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added hmp-template options
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farchaab committed May 8, 2024
1 parent e9c8959 commit 9056e10
Showing 1 changed file with 46 additions and 31 deletions.
77 changes: 46 additions & 31 deletions mess/__main__.py
Original file line number Diff line number Diff line change
Expand Up @@ -26,13 +26,13 @@
click.rich_click.SHOW_METAVARS_COLUMN = False
click.rich_click.APPEND_METAVARS_HELP = True

mess_common_options = (
cmd_common_options = (
{
"name": "Common options",
"options": ["--input", "--output", "--threads", "--taxonkit", "--help"],
},
)
mess_download_options = (
cmd_dl_options = (
{
"name": "Download options",
"options": [
Expand All @@ -52,7 +52,7 @@
],
},
)
mess_simulate_options = (
cmd_sim_options = (
{
"name": "Common simulators options",
"options": [
Expand Down Expand Up @@ -98,13 +98,16 @@
],
},
)
mess_local_sim_options = (
local_sim_options = (
{
"name": "Local genomes options",
"options": ["--asm-summary", "--fasta"],
},
)

cmd_hmp_options = ({"name": "Hmp-template options", "options": ["--site", "--sample"]},)


skip_options = (
{
"name": "Skip options",
Expand All @@ -129,23 +132,32 @@

mess_run = [
options
for options in mess_common_options
+ mess_download_options
+ mess_simulate_options
for options in cmd_common_options
+ cmd_dl_options
+ cmd_sim_options
+ skip_options
+ snakemake_options
]

mess_download = [
options
for options in mess_common_options + mess_download_options + snakemake_options
options for options in cmd_common_options + cmd_dl_options + snakemake_options
]

mess_simulate = [
options
for options in mess_common_options
+ mess_local_sim_options
+ mess_simulate_options
for options in cmd_common_options
+ local_sim_options
+ cmd_sim_options
+ skip_options
+ snakemake_options
]

hmp_options = [
options
for options in cmd_hmp_options
+ cmd_common_options
+ cmd_dl_options
+ cmd_sim_options
+ skip_options
+ snakemake_options
]
Expand All @@ -161,9 +173,7 @@
"mess run": mess_run,
"mess download": mess_download,
"mess simulate": mess_simulate,
"mess hmp-template": [
{"name": "Hmp-template options", "options": ["--site", "--sample"]}
],
"mess hmp-template": hmp_options,
}

click.rich_click.COMMAND_GROUPS = {
Expand Down Expand Up @@ -199,11 +209,11 @@ def cli():
"""
\b
___ ___ _____ _____
| \/ | / ___/ ___|
| . . | ___\ `--.\ `--.
| |\/| |/ _ \`--. \`--. \\
| | | | __/\__/ /\__/ /
\_| |_/\___\____/\____/
| \\/ | / ___/ ___|
| . . | ___\\ `--.\\ `--.
| |\\/| |/ _ \\`--. \\`--. \\
| | | | __/\\__/ /\\__/ /
\\_| |_/\\___\\____/\\____/
\b
For more options:
Expand Down Expand Up @@ -232,37 +242,42 @@ def cli():
"""

help_download = """
\b
\n
Downloads genomes from taxons/accessions in input table(s)
\b
\n
EXAMPLES:
mess download -i [input] -o [output]
"""

help_simulate = """
\b
\n
Simulate reads from local fasta
\b
\n
EXAMPLES:
mess simulate -i [input] --tech [tech] --fasta [fasta-dir] -o [output]
or
\n
or
\n
mess simulate -i [input] --tech [tech] --asm-summary [asm-summary] -o [output]
"""
help_test = """
\b
\n
Test command to run mess from assembly download to read simulation
\b
\n
EXAMPLES:
mess test -o [output]
"""
help_hmp_templates = """
\b
\n
Command to download and simulate healthy human microbiome templates
\b
\n
EXAMPLES:
mess hmp_template --site gut -o gut
\n
mess hmp-template --site gut -o gut
\n
or
mess hmp_template --site buccal_mucosa --sample SRS013506 -o SRS013506
\n
mess hmp-template --site buccal_mucosa --sample SRS013506 -o SRS013506
"""


Expand Down

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