diff --git a/dev/reference/gb2gtf.html b/dev/reference/gb2gtf.html new file mode 100644 index 0000000..5d59fc0 --- /dev/null +++ b/dev/reference/gb2gtf.html @@ -0,0 +1,834 @@ + + + + + + + + + +gb2gtf – CCBR Tools + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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gb2gtf

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gb2gtf

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Module for converting GenBank files to GTF format.

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Usage

+

python gb2gtf.py sequence.gb > sequence.gtf

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+ + + + + + \ No newline at end of file diff --git a/dev/reference/homologfinder.html b/dev/reference/homologfinder.html new file mode 100644 index 0000000..9a1c924 --- /dev/null +++ b/dev/reference/homologfinder.html @@ -0,0 +1,827 @@ + + + + + + + + + +homologfinder – CCBR Tools + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+

homologfinder

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homologfinder

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hf or HomologFinder finds homologs in human and mouse.

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+ + + + + + \ No newline at end of file diff --git a/dev/reference/index.html b/dev/reference/index.html index 9afff38..ea5e4e2 100644 --- a/dev/reference/index.html +++ b/dev/reference/index.html @@ -153,9 +153,33 @@ @@ -213,9 +243,25 @@

Modules

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Modules

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gb2gtfModule for converting GenBank files to GTF format.
homologfinderhf or HomologFinder finds homologs in human and mouse.
intersectFind the intersect of two files, returns the inner join
jobby Display job information for past slurm job IDs
jobinfoGet HPC usage metadata for a list of slurm jobids on biowulf
peek Take a peek at tab-delimited files shell Utility functions for shell command execution.
templatesTemplate files for CCBR Tools.
diff --git a/dev/reference/intersect.html b/dev/reference/intersect.html new file mode 100644 index 0000000..523927b --- /dev/null +++ b/dev/reference/intersect.html @@ -0,0 +1,835 @@ + + + + + + + + + +intersect – CCBR Tools + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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intersect

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intersect

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Find the intersect of two files, returns the inner join

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Original author: Skyler Kuhn (@skchronicles)

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Usage

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intersect file1 file2

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jobinfo

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jobinfo

+

Get HPC usage metadata for a list of slurm jobids on biowulf

+
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About

+

This wrapper script works only on BIOWULF! This script usage the “dashboard_cli” utility on biowulf to get HPC usage metadata for a list of slurm jobids. These slurm jobids can be either provided at command line or extracted from a snakemake.log file. Using snakemake.log file option together with –failonly option lists path to the STDERR files for failed jobs. This can be very useful to debug failed Snakemake workflows.

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Usage

+

$ jobinfo -h

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+
+

Example

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$ jobinfo -j 123456,7891011 $ jobinfo -s /path/to/snakemake.log $ jobinfo -j 123456,7891011 -o /path/to/report.tsv $ jobinfo -s /path/to/snakemake.log –failonly

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Functions

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NameDescription
check_helpcheck if usage needs to be printed
exit_w_msgGracefully exit with proper message
+
+

check_help

+

jobinfo.check_help(parser)

+

check if usage needs to be printed

+
+
+

exit_w_msg

+

jobinfo.exit_w_msg(message)

+

Gracefully exit with proper message

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+
+ +
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+ + + + + + \ No newline at end of file diff --git a/dev/reference/peek.html b/dev/reference/peek.html index 0ad5dae..5916126 100644 --- a/dev/reference/peek.html +++ b/dev/reference/peek.html @@ -124,7 +124,7 @@ - + @@ -153,9 +153,33 @@ diff --git a/dev/reference/pipeline.html b/dev/reference/pipeline.html index 8a0a61b..720729f 100644 --- a/dev/reference/pipeline.html +++ b/dev/reference/pipeline.html @@ -124,7 +124,7 @@ - + @@ -153,9 +153,33 @@ diff --git a/dev/reference/pkg_util.html b/dev/reference/pkg_util.html index 0b589af..ae4303d 100644 --- a/dev/reference/pkg_util.html +++ b/dev/reference/pkg_util.html @@ -124,7 +124,7 @@ - + @@ -153,9 +153,33 @@ diff --git a/dev/reference/shell.html b/dev/reference/shell.html index 8a7bbec..138b5c4 100644 --- a/dev/reference/shell.html +++ b/dev/reference/shell.html @@ -124,7 +124,7 @@ - + @@ -153,9 +153,33 @@ diff --git a/dev/reference/templates.html b/dev/reference/templates.html new file mode 100644 index 0000000..1d14f22 --- /dev/null +++ b/dev/reference/templates.html @@ -0,0 +1,991 @@ + + + + + + + + + +templates – CCBR Tools + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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templates

