biodatatools 0.0.1__tar.gz

biodatatools-0.0.1/PKG-INFO

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+Metadata-Version: 2.1
+Name: biodatatools
+Version: 0.0.1
+Summary: A python package with useful biological data processing methods
+Home-page: https://github.com/aldenleung/biodatatools/
+Author: Alden Leung
+Author-email: alden.leung@gmail.com
+Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
+Description-Content-Type: text/markdown
+
+# biodatatools
+
+A python package that provides multiple useful functions for biological data processing. 
+Many functions from his package require external programs installed.

biodatatools-0.0.1/README.md

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+# biodatatools
+
+A python package that provides multiple useful functions for biological data processing. 
+Many functions from his package require external programs installed.

biodatatools-0.0.1/biodatatools/__init__.py

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+import sys
+import simplevc
+simplevc.register(sys.modules[__name__], "0.0.1")
+
+import tempfile
+import os
+import subprocess
+import shutil
+
+import pysam
+import pyBigWig
+
+from biodata.baseio import BaseWriter
+from biodata.bed import BEDPE
+from biodata.delimited import DelimitedReader, DelimitedWriter
+
+from commonhelper import convert_to_bool, safe_inverse_zip, nested_default_dict
+from mphelper import ProcessWrapPool
+	
+	
+	
+
+def check_binaries_validity(*binary_names): # Change to decorator in the future
+	missing_binary_names = [binary_name for binary_name in binary_names if shutil.which(binary_name) is None]
+	if len(missing_binary_names) > 0:
+		raise Exception("The following binaries are not found: " + ",".join(binary_names))
+	
+def bash_command(cmd):
+	p = subprocess.run(cmd, shell=True, executable='/bin/bash')
+	if p.returncode != 0:
+		raise Exception("Bash command fails: " + cmd)
+	
+	
+@vt(
+	description="A wrapper to bedGraphToBigWig", helps=dict(
+		i="Input bedgraph file", g="chrom size file", o="output bigwig file",
+		autosort="Perform sorting on bedgraph file before running bedGraphToBigWig",
+		filter_chr="Remove chromosomes in bedgraph file that are not present in chrom.sizes file", 
+		nthread="Number of threads used in sorting")
+)
+@vc
+def _convert_bedgraph_to_bigwig_20240423(i:str, g:str, o:str, autosort:convert_to_bool=False, filter_chr:convert_to_bool=False, nthread:int=1):
+	'''
+	Convert bedgraph into bigwig files. Auto sort and filter bedgraphs prior to calling bedGraphToBigWig
+	:param i: Input bedgraph file
+	:param g: chrom.size file
+	:param o: Output bw file
+	:param autosort: Perform sorting on bedgraph file before running bedGraphToBigWig
+	:param filter_chr: Remove chromosomes in bedgraph file that are not present in chrom.sizes file
+	'''
+	check_binaries_validity("zcat", "sort", "bedGraphToBigWig")
+	tmpfiles = []
+	if filter_chr:
+		inputfile = tempfile.NamedTemporaryFile(mode='w+', suffix=".bg", delete=False).name
+		tmpfiles.append(inputfile)
+		with DelimitedReader(g) as dr:
+			chromosomes = set([d[0] for d in dr])
+		with DelimitedReader(i) as dr, DelimitedWriter(inputfile) as dw:
+			for d in dr:
+				if d[0] in chromosomes:
+					dw.write(d)
+		i = inputfile
+	
+	if autosort:
+		inputfile = tempfile.NamedTemporaryFile(mode='w+', suffix=".bg", delete=False).name
+		tmpfiles.append(inputfile)
+		if nthread > 1:
+			added_param = f"--parallel={nthread} "
+		else:
+			added_param = ""
+		if i.endswith(".gz"):
+			result0 = subprocess.run(f"zcat {i} | sort -k1,1 -k2,2n {added_param}> {inputfile}", shell=True)
+		else:
+			result0 = subprocess.run(f"sort -k1,1 -k2,2n {added_param}{i} > {inputfile}", shell=True)
+		if result0.returncode != 0:
+			raise Exception("Exception in sorting bg")
+		i = inputfile
+		
+	result = subprocess.run(f"bedGraphToBigWig {i} {g} {o}", shell=True, executable="/bin/bash")
+	if result.returncode != 0:
+		raise Exception("Exception in running bedGraphToBigWig")
+	for tmpfile in tmpfiles:
+		os.unlink(tmpfile)
+
