anvi-script-as-markdown

Markdownizides TAB-delmited data with headers in terminal..

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Authors

A. Murat Eren (Meren)
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Can consume

This program seems to know what its doing. It needs no input material from its user. Good program.

Can provide

markdown-txt

Usage

A helper script to format TAB-delimited files in markdown for bloggers, tutorial writers, those who wish to share example anvi’o outputs as text on GitHub issues, and so on.

Anvi’o programs often generate TAB-delimited files. While this simple format is useful to pass around to other software or share with others, it is not easily interpretable in visual media. The purpose of this script is to make the sharing part simpler for platforms that can render markdown.

You can pipe any TAB-delimited content to this script:

cat file.txt | anvi-sript-as-markdown

Examples

Assume a TAB-delmited file with many lines:

wc -l additional_view_data.txt

301 additional_view_data.txt

Contents of which look like this:

head -n 10 additional_view_data.txt

contig	categorical_1	categorical_2	text_layer_01	numerical	bars_main!A	bars_main!B	bars_main!C
backrest	b	y	nmwje	2.78	278	23	1
backward	b	x	bqmyujr psrd doefhi	2.49	249	52	2
backwind	b	y	hkfer lchpmzix	2.69	269	32	3
backyard	b	x	advoe bfkyhmg	2.05	205	96	4
bacteria	b	x	lqmcwn hywco	2.63	263	38	5
bacterin	b		vxqdmn	2.98	298	3	6
baetylus	b	x	fkgpydi owgyhfx xwlpj	2.19	219	82	7
bagpiped	b	y	ijmnur	2.12	212	89	8
balconet	b	y	ecizgs	2.89	289	12	9

Default run

head -n 10 additional_view_data.txt | anvi-script-as-markdown

which is rendered as,

contig categorical_1 categorical_2 text_layer_01 numerical bars_main!A bars_main!B bars_main!C
backrest b y nmwje 2.78 278 23 1
backward b x bqmyujr psrd doefhi 2.49 249 52 2
backwind b y hkfer lchpmzix 2.69 269 32 3
backyard b x advoe bfkyhmg 2.05 205 96 4
bacteria b x lqmcwn hywco 2.63 263 38 5
bacterin b   vxqdmn 2.98 298 3 6
baetylus b x fkgpydi owgyhfx xwlpj 2.19 219 82 7
bagpiped b y ijmnur 2.12 212 89 8
balconet b y ecizgs 2.89 289 12 9

Limit the number of lines shown

cat additional_view_data.txt | anvi-script-as-markdown --max-num-lines-to-show 10

which is rendered as,

contig categorical_1 categorical_2 text_layer_01 numerical bars_main!A bars_main!B bars_main!C
backrest b y nmwje 2.78 278 23 1
backward b x bqmyujr psrd doefhi 2.49 249 52 2
backwind b y hkfer lchpmzix 2.69 269 32 3
backyard b x advoe bfkyhmg 2.05 205 96 4
bacteria b x lqmcwn hywco 2.63 263 38 5
bacterin b   vxqdmn 2.98 298 3 6
baetylus b x fkgpydi owgyhfx xwlpj 2.19 219 82 7
bagpiped b y ijmnur 2.12 212 89 8
balconet b y ecizgs 2.89 289 12 9
(…) (…) (…) (…) (…) (…) (…) (…)

Code columns

cat additional_view_data.txt | anvi-script-as-markdown --max-num-lines-to-show 10 \
                                                       --code-column contig

which is rendered as,

contig categorical_1 categorical_2 text_layer_01 numerical bars_main!A bars_main!B bars_main!C
backrest b y nmwje 2.78 278 23 1
backward b x bqmyujr psrd doefhi 2.49 249 52 2
backwind b y hkfer lchpmzix 2.69 269 32 3
backyard b x advoe bfkyhmg 2.05 205 96 4
bacteria b x lqmcwn hywco 2.63 263 38 5
bacterin b   vxqdmn 2.98 298 3 6
baetylus b x fkgpydi owgyhfx xwlpj 2.19 219 82 7
bagpiped b y ijmnur 2.12 212 89 8
balconet b y ecizgs 2.89 289 12 9
(…) (…) (…) (…) (…) (…) (…) (…)

Exclude columns from the output

cat additional_view_data.txt | anvi-script-as-markdown --max-num-lines-to-show 10 \
                                                       --code-column contig \
                                                       --exclude-columns 'bars_main!A,bars_main!B,bars_main!C'

which is rendered as,

contig categorical_1 categorical_2 text_layer_01 numerical
backrest b y nmwje 2.78
backward b x bqmyujr psrd doefhi 2.49
backwind b y hkfer lchpmzix 2.69
backyard b x advoe bfkyhmg 2.05
bacteria b x lqmcwn hywco 2.63
bacterin b   vxqdmn 2.98
baetylus b x fkgpydi owgyhfx xwlpj 2.19
bagpiped b y ijmnur 2.12
balconet b y ecizgs 2.89
(…) (…) (…) (…) (…)

Edit this file to update this information.

Additional Resources

Are you aware of resources that may help users better understand the utility of this program? Please feel free to edit this file on GitHub. If you are not sure how to do that, find the __resources__ tag in this file to see an example.

Copyleft, The anvi'o Project