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templates

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Template files for CCBR Tools.

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Templates

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    +
  • ccbr_tools.templates.submit_slurm.sh
    • +
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Functions

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NameDescription
read_templateRead a template file
use_templateUses a template, formats variables, and writes it to a file.
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read_template

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templates.read_template(template_name)

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Read a template file

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Parameters

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NameTypeDescriptionDefault
template_namestrName of the template filerequired
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Returns

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TypeDescription
strContents of the template file
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+
+
+

use_template

+

templates.use_template(template_name, output_filepath=None, **kwargs)

+

Uses a template, formats variables, and writes it to a file.

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Parameters

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NameTypeDescriptionDefault
template_namestrThe name of the template to use.required
output_filepathstrThe filepath to save the output file. If not provided, it will be written to template_name in the current working directory.None
**kwargsKeyword arguments to fill in the template variables.{}
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Returns

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TypeDescription
None
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+
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Raises

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TypeDescription
FileNotFoundErrorIf the template file is not found.
IOErrorIf there is an error writing the output file.
+
+
+

Examples

+

use_template(“submit_slurm.sh”, output_filepath=“./submit_slurm.sh”, PIPELINE=“CCBR_nxf”, MODULES=“ccbrpipeliner nextflow”, ENV_VARS=““, RUN_COMMAND=”nextflow run main.nf -stub”)

