docs/apps/data2wig.md +++ b/docs/apps/data2wig.md @@ -1,10 +1,12 @@ -# NAME +# Bio::ToolBox -data2wig.pl +|[Home](ReadMe.md)|[Install](AdvancedInstallation.md)|[Libraries](Libraries.md)|[Applications](Applications.md)|[Examples](Examples.md)|[FAQ](FAQ.md)| + +## data2wig.pl A program to convert a generic data file into a wig file. -# SYNOPSIS +## SYNOPSIS data2wig.pl \[--options...\] <filename> @@ -47,11 +49,11 @@ data2wig.pl \[--options...\] <filename> -v --version print version and exit -h --help show extended documentation -# OPTIONS +## OPTIONS The command line flags and descriptions: -## File options +### File options - --in <filename> @@ -80,7 +82,7 @@ The command line flags and descriptions: definition 1-based. This is automatically handled for most input files. Default is false. -## Column indices +### Column indices - --ask @@ -126,7 +128,7 @@ The command line flags and descriptions: from which to take the value (usually 10 or higher) using the --index option. INFO field attributes can also be taken, if desired (use --index 8). -## Wig options +### Wig options - --step \[fixed | variable | bed\] @@ -167,7 +169,7 @@ The command line flags and descriptions: the oligo probes are the same length and you wish to assign the value across the oligo rather than the midpoint. The default is inherently 1 bp. -## Conversion options +### Conversion options - --fast @@ -207,7 +209,7 @@ The command line flags and descriptions: position. Wig files do not tolerate multiple identical positions. Default is mean. -## BigWig options +### BigWig options - --bigwig - --bw @@ -236,7 +238,7 @@ The command line flags and descriptions: environment path for the utility. If found, it will automatically execute the utility to convert the wig file. -## General options +### General options - --gz @@ -251,7 +253,7 @@ The command line flags and descriptions: Display the POD documentation -# DESCRIPTION +## DESCRIPTION This program will convert any tab-delimited data text file into a wiggle formatted text file. This requires that the file contains not only the @@ -285,7 +287,7 @@ http://genome.ucsc.edu/goldenPath/help/bigWig.html. Conversion requires BigWig file support, supplied by the external `wigToBigWig` or `bedGraphToBigWig` utility available from UCSC. -# AUTHOR +## AUTHOR Timothy J. Parnell, PhD Howard Hughes Medical Institute diff --git a/docs/apps/db_setup.md b/docs/apps/db_setup.md index 7e99df2..4335f98 100644 --- a/docs/apps/db_setup.md +++ b/docs/apps/db_setup.md @@ -1,10 +1,12 @@ -# NAME +# Bio::ToolBox -db\_setup.pl +|[Home](ReadMe.md)|[Install](AdvancedInstallation.md)|[Libraries](Libraries.md)|[Applications](Applications.md)|[Examples](Examples.md)|[FAQ](FAQ.md)| + +## db\_setup.pl A program to setup a SeqFeature::Store SQLite database from UCSC data -# SYNOPSIS +## SYNOPSIS db\_setup.pl \[--options...\] @@ -17,7 +19,7 @@ db\_setup.pl \[--options...\] -v --version -h --help -# OPTIONS +## OPTIONS The command line flags and descriptions: @@ -56,7 +58,7 @@ The command line flags and descriptions: Display this POD documentation. -# DESCRIPTION +## DESCRIPTION This program will simplify the task of generating an annotation database. You provide the short name of the UCSC database for the species and genome version @@ -64,7 +66,7 @@ you are interested in, and the script will automatically download gene annotatio and build a _Bio::DB::SeqFeature::Store_ database for use with BioToolBox scripts. -# AUTHOR +## AUTHOR Timothy J. Parnell, PhD Huntsman Cancer Institute diff --git a/docs/apps/db_types.md b/docs/apps/db_types.md index bde2de0..bc7fca0 100644 --- a/docs/apps/db_types.md +++ b/docs/apps/db_types.md @@ -1,10 +1,12 @@ -# NAME +# Bio::ToolBox -db\_types.pl +|[Home](ReadMe.md)|[Install](AdvancedInstallation.md)|[Libraries](Libraries.md)|[Applications](Applications.md)|[Examples](Examples.md)|[FAQ](FAQ.md)| + +## db\_types.pl A program to print out the available feature types in a database. -# SYNOPSIS +## SYNOPSIS db\_types.pl <database> @@ -14,7 +16,7 @@ db\_types.pl <database> --help -# OPTIONS +## OPTIONS The command line flags and descriptions: @@ -33,7 +35,7 @@ The command line flags and descriptions: Display this POD documentation. -# DESCRIPTION +## DESCRIPTION This program will print a list of all of the known feature types present in a [Bio::DB::SeqFeature::Store](https://metacpan.org/pod/Bio%3A%3ADB%3A%3ASeqFeature%3A%3AStore) database. The types are