+@vt(description="Convert GROcap/PROcap/GROseq/PROseq bam file to bigwig files (paired-end reads). Returns 4 bigwig files representing 5' and 3' end of the molecules on plus or minus strand", 
+	helps=dict(i="Input bam file", g="chrom size file", o="output bigwig file prefix",
+			paired_end="True: paired-end sequencing; False: single-end sequencing",
+			rna_strand="Indicate whether RNA strand is forward or reverse. In paired-end, forward represents that first read is 5'."
+			)
+		)
+@vc
+def _process_PROcap_bam_to_bigwig_20240423(i:str, g:str, o:str, paired_end : convert_to_bool, rna_strand : str):
+	'''
+	first_read_is_5 --> strand == Forward
+	'''
+	check_binaries_validity("samtools", "bedtools", "zcat", "sort", "bedGraphToBigWig")
+	
+	tmpfiles = [tempfile.NamedTemporaryFile(mode='w+', suffix=".bg", delete=False).name for _ in range(4)]
+	bg5_pl, bg5_mn, bg3_pl, bg3_mn = tmpfiles
+	thread = 16
+	pwpool = ProcessWrapPool(4)
+	if paired_end:
+		tmpfiles_bam = [tempfile.NamedTemporaryFile(mode='w+', suffix=".bam", delete=False).name for _ in range(2)]
+		bam5, bam3 = tmpfiles_bam		
+		if rna_strand == "forward":
+			bam5_pid = pwpool.run(bash_command, args=[f"samtools view -f 66 --write-index -@ {thread} -o {bam5} {i}"])
+			bam3_pid = pwpool.run(bash_command, args=[f"samtools view -f 130 --write-index -@ {thread} -o {bam3} {i}"])
+		elif rna_strand == "reverse":
+			bam5_pid = pwpool.run(bash_command, args=[f"samtools view -f 130 --write-index -@ {thread} -o {bam5} {i}"])
+			bam3_pid = pwpool.run(bash_command, args=[f"samtools view -f 66 --write-index -@ {thread} -o {bam3} {i}"])
+		else:
+			raise Exception()
+		# Be careful of the strand. We assumed F1R2 setup 
+		bgpl_pid = pwpool.run(bash_command, args=[f"bedtools genomecov -ibam {bam5} -5 -strand + -bg > {bg5_pl}"], dependencies=[bam5_pid])
+		bgmn_pid = pwpool.run(bash_command, args=[f"bedtools genomecov -ibam {bam5} -5 -strand - -bg | awk {{'printf (\"%s\\t%s\\t%s\\t-%s\\n\", $1, $2, $3, $4)'}} > {bg5_mn}"], dependencies=[bam5_pid])
+		bg3pl_pid = pwpool.run(bash_command, args=[f"bedtools genomecov -ibam {bam3} -5 -strand - -bg > {bg3_pl}"], dependencies=[bam3_pid])
+		bg3mn_pid = pwpool.run(bash_command, args=[f"bedtools genomecov -ibam {bam3} -5 -strand + -bg | awk {{'printf (\"%s\\t%s\\t%s\\t-%s\\n\", $1, $2, $3, $4)'}} > {bg3_mn}"], dependencies=[bam3_pid])
+	else:
+		tmpfiles_bam = [] # No bam files needed
+		bgpl_pid = pwpool.run(bash_command, args=[f"bedtools genomecov -ibam {i} -5 -strand + -bg > {bg5_pl}"])
+		bgmn_pid = pwpool.run(bash_command, args=[f"bedtools genomecov -ibam {i} -5 -strand - -bg | awk {{'printf (\"%s\\t%s\\t%s\\t-%s\\n\", $1, $2, $3, $4)'}} > {bg5_mn}"])
+		bg3pl_pid = pwpool.run(bash_command, args=[f"bedtools genomecov -ibam {i} -3 -strand + -bg > {bg3_pl}"])
+		bg3mn_pid = pwpool.run(bash_command, args=[f"bedtools genomecov -ibam {i} -3 -strand - -bg | awk {{'printf (\"%s\\t%s\\t%s\\t-%s\\n\", $1, $2, $3, $4)'}} > {bg3_mn}"])
+		
+	pwpool.run(_convert_bedgraph_to_bigwig_20240423, args=[bg5_pl, g, o + "_5pl.bw"], kwargs=dict(autosort=True, filter_chr=True), dependencies=[bgpl_pid])
+	pwpool.run(_convert_bedgraph_to_bigwig_20240423, args=[bg5_mn, g, o + "_5mn.bw"], kwargs=dict(autosort=True, filter_chr=True), dependencies=[bgmn_pid])
+	pwpool.run(_convert_bedgraph_to_bigwig_20240423, args=[bg3_pl, g, o + "_3pl.bw"], kwargs=dict(autosort=True, filter_chr=True), dependencies=[bg3pl_pid])
+	pwpool.run(_convert_bedgraph_to_bigwig_20240423, args=[bg3_mn, g, o + "_3mn.bw"], kwargs=dict(autosort=True, filter_chr=True), dependencies=[bg3mn_pid])
+	pwpool.get(wait=True)
+	pwpool.close()
+	for tmpfile in tmpfiles + tmpfiles_bam:
+		os.unlink(tmpfile)
+
+@vt(description="Convert GROcap/PROcap/GROseq/PROseq bam file to bed files Returns 2 bed files with the 4th column as a comma separated list of RNA distances from TSS", 
+	helps=dict(i="Input bam file", o="output bed file prefix. Two files, _dpl.bed.gz and _dmn.bed.gz are output",
+			paired_end="True: paired-end sequencing; False: single-end sequencing",