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+ + + + + + \ No newline at end of file diff --git a/dev/search.json b/dev/search.json index ebc94e0..cf96983 100644 --- a/dev/search.json +++ b/dev/search.json @@ -20,12 +20,36 @@ "section": "Tools 0.0.1", "text": "Tools 0.0.1\nThis tag marks the repository state from before refactoring it as a python package." }, + { + "objectID": "reference/intersect.html", + "href": "reference/intersect.html", + "title": "intersect", + "section": "", + "text": "intersect\nFind the intersect of two files, returns the inner join\nOriginal author: Skyler Kuhn (@skchronicles)\n\n\nintersect file1 file2", + "crumbs": [ + "Reference", + "Modules", + "intersect" + ] + }, + { + "objectID": "reference/intersect.html#usage", + "href": "reference/intersect.html#usage", + "title": "intersect", + "section": "", + "text": "intersect file1 file2", + "crumbs": [ + "Reference", + "Modules", + "intersect" + ] + }, { "objectID": "reference/index.html", "href": "reference/index.html", "title": "Function reference", "section": "", - "text": "jobby\nDisplay job information for past slurm job IDs\n\n\npeek\nTake a peek at tab-delimited files\n\n\npipeline\nHelpers for bioinformatics pipelines\n\n\npkg_util\nMiscellaneous utility functions for the package\n\n\nshell\nUtility functions for shell command execution.", + "text": "gb2gtf\nModule for converting GenBank files to GTF format.\n\n\nhomologfinder\nhf or HomologFinder finds homologs in human and mouse.\n\n\nintersect\nFind the intersect of two files, returns the inner join\n\n\njobby\nDisplay job information for past slurm job IDs\n\n\njobinfo\nGet HPC usage metadata for a list of slurm jobids on biowulf\n\n\npeek\nTake a peek at tab-delimited files\n\n\npipeline\nHelpers for bioinformatics pipelines\n\n\npkg_util\nMiscellaneous utility functions for the package\n\n\nshell\nUtility functions for shell command execution.\n\n\ntemplates\nTemplate files for CCBR Tools.", "crumbs": [ "Reference", "Function reference" @@ -36,12 +60,24 @@ "href": "reference/index.html#modules", "title": "Function reference", "section": "", - "text": "jobby\nDisplay job information for past slurm job IDs\n\n\npeek\nTake a peek at tab-delimited files\n\n\npipeline\nHelpers for bioinformatics pipelines\n\n\npkg_util\nMiscellaneous utility functions for the package\n\n\nshell\nUtility functions for shell command execution.", + "text": "gb2gtf\nModule for converting GenBank files to GTF format.\n\n\nhomologfinder\nhf or HomologFinder finds homologs in human and mouse.\n\n\nintersect\nFind the intersect of two files, returns the inner join\n\n\njobby\nDisplay job information for past slurm job IDs\n\n\njobinfo\nGet HPC usage metadata for a list of slurm jobids on biowulf\n\n\npeek\nTake a peek at tab-delimited files\n\n\npipeline\nHelpers for bioinformatics pipelines\n\n\npkg_util\nMiscellaneous utility functions for the package\n\n\nshell\nUtility functions for shell command execution.\n\n\ntemplates\nTemplate files for CCBR Tools.", "crumbs": [ "Reference", "Function reference" ] }, + { + "objectID": "reference/pipeline.html", + "href": "reference/pipeline.html", + "title": "pipeline", + "section": "", + "text": "pipeline\npipeline\nHelpers for bioinformatics pipelines", + "crumbs": [ + "Reference", + "Modules", + "pipeline" + ] + }, { "objectID": "reference/jobby.html", "href": "reference/jobby.html", @@ -174,6 +210,66 @@ "peek" ] }, + { + "objectID": "reference/jobinfo.html", + "href": "reference/jobinfo.html", + "title": "jobinfo", + "section": "", + "text": "jobinfo\nGet HPC usage metadata for a list of slurm jobids on biowulf\n\n\nThis wrapper script works only on BIOWULF! This script usage the “dashboard_cli” utility on biowulf to get HPC usage metadata for a list of slurm jobids. These slurm jobids can be either provided at command line or extracted from a snakemake.log file. Using snakemake.log file option together with –failonly option lists path to the STDERR files for failed jobs. This can be very useful to debug failed Snakemake workflows.