Command Line Interface¶
Commands can be invoked via the command line using mieaa SUBCOMMAND.Help and options for all subcommands can be view with mieaa SUBCOMMAND -h
Supported Species
- hsa - Homo sapiens
- mmu - Mus musculus
- rno - Rattus norvegicus
- ath - Arabidopsis thaliana
- bta - Bos taurus
- cel - Caenorhabditis elegans
- dme - Drosophila melanogaster
- dre - Danio rerio
- gga - Gallus gallus
- ssc - Sus scrofa
Specifying precursorsFor subcommands where you need to specify precursor or mature, mature is always assumed unless the --precursor (-p) flag is set.
Mutually exclusive optionsMost subcommands require one of --mirna-set (-m) or --mirna-set-file (-M) to be specified.
mieaa SUBCOMMAND --mirna-set MIRNA [MIRNA ...]mieaa SUBCOMMAND --mirna-set MIRNAS_STRINGmieaa SUBCOMMAND --mirna-set-file MIRNA_FILE
Subcommands¶
to_precursor¶
Convert miRNA -> precursor
usage: miEAA to_precursor [-h] [-v] [-m MIRNA_SET [MIRNA_SET ...]]
[-M MIRNA_SET_FILE] [-p] [-o OUTFILE]
[--oneline | --newline | --tabsep] [-u]
optional arguments:
-h, --help show this help message and exit
-v, --verbose Always print results to stdout
-p, --precursor, --precursors
Use if running on a set of precursors as opposed to
miRNAs
-o OUTFILE, --outfile OUTFILE
Save results to provided file
--oneline Output style: Multi-mapped ids are separated by a
semicolon (default)
--newline Output style: Multi-mapped ids are separated by a
newline
--tabsep Output style: Tab-separated `original converted` ids
-u, --unique Only output ids that map uniquely
mutually exclusive required arguments:
either a set or file must be provided
-m MIRNA_SET [MIRNA_SET ...], --mirna-set MIRNA_SET [MIRNA_SET ...]
miRNA/precursor target set
-M MIRNA_SET_FILE, --mirna-set-file MIRNA_SET_FILE
Specify miRNA/precursor target set via file
Examples:
$ mieaa to_precursor -m hsa-miR-20b-5p hsa-miR-144-5p --tabsep --unique
$ mieaa to_precursor -m 'hsa-miR-20b-5p,hsa-miR-144-5p' --newline -o precursors.txt
$ mieaa to_precursor -M mirnas.txt --outfile precursors.txt
to_mirna¶
Converting between precursor -> miRNA
usage: miEAA to_mirna [-h] [-v] [-m MIRNA_SET [MIRNA_SET ...]]
[-M MIRNA_SET_FILE] [-p] [-o OUTFILE]
[--oneline | --newline | --tabsep] [-u]
optional arguments:
-h, --help show this help message and exit
-v, --verbose Always print results to stdout
-p, --precursor, --precursors
Use if running on a set of precursors as opposed to
miRNAs
-o OUTFILE, --outfile OUTFILE
Save results to provided file
--oneline Output style: Multi-mapped ids are separated by a
semicolon (default)
--newline Output style: Multi-mapped ids are separated by a
newline
--tabsep Output style: Tab-separated `original converted` ids
-u, --unique Only output ids that map uniquely
mutually exclusive required arguments:
either a set or file must be provided
-m MIRNA_SET [MIRNA_SET ...], --mirna-set MIRNA_SET [MIRNA_SET ...]
miRNA/precursor target set
-M MIRNA_SET_FILE, --mirna-set-file MIRNA_SET_FILE
Specify miRNA/precursor target set via file
Examples:
$ mieaa to_mirna -m hsa-mir-20b hsa-mir-144 --tabsep --unique
$ mieaa to_mirna -m 'hsa-mir-20b,hsa-mir-144' --newline -o mirnas.txt
$ mieaa to_mirna -M precursors.txt --outfile mirnas.txt
convert_mirbase¶
Converting miRBase version
usage: miEAA convert_mirbase [-h] [-v] [-m MIRNA_SET [MIRNA_SET ...]]
