Skip to content

Commit

Permalink
Patch: make the erv family table optional
Browse files Browse the repository at this point in the history
  • Loading branch information
@skchronicles
skchronicles committed May 21, 2024
1 parent 980f277 commit 7aa76fa
Show file tree
Hide file tree
Showing 3 changed files with 64 additions and 21 deletions.
2 changes: 1 addition & 1 deletion VERSION
View file
Original file line number Diff line number Diff line change
@@ -1 +1 @@
0.1.0
0.1.1
74 changes: 56 additions & 18 deletions ervx
View file
Original file line number Diff line number Diff line change
Expand Up @@ -23,11 +23,11 @@ import argparse # potential python3 3rd party package, added in python/3.5

# Pipeline Metadata and globals
__author__ = 'Skyler Kuhn'
__version__ = 'v0.1.0'
__version__ = 'v0.1.1'
__email__ = '[email protected]'
__home__ = os.path.dirname(os.path.abspath(__file__))
_name = os.path.basename(sys.argv[0])
_description = 'a highly-reproducible RNA-seq pipeline'
_description = 'a highly-reproducible ERV RNA-seq pipeline'


class Colors():
Expand Down Expand Up @@ -136,7 +136,7 @@ def permissions(parser, filename, *args, **kwargs):
If file exists and user can read from file
"""
if not exists(filename):
parser.error("File '{}' does not exists! Failed to provide vaild input.".format(filename))
parser.error("File '{}' does not exist! Failed to provide vaild input.".format(filename))

if not os.access(filename, *args, **kwargs):
parser.error("File '{}' exists, but cannot read file due to permissions!".format(filename))
Expand Down Expand Up @@ -985,6 +985,13 @@ def _configure(sub_args, filename, git_repo):
# Resolves if an image needs to be pulled from an OCI registry or
# a local SIF generated from the ervx cache subcommand exists
sif_config = image_cache(sub_args, {})

if sub_args.ervs_fam_table:
ervs_fam_table = os.path.join(sub_args.output, os.path.basename(sub_args.ervs_fam_table))
else:
# ervx family annotation table is not provided,
# set default value to empty string
ervs_fam_table = ''
# Creates config file /path/to/output/config/build.yml
with open(filename, 'w') as fh:
fh.write('GENOME: "{}"\n'.format(sub_args.ref_name))
Expand All @@ -998,7 +1005,7 @@ def _configure(sub_args, filename, git_repo):
fh.write('TMP_DIR: "{}"\n'.format(sub_args.tmp_dir))
fh.write('SHARED_RESOURCES: "{}"\n'.format(sub_args.shared_resources))
fh.write('TELESCOPE_ERVS_GTF: "{}"\n'.format(os.path.join(sub_args.output, os.path.basename(sub_args.ervs_gtf))))
fh.write('ERVS_FAMILY_ANNOTATION_TABLE: "{}"\n'.format(os.path.join(sub_args.output, os.path.basename(sub_args.ervs_fam_table))))
fh.write('ERVS_FAMILY_ANNOTATION_TABLE: "{}"\n'.format(ervs_fam_table))
fh.write('MODE: "{}"\n'.format(sub_args.mode))
fh.write('READLENGTHS:\n')
read_lengths = ['50', '75', '100', '125', '150']
Expand Down Expand Up @@ -1040,7 +1047,13 @@ def configure_build(sub_args, git_repo, output_path):
required_resources = ['workflow', 'resources', 'config']
_cp_r_safe_(source = git_repo, target = output_path, resources = required_resources)
_configure(sub_args = sub_args, filename = os.path.join(output_path, 'config', 'build.yml'), git_repo = git_repo)
additional_bind_paths = _sym_refs(input_data = [sub_args.ref_fa, sub_args.ref_gtf, sub_args.ervs_gtf, sub_args.ervs_fam_table], target = output_path, make_copy = True)

sym_link = [sub_args.ref_fa, sub_args.ref_gtf, sub_args.ervs_gtf]
if sub_args.ervs_fam_table:
# ervx family annotation table is not provided,
# set default value to empty string
sym_link = [sub_args.ref_fa, sub_args.ref_gtf, sub_args.ervs_gtf, sub_args.ervs_fam_table]
additional_bind_paths = _sym_refs(input_data = sym_link, target = output_path, make_copy = True)

return additional_bind_paths

Expand All @@ -1066,7 +1079,7 @@ def build(sub_args):
git_repo = git_repo,
output_path = output_path
)