\n\n\n\n$ jobinfo -h\n\n\n\n$ jobinfo -j 123456,7891011 $ jobinfo -s /path/to/snakemake.log $ jobinfo -j 123456,7891011 -o /path/to/report.tsv $ jobinfo -s /path/to/snakemake.log –failonly\n\n\n\n\n\n\nName\nDescription\n\n\n\n\ncheck_help\ncheck if usage needs to be printed\n\n\nexit_w_msg\nGracefully exit with proper message\n\n\n\n\n\njobinfo.check_help(parser)\ncheck if usage needs to be printed\n\n\n\njobinfo.exit_w_msg(message)\nGracefully exit with proper message", + "crumbs": [ + "Reference", + "Modules", + "jobinfo" + ] + }, + { + "objectID": "reference/jobinfo.html#about", + "href": "reference/jobinfo.html#about", + "title": "jobinfo", + "section": "", + "text": "This wrapper script works only on BIOWULF! This script usage the “dashboard_cli” utility on biowulf to get HPC usage metadata for a list of slurm jobids. These slurm jobids can be either provided at command line or extracted from a snakemake.log file. Using snakemake.log file option together with –failonly option lists path to the STDERR files for failed jobs. This can be very useful to debug failed Snakemake workflows.", + "crumbs": [ + "Reference", + "Modules", + "jobinfo" + ] + }, + { + "objectID": "reference/jobinfo.html#usage", + "href": "reference/jobinfo.html#usage", + "title": "jobinfo", + "section": "", + "text": "$ jobinfo -h", + "crumbs": [ + "Reference", + "Modules", + "jobinfo" + ] + }, + { + "objectID": "reference/jobinfo.html#example", + "href": "reference/jobinfo.html#example", + "title": "jobinfo", + "section": "", + "text": "$ jobinfo -j 123456,7891011 $ jobinfo -s /path/to/snakemake.log $ jobinfo -j 123456,7891011 -o /path/to/report.tsv $ jobinfo -s /path/to/snakemake.log –failonly", + "crumbs": [ + "Reference", + "Modules", + "jobinfo" + ] + }, + { + "objectID": "reference/jobinfo.html#functions", + "href": "reference/jobinfo.html#functions", + "title": "jobinfo", + "section": "", + "text": "Name\nDescription\n\n\n\n\ncheck_help\ncheck if usage needs to be printed\n\n\nexit_w_msg\nGracefully exit with proper message\n\n\n\n\n\njobinfo.check_help(parser)\ncheck if usage needs to be printed\n\n\n\njobinfo.exit_w_msg(message)\nGracefully exit with proper message", + "crumbs": [ + "Reference", + "Modules", + "jobinfo" + ] + }, { "objectID": "index.html", "href": "index.html", @@ -277,15 +373,75 @@ ] }, { - "objectID": "reference/pipeline.html", - "href": "reference/pipeline.html", - "title": "pipeline", + "objectID": "reference/homologfinder.html", + "href": "reference/homologfinder.html", + "title": "homologfinder", "section": "", - "text": "pipeline\npipeline\nHelpers for bioinformatics pipelines", + "text": "homologfinder\nhomologfinder\nhf or HomologFinder finds homologs in human and mouse.", "crumbs": [ "Reference", "Modules", - "pipeline" + "homologfinder" + ] + }, + { + "objectID": "reference/templates.html", + "href": "reference/templates.html", + "title": "templates", + "section": "", + "text": "templates\nTemplate files for CCBR Tools.\n\n\n\nccbr_tools.templates.submit_slurm.sh\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nread_template\nRead a template file\n\n\nuse_template\nUses a template, formats variables, and writes it to a file.\n\n\n\n\n\ntemplates.read_template(template_name)\nRead a template file\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ntemplate_name\nstr\nName of the template file\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nstr\nContents of the template file\n\n\n\n\n\n\n\ntemplates.use_template(template_name, output_filepath=None, **kwargs)\nUses a template, formats variables, and writes it to a file.\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ntemplate_name\nstr\nThe name of the template to use.\nrequired\n\n\noutput_filepath\nstr\nThe filepath to save the output file. If not provided, it will be written to template_name in the current working directory.\nNone\n\n\n**kwargs\n\nKeyword arguments to fill in the template variables.\n{}\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\n\nNone\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nFileNotFoundError\nIf the template file is not found.\n\n\nIOError\nIf there is an error writing the output file.