organized into @@ -42,7 +44,7 @@ groups by their source tag. BigWigSet databases, comprised of a directory of BigWig files and a metadata file, are also supported. -# AUTHOR +## AUTHOR Timothy J. Parnell, PhD Howard Hughes Medical Institute diff --git a/docs/apps/get_binned_data.md b/docs/apps/get_binned_data.md index 543adc1..80bdddb 100644 --- a/docs/apps/get_binned_data.md +++ b/docs/apps/get_binned_data.md @@ -1,10 +1,12 @@ -# NAME +# Bio::ToolBox -get\_binned\_data.pl +|[Home](ReadMe.md)|[Install](AdvancedInstallation.md)|[Libraries](Libraries.md)|[Applications](Applications.md)|[Examples](Examples.md)|[FAQ](FAQ.md)| + +## get\_binned\_data.pl A program to collect data in bins across a list of features. -# SYNOPSIS +## SYNOPSIS get_binned_data.pl [--options] --in --out @@ -48,11 +50,11 @@ A program to collect data in bins across a list of features. -v --version print version and exit -h --help show extended documentation -# OPTIONS +## OPTIONS The command line flags and descriptions: -## Options for data files +### Options for data files - --in <filename> @@ -69,7 +71,7 @@ The command line flags and descriptions: Specify the output file name. Default is to overwrite the input text file. Required if generating a new file from a database. -## Options for new files +### Options for new files - --db <name> @@ -84,7 +86,7 @@ The command line flags and descriptions: feature type, feature type and source expressed as 'type:source'. More than one feature may be included as a comma-delimited list (no spaces). -## Options for data collection +### Options for data collection - --ddb <name | filename> @@ -172,7 +174,7 @@ The command line flags and descriptions: Default is not to format, often leading to more than the intended significant digits. -## Bin specification +### Bin specification - --bins <integer> @@ -199,7 +201,7 @@ The command line flags and descriptions: null values). This is to avoid having bin sizes below the average microarray tiling distance. The default is undefined (no limit). -## Post-processing +### Post-processing - --sum @@ -213,7 +215,7 @@ The command line flags and descriptions: Indicate that windows without values should (not) be interpolated from neighboring values. The default is false. -## General options +### General options - --groups @@ -246,7 +248,7 @@ The command line flags and descriptions: This help text. -# DESCRIPTION +## DESCRIPTION This program will collect data across a gene or feature body into numerous percentile bins. It is used to determine if there is a spatial @@ -255,7 +257,7 @@ of bins may be specified as a command argument (default 10). Additionally, extra bins may be extended on either side of the gene (default 0 on either side). The bin size is determined as a percentage of gene length. -# EXAMPLES +## EXAMPLES These are some examples of some common scenarios for collecting data. @@ -283,7 +285,7 @@ These are some examples of some common scenarios for collecting data. --method count --data alignments.bam --out gene_profile --sum -# AUTHOR +## AUTHOR Timothy J. Parnell, PhD Howard Hughes Medical Institute diff --git a/docs/apps/get_datasets.md b/docs/apps/get_datasets.md index 764abd2..46b9c4d 100644 --- a/docs/apps/get_datasets.md +++ b/docs/apps/get_datasets.md @@ -1,10 +1,12 @@ -# NAME +# Bio::ToolBox -get\_datasets.pl +|[Home](ReadMe.md)|[Install](AdvancedInstallation.md)|[Libraries](Libraries.md)|[Applications](Applications.md)|[Examples](Examples.md)|[FAQ](FAQ.md)| + +## get\_datasets.pl A program to collect data for a list of features -# SYNOPSIS +## SYNOPSIS get\_datasets.pl \[--options...\] <filename> @@ -56,11 +58,11 @@ get\_datasets.pl \[--options...\] --in <filename> <data1> <data2...> -v --version print version and exit -h --help show extended documentation -# OPTIONS +## OPTIONS The command line flags and descriptions: -## Options for data files +### Options for data files - --in <filename> @@ -78,7 +80,7 @@ The command line flags and descriptions: current files. If this is argument is not specified then the input file is overwritten. -## Options for new files +### Options for new files - --db <name | filename> @@ -97,7 +99,7 @@ The command line flags and descriptions: alias to one or more feature types. More than one feature may be included as a comma-delimited list (no spaces). -## Options for feature "genome" +### Options for feature "genome" - --feature genome @@ -136,7 +138,7 @@ The command line