<filename>metawibele/tools/gene_abundance_indexRef.py
#!/usr/bin/env python

"""
MetaWIBELE: gene_abundance_indexRef module
Build reference index and annotation info file

Copyright (c) 2019 Harvard School of Public Health

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.
"""

import sys
import os
import re
import argparse

try:
	from metawibele import config
except ImportError:
	sys.exit("CRITICAL ERROR: Unable to find the MetaWIBELE python package." +
	         " Please check your install.")


#==============================================================
# index with bowtie2
#==============================================================
def bowtie2_index (ref_seq, base_name):
	config.logger.info (">>Running botwie2 to index reference...")
	# Index reference sequences
	config.logger.info ("Run command: " + "bowtie2-build " + ref_seq + " " + base_name + "\n")
	os.system("bowtie2-build " + ref_seq + " " + base_name)
# function bowtie2_index


#==============================================================
# Build SAF (simplified annotation format) info
#==============================================================
def extract_SAF_info_gene (seq_file, bed_out):	# use NR gene category as the reference 
	open_in = open(seq_file, "r")
	outs = {}
	myid = ""
	for line in open_in.readlines():
		line = line.strip()
		if not len(line):
			continue
		if re.search("^>", line):	# new gene
			mym = re.search(">([\S]+)", line)
			myid = mym.group(1)
			outs[myid] = 0
			continue
		else:
			outs[myid] = outs[myid] + len(line)
	# foreach line
	open_in.close()
	
	open_out = open(bed_out, "w")
	open_out.write("GeneID\tChr\tStart\tEnd\tStrand\n")
	for myid in sorted(outs.keys()):
		open_out.write(myid + "\t" + myid + "\t1\t" + str(outs[myid]) + "\t+\n")
	# foreach gene
# extract_SAF_info_gene


#==============================================================
###########  Main processing ############
#==============================================================
def main():
	
	### get arguments ###
	parser=argparse.ArgumentParser()
	parser.add_argument('-r', help='the reference file', required=True)
	parser.add_argument('-b', help='the reference index base name', required=True)
	parser.add_argument('-t', help='the type of reference, e.g. gene | contig', required=True)
	parser.add_argument('-o', help='the output file for simplified annotation file', required=True)
	values=parser.parse_args()

	config.logger.info ("### Start gene_abundance_indexRef step ####")
	
	### Index ###
	config.logger.info ("Bowtie2 index......starting")
	bowtie2_index (values.r, values.b) 
	config.logger.info ("Bowtie2 index......done")
	
	### Getting SAF ###
	config.logger.info ("Extract SAF info......starting")
	if values.t == "gene":
		extract_SAF_info_gene (values.r, values.o)
	config.logger.info ("Extract SAF info......done")

	config.logger.info ("### Finish gene_abundance_indexRef step ####")

# end: main

if __name__ == '__main__':
	main()

<filename>metawibele/tools/gene_abundance_indexRef.py
#!/usr/bin/env python

"""
MetaWIBELE: gene_abundance_indexRef module
Build reference index and annotation info file

Copyright (c) 2019 Harvard School of Public Health

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.
"""

import sys
import os
import re
import argparse

try:
	from metawibele import config
except ImportError:
	sys.exit("CRITICAL ERROR: Unable to find the MetaWIBELE python package." +
	         " Please check your install.")


#==============================================================
# index with bowtie2
#==============================================================
def bowtie2_index (ref_seq, base_name):
	config.logger.info (">>Running botwie2 to index reference...")
	# Index reference sequences
	config.logger.info ("Run command: " + "bowtie2-build " + ref_seq + " " + base_name + "\n")
	os.system("bowtie2-build " + ref_seq + " " + base_name)
# function bowtie2_index


#==============================================================
# Build SAF (simplified annotation format) info
#==============================================================
def extract_SAF_info_gene (seq_file, bed_out):	# use NR gene category as the reference 
	open_in = open(seq_file, "r")
	outs = {}
	myid = ""
	for line in open_in.readlines():
		line = line.strip()
		if not len(line):
			continue
		if re.search("^>", line):	# new gene
			mym = re.search(">([\S]+)", line)
			myid = mym.group(1)
			outs[myid] = 0
			continue
		else:
			outs[myid] = outs[myid] + len(line)
	# foreach line
	open_in.close()
	
	open_out = open(bed_out, "w")
	open_out.write("GeneID\tChr\tStart\tEnd\tStrand\n")
	for myid in sorted(outs.keys()):
		open_out.write(myid + "\t" + myid + "\t1\t" + str(outs[myid]) + "\t+\n")
	# foreach gene
# extract_SAF_info_gene


#==============================================================
###########  Main processing ############
#==============================================================
def main():
	
	### get arguments ###
	parser=argparse.ArgumentParser()
	parser.add_argument('-r', help='the reference file', required=True)
	parser.add_argument('-b', help='the reference index base name', required=True)
	parser.add_argument('-t', help='the type of reference, e.g. gene | contig', required=True)
	parser.add_argument('-o', help='the output file for simplified annotation file', required=True)
	values=parser.parse_args()

	config.logger.info ("### Start gene_abundance_indexRef step ####")
	
	### Index ###
	config.logger.info ("Bowtie2 index......starting")
	bowtie2_index (values.r, values.b) 
	config.logger.info ("Bowtie2 index......done")
	
	### Getting SAF ###
	config.logger.info ("Extract SAF info......starting")
	if values.t == "gene":
		extract_SAF_info_gene (values.r, values.o)
	config.logger.info ("Extract SAF info......done")

	config.logger.info ("### Finish gene_abundance_indexRef step ####")

# end: main

if __name__ == '__main__':
	main()

#!/usr/bin/env python MetaWIBELE: gene_abundance_indexRef module Build reference index and annotation info file  Copyright (c) 2019 Harvard School of Public Health  Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:  The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. #============================================================== # index with bowtie2 #============================================================== # Index reference sequences # function bowtie2_index #============================================================== # Build SAF (simplified annotation format) info #============================================================== # use NR gene category as the reference # new gene # foreach line # foreach gene # extract_SAF_info_gene #============================================================== ###########  Main processing ############ #============================================================== ### get arguments ### ## Start gene_abundance_indexRef step ####") ### Index ### ### Getting SAF ### ## Finish gene_abundance_indexRef step ####") # end: main