\n\n\n\n\n\n\nuse_template(“submit_slurm.sh”, output_filepath=“./submit_slurm.sh”, PIPELINE=“CCBR_nxf”, MODULES=“ccbrpipeliner nextflow”, ENV_VARS=““, RUN_COMMAND=”nextflow run main.nf -stub”)", + "crumbs": [ + "Reference", + "Modules", + "templates" + ] + }, + { + "objectID": "reference/templates.html#templates", + "href": "reference/templates.html#templates", + "title": "templates", + "section": "", + "text": "ccbr_tools.templates.submit_slurm.sh", + "crumbs": [ + "Reference", + "Modules", + "templates" + ] + }, + { + "objectID": "reference/templates.html#functions", + "href": "reference/templates.html#functions", + "title": "templates", + "section": "", + "text": "Name\nDescription\n\n\n\n\nread_template\nRead a template file\n\n\nuse_template\nUses a template, formats variables, and writes it to a file.\n\n\n\n\n\ntemplates.read_template(template_name)\nRead a template file\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ntemplate_name\nstr\nName of the template file\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nstr\nContents of the template file\n\n\n\n\n\n\n\ntemplates.use_template(template_name, output_filepath=None, **kwargs)\nUses a template, formats variables, and writes it to a file.\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ntemplate_name\nstr\nThe name of the template to use.\nrequired\n\n\noutput_filepath\nstr\nThe filepath to save the output file. If not provided, it will be written to template_name in the current working directory.\nNone\n\n\n**kwargs\n\nKeyword arguments to fill in the template variables.\n{}\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\n\nNone\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nFileNotFoundError\nIf the template file is not found.\n\n\nIOError\nIf there is an error writing the output file.\n\n\n\n\n\n\nuse_template(“submit_slurm.sh”, output_filepath=“./submit_slurm.sh”, PIPELINE=“CCBR_nxf”, MODULES=“ccbrpipeliner nextflow”, ENV_VARS=““, RUN_COMMAND=”nextflow run main.nf -stub”)", + "crumbs": [ + "Reference", + "Modules", + "templates" + ] + }, + { + "objectID": "reference/gb2gtf.html", + "href": "reference/gb2gtf.html", + "title": "gb2gtf", + "section": "", + "text": "gb2gtf\nModule for converting GenBank files to GTF format.\n\n\npython gb2gtf.py sequence.gb > sequence.gtf", + "crumbs": [ + "Reference", + "Modules", + "gb2gtf" + ] + }, + { + "objectID": "reference/gb2gtf.html#usage", + "href": "reference/gb2gtf.html#usage", + "title": "gb2gtf", + "section": "", + "text": "python gb2gtf.py sequence.gb > sequence.gtf", + "crumbs": [ + "Reference", + "Modules", + "gb2gtf" ] }, { diff --git a/dev/sitemap.xml b/dev/sitemap.xml index d5fc5ba..05565a1 100644 --- a/dev/sitemap.xml +++ b/dev/sitemap.xml @@ -2,38 +2,58 @@ https://ccbr.github.io/Tools/CHANGELOG.html - 2024-09-11T16:43:53.849Z + 2024-09-11T16:56:43.725Z + + + https://ccbr.github.io/Tools/reference/intersect.html + 2024-09-11T16:57:13.380Z https://ccbr.github.io/Tools/reference/index.html - 2024-09-11T16:44:20.305Z + 2024-09-11T16:57:13.368Z + + + https://ccbr.github.io/Tools/reference/pipeline.html + 2024-09-11T16:57:13.444Z https://ccbr.github.io/Tools/reference/jobby.html - 2024-09-11T16:44:20.353Z + 2024-09-11T16:57:13.420Z https://ccbr.github.io/Tools/reference/peek.html - 2024-09-11T16:44:20.369Z + 2024-09-11T16:57:13.440Z + + + https://ccbr.github.io/Tools/reference/jobinfo.html + 2024-09-11T16:57:13.428Z https://ccbr.github.io/Tools/index.html - 2024-09-11T16:43:53.849Z + 2024-09-11T16:56:43.725Z https://ccbr.github.io/Tools/reference/shell.html - 2024-09-11T16:44:20.417Z + 2024-09-11T16:57:13.492Z https://ccbr.github.io/Tools/reference/pkg_util.html - 2024-09-11T16:44:20.401Z + 2024-09-11T16:57:13.476Z - https://ccbr.github.io/Tools/reference/pipeline.html - 2024-09-11T16:44:20.369Z + https://ccbr.github.io/Tools/reference/homologfinder.html + 2024-09-11T16:57:13.380Z + + + https://ccbr.github.io/Tools/reference/templates.html + 2024-09-11T16:57:13.504Z + + + https://ccbr.github.io/Tools/reference/gb2gtf.html + 2024-09-11T16:57:13.380Z https://ccbr.github.io/Tools/CONTRIBUTING.html - 2024-09-11T16:43:53.849Z + 2024-09-11T16:56:43.721Z