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process_CHiC.py
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process_CHiC.py
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#!/usr/bin/env python
"""
.. See the NOTICE file distributed with this work for additional information
regarding copyright ownership.
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
"""
from __future__ import print_function
#Required for ReadTheDocs
import argparse
from basic_modules.workflow import Workflow
from utils import logger
from CHiC.tool.rmap_tool import makeRmapFile
from CHiC.tool.makeBaitmap import makeBaitmapTool
from CHiC.tool.makeDesignFiles import makeDesignFilesTool
from CHiC.tool.hicup_tool import hicup
from CHiC.tool.bam2chicago_tool import bam2chicagoTool
from CHiC.tool.run_chicago import ChicagoTool
################################################
class process_CHiC(Workflow):
"""
This class output chromatin contacts from capture HiC from
pair fastq reads, baits and RE
"""
def __init__(self, configuration=None):
"""
initiate the class
Parameters
----------
configuration: dict
"RE_truncater" : str - format A^AGCT (Truncater),
"RE" : {"HindIII" : 'A|AGCTT'},
"""
logger.info("Initialising process_chicago_CHiC")
if configuration is None:
configuration = {}
self.configuration.update(configuration)
def run(self, input_files, metadata, output_files):
"""
This is the main function that run the tools to create
.baitmap.
Parameters
----------
input_files: dict
fastq1: str
fastq2: str
genome_fa: str
genome in fasta format
input_metadata: dict
input metadata
output_files: dict
Returns
-------
output_files
output_metadata
"""
self.configuration["bowtie2_fasta_input"] = "True"
if "genome_fa_public" in input_files:
input_files["genome_fa"] = input_files.pop("genome_fa_public")
metadata["genome_fa"] = metadata.pop("genome_fa_public")
input_files["bowtie_gen_idx"] = input_files.pop("bowtie_gen_idx_public")
metadata["bowtie_gen_idx"] = metadata.pop("bowtie_gen_idx_public")
#call hicup
try:
hicup_caller = hicup(self.configuration)
output_files_hicup, output_metadata_hicup = hicup_caller.run(
{
"genome_fa": input_files["genome_fa"],
"fastq1": input_files["fastq1"],
"fastq2" : input_files["fastq2"],
"bowtie_gen_idx": input_files["bowtie_gen_idx"]
},
{
"genome_fa": metadata["genome_fa"],
"fastq1": metadata["fastq1"],
"fastq2": metadata["fastq2"]
},
{
"hicup_outdir_tar" : output_files["hicup_outdir_tar"]
}
)
logger.info("hicup runned succesfully =)")
except IOError:
logger.fatal("hicup failed to run succesfully =(")
#call ramp
try:
rmap_caller = makeRmapFile(self.configuration)
output_files_rmap, output_metadata_rmap = rmap_caller.run(
{
"genome_fa" : input_files["genome_fa"]
},
{
"genome_fa" : metadata["genome_fa"]
},
{
}
)
logger.info(".rmap file generated succesfully")
except IOError:
logger.fatal("rmap_tool failed to generate .rmap file")
#produce Baitmap file
try:
baitmap_caller = makeBaitmapTool(self.configuration)
output_files_baitmap, output_metadata_baitmap = baitmap_caller.run(
{
"bowtie_gen_idx" : input_files["bowtie_gen_idx"],
"probes_fa": input_files["probes_fa"],
"genome_fa" : input_files["genome_fa"],
},
{
"genome_fa" : metadata["genome_fa"],
"probes_fa" : metadata["probes_fa"],
"bowtie_gen_idx": metadata["bowtie_gen_idx"]
},
{
}
)
logger.info(".baitmap file generated succesfully")
except IOError:
logger.fatal("generate_CHiCAGO_baitmap failed to generate .baitmap file")
try:
design_caller = makeDesignFilesTool(self.configuration)
design_out, design_meta = design_caller.run(
{
},
{
},
{
}
)
logger.info("design files succesfully generated =)")
except IOError:
logger.fatal("process_makeDesign failed to" +
"generate design files")
try:
bam2chicago_caller = bam2chicagoTool(self.configuration)
output_files_bam2chicago, output_metadata_bam2chicago = bam2chicago_caller.run(
input_files, metadata, output_files
)
logger.info("bam2chicago_tool succesfully generate chinput files =)")
except IOError:
logger.fatal("process_bam2chicago failed to generate .chinput files")
try:
chicago_caller = ChicagoTool(self.configuration)
output_files_chicago, output_metadata_chicago = chicago_caller.run(
input_files, metadata, output_files)
except IOError:
logger.info("chicago failed to generate output files =(")
output_files = {}
output_metadata = {}
output_files.update(output_files_rmap)
output_files.update(output_files_baitmap)
output_files.update(design_out)
output_files.update(output_files_hicup)
output_files.update(output_files_bam2chicago)
output_files.update(output_files_chicago)
output_metadata.update(output_metadata_rmap)
output_metadata.update(output_metadata_baitmap)
output_metadata.update(design_meta)
output_metadata.update(output_metadata_hicup)
output_metadata.update(output_metadata_bam2chicago)
output_metadata.update(output_metadata_chicago)
return output_files, output_metadata
#############################################################
def main_json(config, in_metadata, out_metadata):
"""
Alternative main function
This function launch the app using the configuration written
in two json files: config_process_rmapBaitmap.json and
input_process_rmapBaitmap.json
"""
#Instantiate and lauch the app
print("1. Instantiate and launch the App")
from apps.jsonapp import JSONApp
app = JSONApp()
results = app.launch(process_CHiC,
config,
in_metadata,
out_metadata)
#2. The App has finished
print("2. Execution finished: see " + out_metadata)
print(results)
return results
#########################################################################
if __name__ == "__main__":
#set up the command line parameters
PARSER = argparse.ArgumentParser(
description="Pipeline to generate .baitmap file")
PARSER.add_argument("--config", help="Configuration file")
PARSER.add_argument(
"--in_metadata", help="Location of metadata file")
PARSER.add_argument(
"--out_metadata", help="Location of output metadata file")
PARSER.add_argument(
"--local", action="store_const", const=True, default=False)
#Get matching parameters from the command line
ARGS = PARSER.parse_args()
CONFIG = ARGS.config
IN_METADATA = ARGS.in_metadata
OUT_METADATA = ARGS.out_metadata
LOCAL = ARGS.local
if LOCAL:
import sys
sys._run_from_cmdl = True # pylint: disable=protected-access
RESULTS = main_json(CONFIG, IN_METADATA, OUT_METADATA)
print(RESULTS)