apollo_annotator_utilities.py

#!/usr/bin/env python3

name = 'apollo_annotator_utilities.py'
version = '0.3.0'
updated = '2023-06-24'

usage = f"""
NAME		{name}
VERSION		{version}
UPDATED		{updated}
SYNOPSIS	Interface between Apollo Arrow, Apollo, and the user that minimizes intermidiate steps.

REQUIRES	Apollo (https://github.com/GMOD/Apollo)
		python-apollo (https://github.com/galaxy-genome-annotation/python-apollo)
		$APOLLO enviromental variable (/path/to/Apollo_distribution)

------------------------------------------------------------------------------------------------------------------------
Add an Organism
------------------------------------------------------------------------------------------------------------------------

COMMAND		{name} --add_organism \\
		 -f 50507.fasta \\
		 -g Encephalitozoon \\
		 -s intestinalis \\
		 -i E_intestinalis_50507

-f (--fasta)	Assembly fasta file
-g (--genus)	Genus
-s (--species)	Species
-i (--id)	Organism ID

------------------------------------------------------------------------------------------------------------------------
Delete an Organism
------------------------------------------------------------------------------------------------------------------------

COMMAND		{name} --delete_organism \\
		 -i E_intestinalis_50507

-i (--id)	Organism ID

------------------------------------------------------------------------------------------------------------------------
Load Annotations
------------------------------------------------------------------------------------------------------------------------

COMMAND		{name} --load_annotations \\
		 -i E_intestinalis_50507 \\
		 -a proteins.long.gff

-i (--id)	Organism ID
-a (--annot)	Annotation gff file

------------------------------------------------------------------------------------------------------------------------
Remove Annotations
------------------------------------------------------------------------------------------------------------------------

COMMAND		{name} --remove_annotations \\
		 -i E_intestinalis_50507

-i (--id)	Organism ID

------------------------------------------------------------------------------------------------------------------------
Add a Reference
------------------------------------------------------------------------------------------------------------------------

COMMAND		{name} --add_reference \\
		 -r E_intestinalis_50506.blast.gff \\
		 -t match,match_part \\
		 -l E_intestinalis_50506 \\
		 -d -d /media/FatCat/apollo_data/E_intestinalis_50507

-r (--ref)	Reference gff file
-t (--type)	Reference type (CDS;match,match_part;tRNA)
-l (--label)	Reference label
-c (--color)	Track color

------------------------------------------------------------------------------------------------------------------------
Remove a Track
------------------------------------------------------------------------------------------------------------------------

COMMAND		{name} --remove_track \\
		 -l E_intestinalis_50506 \\
		 -d /media/FatCat/apollo_data/E_intestinalis_50507

-l (--label)	Track label

------------------------------------------------------------------------------------------------------------------------
Upload BAM file
------------------------------------------------------------------------------------------------------------------------

COMMAND		{name} --add_bam \\

-b (--bam)	BAM file
-l (--label)	BAM label
-t (--type)	Track type (alignment or coverage) [Default: alignment]
-n (--min_cov)	Minimum coverage (Applicable if --type coverage) [Default: 0]
-x (--max_cov)	Maximum coverage (Applicable if --type coverage) [Default: 50]

------------------------------------------------------------------------------------------------------------------------
"""

from sys import argv

if len(argv) < 2:
	print(f"\n{usage}")
	exit()

from argparse import ArgumentParser
from subprocess import run
from os import environ, makedirs
from os.path import isdir, dirname, isfile, basename
from shutil import copy

GetOptions = ArgumentParser()
group = GetOptions.add_mutually_exclusive_group(required=True)

group.add_argument("--add_organism",default=False,action='store_true')
group.add_argument("--delete_organism",default=False,action='store_true')

group.add_argument("--load_annotations",default=False,action='store_true')
group.add_argument("--remove_annotations",default=False,action='store_true')

group.add_argument("--add_reference",default=False,action='store_true')

group.add_argument("--remove_track",default=False,action='store_true')

group.add_argument("--add_bam",default=False,action='store_true')