flags and descriptions: Provide a text string to prefix the name of generated genomic windows. Names will be appended with an incrementing, unformatted digit. -## Options for data collection +### Options for data collection - --ddb <name> @@ -282,7 +284,7 @@ The command line flags and descriptions: that were newly collected. For more advanced filtering, see [manipulate\_datasets.pl](https://metacpan.org/pod/manipulate_datasets.pl). -## Adjustments to features +### Adjustments to features - --extend <integer> @@ -328,7 +330,7 @@ The command line flags and descriptions: region. Used in combination with fstart and fstop to prevent taking a subregion from a region too small to support it. The default is 10 bp. -## General options +### General options - --gz @@ -356,7 +358,7 @@ The command line flags and descriptions: Display the POD documentation for this program. -# DESCRIPTION +## DESCRIPTION This program will collect dataset values from a variety of sources, including features in a BioPerl Bio::DB::SeqFeature::Store database, binary wig files @@ -383,7 +385,7 @@ Stranded data may be collected, if the dataset supports stranded information. Also, two or more datasets may be combined and treated as one. Note that collecting stranded data may significantly slow down data collection. -# EXAMPLES +## EXAMPLES These are some examples of some common scenarios for collecting data. @@ -476,7 +478,7 @@ These are some examples of some common scenarios for collecting data. --data scores.bw -# AUTHOR +## AUTHOR Timothy J. Parnell, PhD Howard Hughes Medical Institute diff --git a/docs/apps/get_feature_info.md b/docs/apps/get_feature_info.md index 47680fc..595079f 100644 --- a/docs/apps/get_feature_info.md +++ b/docs/apps/get_feature_info.md @@ -1,10 +1,12 @@ -# NAME +# Bio::ToolBox -get\_feature\_info.pl +|[Home](ReadMe.md)|[Install](AdvancedInstallation.md)|[Libraries](Libraries.md)|[Applications](Applications.md)|[Examples](Examples.md)|[FAQ](FAQ.md)| + +## get\_feature\_info.pl A program to collect feature information from a BioPerl SeqFeature::Store db. -# SYNOPSIS +## SYNOPSIS get\_feature\_info.pl <filename> @@ -46,11 +48,11 @@ get\_feature\_info.pl <filename> Primary_ID -# OPTIONS +## OPTIONS The command line flags and descriptions: -## File options +### File options - --in <filename> @@ -66,7 +68,7 @@ The command line flags and descriptions: Optionally specify an alternate output file name. The default is to overwrite the input file. -## Database options +### Database options - --db <name> @@ -122,7 +124,7 @@ The command line flags and descriptions: may be provided. This is especially useful to restrict the database search when there are multiple features with the same name. -## General options +### General options - --gz @@ -138,14 +140,14 @@ The command line flags and descriptions: Display this help. -# DESCRIPTION +## DESCRIPTION This program will collect attributes for a list of features from the database. The attributes may be general attributes, such as chromsome, start, stop, strand, etc., or feature specific attributes stored in the original group field of the original source GFF file. -# AUTHOR +## AUTHOR Timothy J. Parnell, PhD Howard Hughes Medical Institute diff --git a/docs/apps/get_features.md b/docs/apps/get_features.md index 19ac277..fc12113 100644 --- a/docs/apps/get_features.md +++ b/docs/apps/get_features.md @@ -1,10 +1,12 @@ -# NAME +# Bio::ToolBox -get\_features.pl +|[Home](ReadMe.md)|[Install](AdvancedInstallation.md)|[Libraries](Libraries.md)|[Applications](Applications.md)|[Examples](Examples.md)|[FAQ](FAQ.md)| + +## get\_features.pl A program to collect and filter annotated features from source files. -# SYNOPSIS +## SYNOPSIS get\_features.pl --in <filename> --out <filename> @@ -51,11 +53,11 @@ get\_features.pl --db <name> --out <filename> -v --version print version and exit -h --help show full documentation -# OPTIONS +## OPTIONS The command line flags and descriptions: -## Source data +### Source data - --db <text> @@ -70,7 +72,7 @@ The command line flags and descriptions: or a UCSC-formatted file including, refFlat, genePred, or knownGene. The file may be gzip compressed. Used as an alternate to a database. -## Selection +### Selection - --feature <type> @@ -88,7 +90,7 @@ The command line flags and descriptions: turned off with `--nosub`. With BED output, it will force a BED12 file to be written. It has no effect with standard