[-M MIRNA_SET_FILE] [-p] [-o OUTFILE]
[--oneline | --newline | --tabsep] [--to TO]
FROM
positional arguments:
FROM mirBase version to convert miRNAs/precursors from
optional arguments:
-h, --help show this help message and exit
-v, --verbose Always print results to stdout
-p, --precursor, --precursors
Use if running on a set of precursors as opposed to
miRNAs
-o OUTFILE, --outfile OUTFILE
Save results to provided file
--oneline Output style: Multi-mapped ids are separated by a
semicolon (default)
--newline Output style: Multi-mapped ids are separated by a
newline
--tabsep Output style: Tab-separated `original converted` ids
--to TO mirBase version to convert miRNAs/precursors from
(default=22)
mutually exclusive required arguments:
either a set or file must be provided
-m MIRNA_SET [MIRNA_SET ...], --mirna-set MIRNA_SET [MIRNA_SET ...]
miRNA/precursor target set
-M MIRNA_SET_FILE, --mirna-set-file MIRNA_SET_FILE
Specify miRNA/precursor target set via file
Examples:
$ mieaa convert_mirbase 16 -m hsa-miR-642b,hsa-miR-550b
$ mieaa convert_mirbase 16 --to 22 -m hsa-miR-642b hsa-miR-550b
$ mieaa convert_mirbase 16 -M version_16.txt -o version_22.txt
gsea¶
Gene Set Enrichment Analysis (GSEA)
usage: miEAA gsea [-h] [-v] [-m MIRNA_SET [MIRNA_SET ...]] [-M MIRNA_SET_FILE]
[-p] [-o OUTFILE] [-x] [-c CATEGORIES [CATEGORIES ...]]
[-C CATEGORIES_FILE] [-t THRESHOLD] [-s SIGNIFICANCE] [-g]
[-a {none,fdr,bonferroni,BY,holm,hochberg,hommel}]
[--csv | --json]
{hsa,mmu,rno,ath,bta,cel,dme,dre,gga,ssc}
positional arguments:
{hsa,mmu,rno,ath,bta,cel,dme,dre,gga,ssc}
Species
optional arguments:
-h, --help show this help message and exit
-v, --verbose Always print results to stdout
-p, --precursor, --precursors
Use if running on a set of precursors as opposed to
miRNAs
-o OUTFILE, --outfile OUTFILE
Save results to provided file
-x, --no-results Do not monitor progress or obtain results. Can
retrieve later using Job ID.
-t THRESHOLD, --threshold THRESHOLD
Filter out subcategories that contain less than this
many miRNAs/precursors (default=2)
-s SIGNIFICANCE, --significance SIGNIFICANCE, --alpha SIGNIFICANCE
Significance level (default=0.05)
-g, --group-adjust Adjust p-values over aggregated groups (By default
each group is adjusted independently)
-a {none,fdr,bonferroni,BY,holm,hochberg,hommel}, --adjustment {none,fdr,bonferroni,BY,holm,hochberg,hommel}
p-value adjustment method (default='fdr')
--csv Store results in output file in csv format (default)
--json Store results in output file in json format (default
is csv)
mutually exclusive required arguments:
either a set or file must be provided
-m MIRNA_SET [MIRNA_SET ...], --mirna-set MIRNA_SET [MIRNA_SET ...]
miRNA/precursor target set
-M MIRNA_SET_FILE, --mirna-set-file MIRNA_SET_FILE
Specify miRNA/precursor target set via file
mutually exclusive optional arguments:
either a set or file may be provided
-c CATEGORIES [CATEGORIES ...], --categories CATEGORIES [CATEGORIES ...]
Set of categories to include in analysis, can include
`all`, `default`, `expert` or specific categories
-C CATEGORIES_FILE, --categories-file CATEGORIES_FILE
File specifying categories to include in analysis
Examples:
$ mieaa gsea hsa --precursors -M precursors.txt -C categories.txt -o results.csv
$ mieaa gsea hsa -p -M precursors.txt -c HMDD MNDR > results.csv
$ mieaa gsea mmu -M mirnas.txt -C categories.txt --adjustment none
$ mieaa gsea rno -M mirnas.txt -C categories.txt -a bonferroni --json -o results.json
ora¶
Over-representation Analysis (ORA)
usage: miEAA ora [-h] [-v] [-m MIRNA_SET [MIRNA_SET ...]] [-M MIRNA_SET_FILE]
[-p] [-o OUTFILE] [-x] [-c CATEGORIES [CATEGORIES ...]]