# Add any additional bindpaths
if sub_args.shared_resources:
# Check if shared resource path
Expand Down Expand Up @@ -1257,7 +1270,7 @@ def parsed_arguments(name, description):
{1}{2}Synopsis:{4}
$ {0} run [--help] \\
[--prokaryote] [--small-rna] [--star-2-pass-basic] \\
[--dry-run] [--mode {{slurm, local}}] \\
[--dry-run] [--mode {{slurm, uge, local}}] \\
[--shared-resources SHARED_RESOURCES] \\
[--singularity-cache SINGULARITY_CACHE] \\
[--sif-cache SIF_CACHE] \\
Expand Down Expand Up @@ -1349,7 +1362,7 @@ def parsed_arguments(name, description):
the pipeline remain or will be run.
Example: --dry-run
--mode {{slurm,uge,local}}
--mode {{slurm, uge, local}}
Method of execution. Defines the mode of execution.
Vaild options for this mode include: local or slurm.
Additional modes of exection are coming soon, default:
Expand Down Expand Up @@ -1633,15 +1646,16 @@ def parsed_arguments(name, description):
{1}{2}Synopsis:{4}
$ {0} build [--help] \\
[--shared-resources SHARED_RESOURCES] [--small-genome] \\
[--dry-run] [--singularity-cache SINGULARITY_CACHE] \\
[--dry-run] [--mode {{slurm, uge, local}}] \\
[--singularity-cache SINGULARITY_CACHE] \\
[--sif-cache SIF_CACHE] [--tmp-dir TMP_DIR] \\
[--ervs-fam-table ERVS_FAM_TABLE] \\
--ref-fa REF_FA \\
--ref-name REF_NAME \\
--ref-gtf REF_GTF \\
--gtf-ver GTF_VER \\
--output OUTPUT \\
--ervs-gtf ERVS_GTF \\
--ervs-fam-table ERVS_FAM_TABLE
--ervs-gtf ERVS_GTF
{1}{2}Description:{4}
Builds the reference files for the RNA-seek pipeline from a genomic FASTA
Expand Down Expand Up @@ -1691,16 +1705,16 @@ def parsed_arguments(name, description):
also known as Endogenous Retroviruses (ERVS). Such GTF files
can be downloaded from the following source
http://geve.med.u-tokai.ac.jp/download/ . Typically these GTFs
need to be reformatted using ./resources/clean_gtf.py .
need to be reformatted using "./resources/clean_gtf.py".
Example: --ervs-gtf Mmus38.geve.v1.polished.gtf
{1}{2}Build options:{4}
--ervs-fam-table ERVS_FAM_TABLE
Annotation CSV file for transposable elements. This file is used
in the telescope rule to assign family to ervs, and was downloaded
from http://geve.med.u-tokai.ac.jp/download/ .
Example: --ervs-fam-table Mmus38.csv
{1}{2}Build options:{4}
Example: --ervs-fam-table Mmus38.csv
--shared-resources SHARED_RESOURCES
Path to download shared resources. The pipeline uses a
set of shared reference files that can be re-used across
Expand All @@ -1727,6 +1741,28 @@ def parsed_arguments(name, description):
--dry-run Does not execute anything. Only displays what steps in
the pipeline remain or will be run.
Example: --dry-run
--mode {{slurm,uge,local}}
Method of execution. Defines the mode of execution.
Vaild options for this mode include: local or slurm.
Additional modes of exection are coming soon, default:
slurm.
Here is a brief description of each mode:
• local: uses local method of execution. local runs
will run serially on compute instance. This is useful
for testing, debugging, or when a users does not have
access to a high performance computing environment.
If this option is not provided, it will default to a
slurm mode of execution.
• slurm: uses slurm execution backend. This method
will submit jobs to a cluster using sbatch. It is
recommended running the pipeline in this mode as it
will be significantly faster.
Example: --mode slurm
• uge: uses UGE execution backend. This method will
submit jobs to a cluster using qsub. Please set the
mode to uge when running the pipeline on LOCUS.
Example: --mode uge
--singularity-cache SINGULARITY_CACHE
Overrides the $SINGULARITY_CACHEDIR variable. Images
Expand Down Expand Up @@ -1869,7 +1905,8 @@ def parsed_arguments(name, description):
'--ervs-fam-table',
# Check if the file exists and if it is readable
type = lambda file: permissions(parser, file, os.R_OK),
required = True,
required = False,
default = None,
help = argparse.SUPPRESS
)

Expand All @@ -1879,8 +1916,9 @@ def parsed_arguments(name, description):
subparser_build.add_argument(
'--mode',
type = str,
required = True,
required = False,
choices = ['slurm', 'uge', 'local'],
default = 'slurm',
help = argparse.SUPPRESS
)

Expand Down
9 changes: 7 additions & 2 deletions workflow/rules/build.smk
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
from os.path import join, basename
import json

# Helper Functions
def allocated(resource, rule, lookup, default="__default__"):
Expand Down Expand Up @@ -73,8 +74,10 @@ OUTDIR=config["OUTDIR"]
SCRIPTSDIR=config["SCRIPTSDIR"]
tmpdir=config["TMP_DIR"]
TELESCOPE_ERVS_GTF=config["TELESCOPE_ERVS_GTF"]
ERVS_FAMILY_ANNOTATION_TABLE=config["ERVS_FAMILY_ANNOTATION_TABLE"]
MODE=config["MODE"]
ERVS_FAMILY_ANNOTATION_TABLE=config["ERVS_FAMILY_ANNOTATION_TABLE"] \
if config["ERVS_FAMILY_ANNOTATION_TABLE"] and config["ERVS_FAMILY_ANNOTATION_TABLE"] !='None' \
else []
workdir:OUTDIR

# Read in resource information,
Expand Down Expand Up @@ -682,6 +685,8 @@ rule jsonmaker:
rname='bl_jsonmaker',
workdir=OUTDIR,
genome=GENOME,
ervs_fam_table=lambda _: ERVS_FAMILY_ANNOTATION_TABLE \
if ERVS_FAMILY_ANNOTATION_TABLE else '',
run:
import json
outdir=params.workdir
Expand All @@ -707,7 +712,7 @@ rule jsonmaker:
refdict["references"]["rnaseq"]["ORGANISM"] = wildcards.genome
refdict["references"]["rnaseq"]["TINREF"] = outdir+"transcripts.protein_coding_only.bed12"
refdict["references"]["rnaseq"]["TELESCOPE_ERVS_GTF"] = input.ervs_gtf
refdict["references"]["rnaseq"]["ERVS_FAMILY_ANNOTATION_TABLE"]=input.ervs_fam_table
refdict["references"]["rnaseq"]["ERVS_FAMILY_ANNOTATION_TABLE"]=params.ervs_fam_table

# Try to infer which Arriba reference files to add a user defined reference genome
if 'hg19' in params.genome.lower() or \
Expand Down

0 comments on commit 7aa76fa

Please sign in to comment.