text. -## Filter features +### Filter features - --list <file> @@ -162,7 +164,7 @@ The command line flags and descriptions: marked as part of the GENCODE set. Transcripts not marked as such usually lack sufficient experimental evidence. -## Adjustments +### Adjustments - --start=<integer> - --stop=<integer> @@ -193,7 +195,7 @@ The command line flags and descriptions: introns, where appropriate. Genes without alternate transcripts are not collapsed. -## Report format options +### Report format options - --bed @@ -229,7 +231,7 @@ The command line flags and descriptions: in other formats. This is automatically included when adjusting coordinate positions. -## General options +### General options - --out <filename> @@ -257,7 +259,7 @@ The command line flags and descriptions: Display this POD documentation. -# DESCRIPTION +## DESCRIPTION This program will extract a list of features from a database or input annotation file and write them out to a file. Features may be selected @@ -277,7 +279,7 @@ metadata for use in subsequent programs. Coordinates may be optionally included in the text file, which preempts using parsed features in other tools. -## Coordinate adjustments +### Coordinate adjustments Coordinates of the features may be adjusted as desired when writing to text or BED file formats. Adjustments may be made relative to either @@ -307,7 +309,7 @@ are based on the feature strand. Use the following examples as a guide. Note that positions are always in base coordinates, and the resulting regions may be 1 bp longer depending on whether the reference base was included or not. -# AUTHOR +## AUTHOR Timothy J. Parnell, PhD Dept of Oncological Sciences diff --git a/docs/apps/get_gene_regions.md b/docs/apps/get_gene_regions.md index 453f3bc..66b412a 100644 --- a/docs/apps/get_gene_regions.md +++ b/docs/apps/get_gene_regions.md @@ -1,10 +1,12 @@ -# NAME +# Bio::ToolBox -get\_gene\_regions.pl +|[Home](ReadMe.md)|[Install](AdvancedInstallation.md)|[Libraries](Libraries.md)|[Applications](Applications.md)|[Examples](Examples.md)|[FAQ](FAQ.md)| + +## get\_gene\_regions.pl A program to collect specific, often un-annotated, regions from genes. -# SYNOPSIS +## SYNOPSIS get\_gene\_regions.pl \[--options...\] --in <filename> --out <filename> @@ -49,11 +51,11 @@ get\_gene\_regions.pl \[--options...\] --db <text> --out <filename> -v --version print version and exit -h --help -# OPTIONS +## OPTIONS The command line flags and descriptions: -## Source data +### Source data - --in <filename> @@ -67,7 +69,7 @@ The command line flags and descriptions: from which gene or feature annotation may be obtained. Only required if an input gene table is not provided. -## Feature selection +### Feature selection - --feature <type> @@ -187,7 +189,7 @@ The command line flags and descriptions: 'scaffold.+' 'chr.+alt|chrUn.+|chr.+_random' -## Adjustments +### Adjustments - --start <integer> - --begin <integer> @@ -201,7 +203,7 @@ The command line flags and descriptions: a start adjustment will always modify the feature's 5'end, either the feature startpoint or endpoint, depending on its orientation. -## General options +### General options - --bed @@ -223,7 +225,7 @@ The command line flags and descriptions: Display this POD documentation. -# DESCRIPTION +## DESCRIPTION This program will collect specific regions from annotated genes and/or transcripts. Often these regions are not explicitly defined in the @@ -243,7 +245,7 @@ This may be converted into a standard BED or GFF file using the appropriate biotoolbox scripts. The file may also be used directly in data collection. -# AUTHOR +## AUTHOR Timothy J. Parnell, PhD Howard Hughes Medical Institute diff --git a/docs/apps/get_intersecting_features.md b/docs/apps/get_intersecting_features.md index aec379a..73f2fd3 100644 --- a/docs/apps/get_intersecting_features.md +++ b/docs/apps/get_intersecting_features.md @@ -1,10 +1,12 @@ -# NAME +# Bio::ToolBox -get\_intersecting\_features.pl +|[Home](ReadMe.md)|[Install](AdvancedInstallation.md)|[Libraries](Libraries.md)|[Applications](Applications.md)|[Examples](Examples.md)|[FAQ](FAQ.md)| + +## get\_intersecting\_features.pl A program to pull out overlapping features from the database. -# SYNOPSIS +## SYNOPSIS get\_intersecting\_features.pl \[--options\] <filename> @@ -28,11 +30,11 @@ get\_intersecting\_features.pl \[--options\] <filename> -v --version print version and exit -h --help show extended documentation -# OPTIONS +## OPTIONS The command line flags and descriptions: -## File options: +### File options: - --in <filename> @@ -49,7 +51,7 @@ The command line flags and descriptions: Optionally specify a new filename. A standard tim data text file is written. The default is to rewrite the input file. -## Database options +### Database options - --db <database> @@ -68,7 +70,7 @@ The command line flags and descriptions: will be queried for potential GFF types and a list presented to the user to select one. -## Modify search range +### Modify search range - --start <integer> - --stop <integer> @@ -101,7 +103,7 @@ The command line flags and descriptions: features. Valid options include "start" (or 5' end for stranded features) and "mid" (for midpoint). Default is "start". -## General options +### General options - --gz @@ -115,7 +117,7 @@ The command line flags and descriptions: Display the POD documentation -# DESCRIPTION +## DESCRIPTION This program will take a list of reference features and identify target features which intersect them. The reference features @@ -136,7 +138,7 @@ of the features, or optionally the midpoints. Note that the distance measurement is relative to the coordinates after adjustment with the --start, \--stop, and --extend options. -# AUTHOR +## AUTHOR Timothy J. Parnell, PhD Howard Hughes Medical Institute diff --git a/docs/apps/get_relative_data.md b/docs/apps/get_relative_data.md index 8ced3f7..1a4c8b3 100644 --- a/docs/apps/get_relative_data.md +++ b/docs/apps/get_relative_data.md @@ -1,10 +1,12 @@ -# NAME +# Bio::ToolBox -get\_relative\_data.pl +|[Home](ReadMe.md)|[Install](AdvancedInstallation.md)|[Libraries](Libraries.md)|[Applications](Applications.md)|[Examples](Examples.md)|[FAQ](FAQ.md)| + +## get\_relative\_data.pl A program to collect data in bins around a relative position. -# SYNOPSIS +## SYNOPSIS get\_relative\_data.pl \[--options\] --in <filename> --out <filename> @@ -50,11 +52,11 @@ get\_relative\_data.pl \[--options\] -i <filename> <data1> <data2...> -v --version print version and exit -h --help show extended documentation -# OPTIONS +## OPTIONS The command line flags and descriptions: -## Options for data files +### Options for data files - --in <filename> @@ -71,7 +73,7 @@ The command line flags and descriptions: Specify the output file name. Required for new files; otherwise, input files will be overwritten unless specified. -## Options for new files +### Options for new files - --db <name | filename> @@ -89,7 +91,7 @@ The command line flags and descriptions: of features will be automatically generated from the database. This is only required when an input file is not specified. -## Options for data collection +### Options for data collection - --ddb <name | filename> @@ -193,7 +195,7 @@ The command line flags and descriptions: Default is not to format, often leading to more than the intended significant digits. -## Bin specification +### Bin specification - --win <integer> @@ -220,7 +222,7 @@ The command line flags and descriptions: indicates the middle of the feature is used. The default is to use the 5' end, or the start position of unstranded features. -## Post-processing +### Post-processing - --(no)sum @@ -234,7 +236,7 @@ The command line flags and descriptions: Indicate that windows without values should (not) be interpolated from neighboring values. The default is false (nosmooth). -## General options +### General options - --groups @@ -267,7 +269,7 @@ The command line flags and descriptions: Display this help -# DESCRIPTION +## DESCRIPTION This program will collect data around a relative coordinate of a genomic feature or region. The data is collected in a series of windows flanking the @@ -285,7 +287,7 @@ orientation. When features overlap, or the collection windows of one feature overlaps with another feature, then data may be ignored and not collected (--avoid). -# EXAMPLES +## EXAMPLES These are some examples of some common scenarios for collecting data. @@ -315,7 +317,7 @@ These are some examples of some common scenarios for collecting data. sense --method count --data alignments.bam --out gene_tss -# AUTHOR +## AUTHOR Timothy J. Parnell, PhD Howard Hughes Medical Institute diff --git a/docs/apps/join_data_file.md b/docs/apps/join_data_file.md index 409f53d..2631855 100644 --- a/docs/apps/join_data_file.md +++ b/docs/apps/join_data_file.md @@ -1,10 +1,12 @@ -# NAME +# Bio::ToolBox -join\_data\_file.pl +|[Home](ReadMe.md)|[Install](AdvancedInstallation.md)|[Libraries](Libraries.md)|[Applications](Applications.md)|[Examples](Examples.md)|[FAQ](FAQ.md)| + +## join\_data\_file.pl A program to join two or more data files and concatenate rows. -# SYNOPSIS +## SYNOPSIS join\_data\_file.pl \[--options\] <file1> <file2> ... @@ -14,7 +16,7 @@ join\_data\_file.pl \[--options\] <file1> <file2> ... -v --version print version and exit -h --help show extended documentation -# OPTIONS +## OPTIONS The command line flags and descriptions: @@ -39,7 +41,7 @@ The command line flags and descriptions: Display the POD documentation -# DESCRIPTION +## DESCRIPTION This program will join two or or more data files, essentially concatanating the files but intelligently dealing with the metadata and column headers. @@ -51,7 +53,7 @@ the program 'merge\_datasets.pl' for that. This program is intended as the complement to 'split\_data\_files.pl'. -# AUTHOR +## AUTHOR Timothy J. Parnell, PhD Howard Hughes Medical Institute diff --git a/docs/apps/manipulate_datasets.md b/docs/apps/manipulate_datasets.md index f514843..c3132af 100644 --- a/docs/apps/manipulate_datasets.md +++ b/docs/apps/manipulate_datasets.md @@ -1,10 +1,12 @@ -# NAME +# Bio::ToolBox -manipulate\_datasets.pl +|[Home](ReadMe.md)|[Install](AdvancedInstallation.md)|[Libraries](Libraries.md)|[Applications](Applications.md)|[Examples](Examples.md)|[FAQ](FAQ.md)| + +## manipulate\_datasets.pl A progam to manipulate tab-delimited data files. -# SYNOPSIS +## SYNOPSIS manipulate\_datasets.pl \[--options ...\] <filename> @@ -39,11 +41,11 @@ manipulate\_datasets.pl \[--options ...\] <filename> -v --version print version and exit -h --help show extended documentation -# OPTIONS +## OPTIONS The command line flags and descriptions: -## File options +### File options - --in <filename> @@ -73,7 +75,7 @@ The command line flags and descriptions: headers will be provided. Not necessary for BED, GFF, or recognized UCSC file formats. -## Non-interactive functions +### Non-interactive functions - --func <function> @@ -98,7 +100,7 @@ The command line flags and descriptions: dash between the start and stop. For example, '1,2,5-7,9' would indicate datasets '1, 2, 5, 6, 7, and 9'. -## Operation options +### Operation options - --exp <integer> - --num <integer> @@ -159,7 +161,7 @@ The command line flags and descriptions: accurate mathematical calculations in some manipulations. This is not necessary when the log status is appropriately recorded in the dataset metadata. -## General options +### General options - --gz @@ -179,7 +181,7 @@ The command line flags and descriptions: Display the POD documentation using perldoc. -# DESCRIPTION +## DESCRIPTION This program allows some common mathematical and other manipulations on one or more columns in a datafile. The program is designed as a simple @@ -202,7 +204,7 @@ any are performed, will write out to file the changed data. Unless an output file name is provided, it will overwrite the input file (NO backup is made!). -# FUNCTIONS +## FUNCTIONS This is a list of the functions available for manipulating columns. These may be selected interactively from the main menu (note the case sensitivity!), @@ -547,7 +549,7 @@ or specified on the command line using the --func option. write an intermediate file during numerous interactive manipulations. Consider this as a 'Save as...'. -# AUTHOR +## AUTHOR Timothy J. Parnell, PhD Howard Hughes Medical Institute diff --git a/docs/apps/manipulate_wig.md b/docs/apps/manipulate_wig.md index d49a72f..93f018c 100644 --- a/docs/apps/manipulate_wig.md +++ b/docs/apps/manipulate_wig.md @@ -1,10 +1,12 @@ -# NAME +# Bio::ToolBox -manipulate\_wig.pl +|[Home](ReadMe.md)|[Install](AdvancedInstallation.md)|[Libraries](Libraries.md)|[Applications](Applications.md)|[Examples](Examples.md)|[FAQ](FAQ.md)| + +## manipulate\_wig.pl A progam to manipulate wiggle files. -# SYNOPSIS +## SYNOPSIS manipulate\_wig.pl \[options\] -i <file1.wig> -o <file1.out.wig> @@ -39,11 +41,11 @@ manipulate\_wig.pl \[options\] -i <file1.wig> -o <file1.out.wig> -v --version print version and exit -h --help show extended documentation -# OPTIONS +## OPTIONS The command line flags and descriptions: -## File options +### File options - --in <file> @@ -60,7 +62,7 @@ The command line flags and descriptions: file is provided. Alternatively, the output may be sent to standard output by specifying 'stdout' as