+			rna_strand="Indicate whether RNA strand is forward or reverse. In paired-end, forward represents that first read is 5'.",
+			min_rna_len="Minimum RNA length to record",
+			max_rna_len="Maximum RNA length to record"
+			)
+		)
+@vc
+def _process_PROcap_bam_to_TSS_RNA_len_20240423(i, o, paired_end, rna_strand, min_rna_len=0, max_rna_len=100000, target_chromosomes:str=None): 
+	'''
+	'''
+	check_binaries_validity("bgzip")
+	def _to_position(alignment):
+		position = alignment.reference_end if alignment.is_reverse else (alignment.reference_start + 1)
+		strand = "-" if alignment.is_reverse else "+"
+		return (alignment.reference_name, position, strand)
+
+	if not paired_end:
+		raise Exception("Single-end not supported yet.")
+	saved_reads = {}
+	TSS_counter = nested_default_dict(3, list)
+	with pysam.AlignmentFile(i) as samfh: 
+		for alignment in samfh:
+# 			if target_chromosomes is not None and alignment.reference_name not in target_chromosomes:
+# 				continue
+			if alignment.query_name in saved_reads:
+				prev_alignment = saved_reads.pop(alignment.query_name)
+				alignment1 = prev_alignment if prev_alignment.is_read1 else alignment
+				alignment2 = prev_alignment if prev_alignment.is_read2 else alignment
+				p1 = _to_position(alignment1) # read1: Pol
+				p2 = _to_position(alignment2) # read2: TSS
+				
+				b = BEDPE(p1[0], p1[1] - 1, p1[1], p2[0], p2[1] - 1, p2[1], strand1 = p1[2], strand2 = p2[2])
+				if (b.chrom1 == b.chrom2
+					and (   (b.strand1 == "+" and b.strand2 == "-" and b.start1 <= b.start2 and b.stop1 <= b.stop2 and min_rna_len <= b.stop2 - b.start1 <= max_rna_len)
+						 or (b.strand1 == "-" and b.strand2 == "+" and b.start2 <= b.start1 and b.stop2 <= b.stop1 and min_rna_len <= b.stop1 - b.start2 <= max_rna_len))):
+					
+					
+					d = b.stop2 - b.start1 if b.strand1 == "+" else b.stop1 - b.start2
+					if rna_strand == "forward":
+						strand = b.strand1
+						if strand == "+":
+							TSS_counter[strand][b.chrom1][b.genomic_pos1.start].append(d)
+						else:
+							TSS_counter[strand][b.chrom1][b.genomic_pos1.stop].append(d)
+					elif rna_strand == "reverse":
+						strand = b.strand2
+						if strand == "+":
+							TSS_counter[strand][b.chrom1][b.genomic_pos2.stop].append(d)
+						else:
+							TSS_counter[strand][b.chrom1][b.genomic_pos2.start].append(d)
+					else:
+						raise Exception()
+
+			else:
+				saved_reads[alignment.query_name] = alignment
+		for output_file, strand in zip([f"{o}_dpl.bed.gz", f"{o}_dmn.bed.gz"], ["+", "-"]):
+			with BaseWriter(output_file) as bwd:
+				regions = TSS_counter[strand]
+				for r in sorted(regions.keys()):
+					positions = regions[r]
+					for p in sorted(positions.keys()):
+						v = sorted(positions[p])
+						bwd.write(f"{r}\t{p - 1}\t{p}\t{','.join(list(map(str, v)))}\n")
+						
+						
+
+
+	
+@vt(description="Modify bigwig files according to the func", 
+helps=dict(i="Input bigwig file", o="Output bigwig file", func="Function to modify bigwig. Either a python function or a string to be evaluated as python lambda function. For example, to convert all positive values into negative values, 'lambda x: x * -1'")
+													)
+
+@vc
+def _modify_bigwig_values_20240423(i:str, o:str, func:str):
+	'''
+	Extract all intervals that overlap with the selected regions
+	'''
+	if isinstance(func, str):
+		func = eval(func, {}) # While unsafe to use eval, disable access to global variables to make it a little bit safer..
+	input_bw = pyBigWig.open(i)
+	def _get_pyBigWig_all_interval_generator(bw):
+		for chrom in bw.chroms():
+			if bw.intervals(chrom) is not None:
+				for interval in bw.intervals(chrom):
+					yield (chrom, *interval)
+	output_bw = pyBigWig.open(o, "w")
+	output_bw.addHeader(list(input_bw.chroms().items()))
+	all_intervals = list(_get_pyBigWig_all_interval_generator(input_bw))
+	chroms, starts, ends, values = safe_inverse_zip(all_intervals, 4)
+	values = list(map(func, values))
+	output_bw.addEntries(list(chroms), list(starts), ends=list(ends), values=list(values))
+	output_bw.close()
+	input_bw.close()
+	
+	
+if __name__ == "__main__":
+	main()
+
+		