[-C CATEGORIES_FILE] [-t THRESHOLD] [-s SIGNIFICANCE] [-g]
[-a {none,fdr,bonferroni,BY,holm,hochberg,hommel}]
[--csv | --json] [-r REFERENCE_SET [REFERENCE_SET ...]]
[-R REFERENCE_SET_FILE]
{hsa,mmu,rno,ath,bta,cel,dme,dre,gga,ssc}
positional arguments:
{hsa,mmu,rno,ath,bta,cel,dme,dre,gga,ssc}
Species
optional arguments:
-h, --help show this help message and exit
-v, --verbose Always print results to stdout
-p, --precursor, --precursors
Use if running on a set of precursors as opposed to
miRNAs
-o OUTFILE, --outfile OUTFILE
Save results to provided file
-x, --no-results Do not monitor progress or obtain results. Can
retrieve later using Job ID.
-t THRESHOLD, --threshold THRESHOLD
Filter out subcategories that contain less than this
many miRNAs/precursors (default=2)
-s SIGNIFICANCE, --significance SIGNIFICANCE, --alpha SIGNIFICANCE
Significance level (default=0.05)
-g, --group-adjust Adjust p-values over aggregated groups (By default
each group is adjusted independently)
-a {none,fdr,bonferroni,BY,holm,hochberg,hommel}, --adjustment {none,fdr,bonferroni,BY,holm,hochberg,hommel}
p-value adjustment method (default='fdr')
--csv Store results in output file in csv format (default)
--json Store results in output file in json format (default
is csv)
mutually exclusive required arguments:
either a set or file must be provided
-m MIRNA_SET [MIRNA_SET ...], --mirna-set MIRNA_SET [MIRNA_SET ...]
miRNA/precursor target set
-M MIRNA_SET_FILE, --mirna-set-file MIRNA_SET_FILE
Specify miRNA/precursor target set via file
mutually exclusive optional arguments:
either a set or file may be provided
-c CATEGORIES [CATEGORIES ...], --categories CATEGORIES [CATEGORIES ...]
Set of categories to include in analysis, can include
`all`, `default`, `expert` or specific categories
-C CATEGORIES_FILE, --categories-file CATEGORIES_FILE
File specifying categories to include in analysis
mutually exclusive optional arguments:
either a set or file may be provided
-r REFERENCE_SET [REFERENCE_SET ...], --reference-set REFERENCE_SET [REFERENCE_SET ...]
(Optional) Set of background miRNAs/precursors
-R REFERENCE_SET_FILE, --reference-set-file REFERENCE_SET_FILE
(Optional) File specifying background
miRNAs/precursors
Examples:
$ mieaa ora hsa --precursors -M precursors.txt -C categories.txt > results.csv
$ mieaa ora hsa -p -M precursors.txt -c HMDD MNDR -o results.csv
$ mieaa ora hsa -p -M precursors.txt -C categories.txt -R reference.txt
$ mieaa ora mmu -M mirnas.txt -C categories.txt --adjustment none
$ mieaa ora rno -M mirnas.txt -C categories.txt -a bonferroni --json -o results.json
open¶
Open the specified mieaa web tool page in browser
usage: miEAA open [-h] [-v] [-j JOB_ID] {input,progress,results}
positional arguments:
{input,progress,results}
Open MiEAA interface in browser
optional arguments:
-h, --help show this help message and exit
-v, --verbose Always print results to stdout
-j JOB_ID, --jobid JOB_ID
Job ID
Examples:
$ mieaa open input
$ mieaa open progress -j 31b41542-7856-40be-91b2-fd6afe28fa0b
$ mieaa open results --jobid 31b41542-7856-40be-91b2-fd6afe28fa0b