the file name. -## Selection functions +### Selection functions - --skip <regex> @@ -74,7 +76,7 @@ The command line flags and descriptions: provided regular expression, leaving remaining lines untouched. For example, to apply a normalization to the X chromosome, use 'chrX'. -## Manipulation functions +### Manipulation functions - --null @@ -119,7 +121,7 @@ The command line flags and descriptions: Discard lines with a score value of zero. -## BigWig support +### BigWig support - chromo <file> @@ -146,7 +148,7 @@ The command line flags and descriptions: If the UCSC `wigToBigWig` utility is not in your environment `PATH`, provide the path with this option. -## General functions +### General functions - --stats @@ -163,7 +165,7 @@ The command line flags and descriptions: Display the POD documentation using perldoc. -# DESCRIPTION +## DESCRIPTION A program to manipulate the score value of wig files. This will process all forms of text based wig files, including fixedStep, variableStep, and bedGraph. @@ -175,7 +177,7 @@ available. in which the score is manipulated. If they are not in the order you want, you may have to pipe to sequential instances. Use 'stdin' and 'stdout' for filenames. -# AUTHOR +## AUTHOR Timothy J. Parnell, PhD Dept of Oncological Sciences diff --git a/docs/apps/merge_datasets.md b/docs/apps/merge_datasets.md index 94d3658..e1f1759 100644 --- a/docs/apps/merge_datasets.md +++ b/docs/apps/merge_datasets.md @@ -1,10 +1,12 @@ -# NAME +# Bio::ToolBox -merge\_datasets.pl +|[Home](ReadMe.md)|[Install](AdvancedInstallation.md)|[Libraries](Libraries.md)|[Applications](Applications.md)|[Examples](Examples.md)|[FAQ](FAQ.md)| + +## merge\_datasets.pl A program to merge columns of two or more data files. -# SYNOPSIS +## SYNOPSIS merge\_datasets.pl \[--options...\] <file1> <file2> ... @@ -22,11 +24,11 @@ merge\_datasets.pl \[--options...\] <file1> <file2> ... -v --version print version and exit -h --help show full documentation -# OPTIONS +## OPTIONS The command line flags and descriptions: -## Merge options +### Merge options - --lookup @@ -73,7 +75,7 @@ The command line flags and descriptions: with coordinate files, such as BED and GFF. This may be disabled by specifying --nocoordinate, or simply specifying a column lookup name. -## General options +### General options - --out <filename> @@ -92,7 +94,7 @@ The command line flags and descriptions: Display this POD documentation. -# DESCRIPTION +## DESCRIPTION This program will merge two or more tab-delimited data files into one file. Datasets or columns from each file are merged together into an output file. @@ -128,7 +130,7 @@ values are recorded when no match is found in the second file. After merging in interactive mode only, an opportunity for interactively renaming the dataset names is presented. -# AUTHOR +## AUTHOR Timothy J. Parnell, PhD Howard Hughes Medical Institute diff --git a/docs/apps/pull_features.md b/docs/apps/pull_features.md index 1a37f3c..4ca4a18 100644 --- a/docs/apps/pull_features.md +++ b/docs/apps/pull_features.md @@ -1,10 +1,12 @@ -# NAME +# Bio::ToolBox -pull\_features.pl +|[Home](ReadMe.md)|[Install](AdvancedInstallation.md)|[Libraries](Libraries.md)|[Applications](Applications.md)|[Examples](Examples.md)|[FAQ](FAQ.md)| + +## pull\_features.pl A program to pull out a specific list of data rows from a data file. -# SYNOPSIS +## SYNOPSIS pull\_features.pl --data <filename> --list <filename> --out <filename> @@ -30,11 +32,11 @@ pull\_features.pl --data <filename> --list <filename> --out <filename> -v --version print version and exit -h --help show full documentation -# OPTIONS +## OPTIONS The command line flags and descriptions: -## File options +### File options - --data @@ -53,7 +55,7 @@ The command line flags and descriptions: Specify the output file name. -## Column index options +### Column index options - --dindex <integer> - --lindex <integer> @@ -72,7 +74,7 @@ The command line flags and descriptions: 'group' will automatically be identified. A .kgg file will automatically use the Cluster column as the group index. -## Output options +### Output options - --order \[list | data\] @@ -111,7 +113,7 @@ The command line flags and descriptions: The data is in log2 space. Only necessary when re-summarizing the pulled data. -## General options +### General options - --version @@ -121,7 +123,7 @@ The command line flags and descriptions: Display this POD documentation. -# DESCRIPTION +## DESCRIPTION Given a list of requested unique feature identifiers, this program will pull out those features (rows) from a datafile and write a new file. This @@ -144,7 +146,7 @@ in the specified data columns are averaged and written out as rows in a separate data file. Compare this function to the summary option in the biotoolbox scripts [get\_relative\_data.pl](https://metacpan.org/pod/get_relative_data.pl) or [average\_gene.pl](https://metacpan.org/pod/average_gene.pl). -# AUTHOR +## AUTHOR Timothy J. Parnell, PhD Howard Hughes Medical Institute diff --git a/docs/apps/split_data_file.md b/docs/apps/split_data_file.md index b759f9c..5d0b78a 100644 --- a/docs/apps/split_data_file.md +++ b/docs/apps/split_data_file.md @@ -1,10 +1,12 @@ -# NAME +# Bio::ToolBox -split\_data\_file.pl +|[Home](ReadMe.md)|[Install](AdvancedInstallation.md)|[Libraries](Libraries.md)|[Applications](Applications.md)|[Examples](Examples.md)|[FAQ](FAQ.md)| + +## split\_data\_file.pl A program to split a data file by rows based on common data values. -# SYNOPSIS +## SYNOPSIS split\_data\_file.pl \[--options\] <filename> @@ -23,11 +25,11 @@ split\_data\_file.pl \[--options\] <filename> -v --version print version and exit -h --help show extended documentation -# OPTIONS +## OPTIONS The command line flags and descriptions: -## File options +### File options - --in <filename> @@ -46,7 +48,7 @@ The command line flags and descriptions: headers will be provided. Not necessary for BED, GFF, or recognized UCSC file formats. -## Splitting options +### Splitting options - --index <column\_index> @@ -68,7 +70,7 @@ The command line flags and descriptions: Enter as an integer; underscores may be used as thousands separator, e.g. 100\_000. -## General options +### General options - --gz @@ -84,7 +86,7 @@ The command line flags and descriptions: Display the POD documentation -# DESCRIPTION +## DESCRIPTION This program will split a data file into multiple files based on common values in the data table. All rows with the same value will be @@ -117,7 +119,7 @@ metadata. The original file is preserved. This program is intended as the complement to 'join\_data\_files.pl'. -# AUTHOR +## AUTHOR Timothy J. Parnell, PhD Howard Hughes Medical Institute diff --git a/docs/apps/ucsc_table2gff3.md b/docs/apps/ucsc_table2gff3.md index a9aa7c6..a7c6d9d 100644 --- a/docs/apps/ucsc_table2gff3.md +++ b/docs/apps/ucsc_table2gff3.md @@ -1,10 +1,12 @@ -# NAME +# Bio::ToolBox -ucsc\_table2gff3.pl +|[Home](ReadMe.md)|[Install](AdvancedInstallation.md)|[Libraries](Libraries.md)|[Applications](Applications.md)|[Examples](Examples.md)|[FAQ](FAQ.md)| + +## ucsc\_table2gff3.pl A program to convert UCSC gene tables to GFF3 or GTF annotation. -# SYNOPSIS +## SYNOPSIS ucsc_table2gff3.pl --ftp --db @@ -37,11 +39,11 @@ A program to convert UCSC gene tables to GFF3 or GTF annotation. -v --version print version and exit -h --help show extended documentation -# OPTIONS +## OPTIONS The command line flags and descriptions: -## UCSC database options +### UCSC database options - --ftp \[refgene|known|all\] @@ -63,7 +65,7 @@ The command line flags and descriptions: Optionally provide the host FTP address for downloading the current gene table files. The default is 'hgdownload.cse.ucsc.edu'. -## Input file options +### Input file options - --table <filename> @@ -87,7 +89,7 @@ The command line flags and descriptions: output GFF file (when processing a single table) or written as a separate file (when processing multiple tables). The file may be gzipped. -## Conversion options +### Conversion options - --source <text> @@ -148,7 +150,7 @@ The command line flags and descriptions: GFF3. Yes, the name of the program says GFF3, but now we can output GTF too, and changing the name of the program is too late now. -## General options +### General options - --gz @@ -162,7 +164,7 @@ The command line flags and descriptions: Display the POD documentation -# DESCRIPTION +## DESCRIPTION This program will convert a UCSC gene or gene prediction table file into a GFF3 (or optionally GTF) format file. It will build canonical @@ -193,7 +195,7 @@ If you need to set up a database using UCSC annotation, you should first take a look at the BioToolBox script [db\_setup.pl](https://metacpan.org/pod/db_setup.pl), which provides a convenient automated database setup based on UCSC annotation. -# AUTHOR +## AUTHOR Timothy J. Parnell, PhD Huntsman Cancer Institute