biodatatools-0.0.1/biodatatools.egg-info/PKG-INFO

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+Metadata-Version: 2.1
+Name: biodatatools
+Version: 0.0.1
+Summary: A python package with useful biological data processing methods
+Home-page: https://github.com/aldenleung/biodatatools/
+Author: Alden Leung
+Author-email: alden.leung@gmail.com
+Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
+Description-Content-Type: text/markdown
+
+# biodatatools
+
+A python package that provides multiple useful functions for biological data processing. 
+Many functions from his package require external programs installed.

biodatatools-0.0.1/biodatatools.egg-info/SOURCES.txt

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+README.md
+setup.py
+biodatatools/__init__.py
+biodatatools.egg-info/PKG-INFO
+biodatatools.egg-info/SOURCES.txt
+biodatatools.egg-info/dependency_links.txt
+biodatatools.egg-info/entry_points.txt
+biodatatools.egg-info/requires.txt
+biodatatools.egg-info/top_level.txt

biodatatools-0.0.1/biodatatools.egg-info/dependency_links.txt

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+

biodatatools-0.0.1/biodatatools.egg-info/entry_points.txt

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+[console_scripts]
+biodatatools = biodatatools:main

biodatatools-0.0.1/biodatatools.egg-info/requires.txt

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+genomictools>=0.0.7
+biodata>=0.0.6
+pysam>=0.22.1
+pyBigWig>=0.3.22
+simplevc>=0.0.2
+commonhelper>=0.0.1
+mphelper>=0.0.1

biodatatools-0.0.1/biodatatools.egg-info/top_level.txt

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+biodatatools

biodatatools-0.0.1/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

biodatatools-0.0.1/setup.py

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+from setuptools import setup, find_packages
+
+with open("README.md", "r") as readme_file:
+	readme = readme_file.read()
+
+requirements = ["genomictools>=0.0.7", "biodata>=0.0.6", "pysam>=0.22.1", "pyBigWig>=0.3.22", "simplevc>=0.0.2", "commonhelper>=0.0.1", "mphelper>=0.0.1"]
+
+setup(
+	name="biodatatools",
+	version="0.0.1",
+	author="Alden Leung",
+	author_email="alden.leung@gmail.com",
+	description="A python package with useful biological data processing methods",
+	long_description=readme,
+	long_description_content_type="text/markdown",
+	url="https://github.com/aldenleung/biodatatools/",
+	packages=find_packages(),
+	install_requires=requirements,
+	classifiers=[
+		"Programming Language :: Python :: 3.7",
+		"Programming Language :: Python :: 3.8",
+		"Programming Language :: Python :: 3.9",
+		"Programming Language :: Python :: 3.10",
+		"Programming Language :: Python :: 3.11",
+		"License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+	],
+	entry_points = {
+		'console_scripts': [
+			'biodatatools = biodatatools:main',
+		],
+	}	
+)