GetOptions.add_argument("-i","--id",required=True)

args = GetOptions.parse_known_args()[0]

add_org = args.add_organism
del_org = args.delete_organism
load_annot = args.load_annotations
rem_annot = args.remove_annotations
add_ref = args.add_reference
rem_ref = args.remove_track
add_bam = args.add_bam
org_id = args.id

APOLLO = environ['APOLLO']

path = f"{APOLLO}/ORGANISMS/{org_id}"

if add_org:

	GetOptions = ArgumentParser()

	GetOptions.add_argument("-f","--fasta",required=True)
	GetOptions.add_argument("-g","--genus",required=True)
	GetOptions.add_argument("-s","--species",required=True)

	args = GetOptions.parse_known_args()[0]

	fasta = args.fasta
	genus = args.genus
	species = args.species

	if not isdir(path):
		makedirs(path)

	run([f"{APOLLO}/web-app/jbrowse/bin/prepare-refseqs.pl","--fasta",fasta,"--out",path])

	run(["arrow","organisms","add_organism","--genus",genus,"--species",species,org_id,path])

if del_org:

	GetOptions = ArgumentParser()

	run(["arrow","organisms","delete_features",org_id])
	run(["arrow","organisms","delete_organism",org_id])

if load_annot:

	GetOptions = ArgumentParser()

	GetOptions.add_argument("-a","--annot",required=True)

	args = GetOptions.parse_known_args()[0]

	annot = args.annot

	run(['arrow','annotations','load_gff3',org_id,annot])

if rem_annot:

	run(["arrow","organisms","delete_features",org_id])

if add_ref:

	GetOptions = ArgumentParser()

	GetOptions.add_argument("-r","--ref",required=True)
	GetOptions.add_argument("-t","--type",required=True)
	GetOptions.add_argument("-l","--label",required=True)
	GetOptions.add_argument("-c","--color",default='blue')

	args = GetOptions.parse_known_args()[0]

	ref = args.ref
	type = args.type
	label = args.label
	color = args.color

	run([f'{APOLLO}/web-app/jbrowse/bin/flatfile-to-json.pl','--gff',ref,'--type',type,'--trackLabel',label,'--out',path])#,'--subfeatureClasses',f"{{\"match_part\":\"{color}\"}}"])

if rem_ref:

	GetOptions = ArgumentParser()

	GetOptions.add_argument("-l","--label",required=True)

	args = GetOptions.parse_known_args()[0]

	label = args.label

	run([f"{APOLLO}/web-app/jbrowse/bin/remove-track.pl",'--trackLabel',label,'--delete','--dir',path])

if add_bam:

	GetOptions = ArgumentParser()
	
	GetOptions.add_argument("-b","--bam",required=True)
	GetOptions.add_argument("-l","--label",required=True)
	GetOptions.add_argument("-c","--coverage",default=False,action='store_true')

	args = GetOptions.parse_known_args()[0]
	
	bam = args.bam
	label = args.label
	coverage = args.coverage

	bam_name = basename(bam)
	bam_path = dirname(bam)
	if bam_path == "":
		bam_path = "."

	
	if not isfile(f"{bam_path}/{bam_name}.bai"):
		print(f"  [E] Could not find the index file ({bam_name}.bai) for the provided bam file ({bam})")

	copy(bam,f"{path}/")
	copy(f"{bam_path}/{bam_name}.bai",f"{path}/")

	if coverage:
	
		GetOptions.add_argument("-n","--minimum",type=int,default=0)
		GetOptions.add_argument("-x","--maximum",type=int,default=500)

		args = GetOptions.parse_known_args()[0]

		minimum = args.minimum
		maximum = args.maximum
		
		run([f"{APOLLO}/web-app/jbrowse/bin/add-bam-track.pl",
				"--in", f"{path}/trackList.json",
				"--bam_url", f"{bam_name}",
				"--label", f"{label}",
				"--coverage",
				"--min_score", f"{minimum}",
				"--max_score", f"{maximum}"])

	else:

		run([f"{APOLLO}/web-app/jbrowse/bin/add-bam-track.pl",
				"--in", f"{path}/trackList.json",
				"--bam_url", f"{bam_name}",
				"--label", f"{label}"])