Merge pull request #28 from karel-brinda/liftover_genomeid

Minor update

requirements.txt

@@ -1,8 +1,8 @@
 pysam>=0.8.3
-pbr>=1.4.0
+pbr>=1.8.0
 termcolor>=1.1.0
 sphinx>=1.3.0
 sphinxcontrib-napoleon>=0.3.3
 sphinx_rtd_theme>=0.1.8
-snakemake>=3.3
-smbl>=0.1.1.dev47
+snakemake>=3.4.2
+smbl>=1.3.0

rnftools/rnfformat/RnfLifter.py

@@ -1,7 +1,7 @@
 import rnftools
 import pysam
 
-import re
+import re,sys
 
 class RnfLifter:
 
@@ -29,40 +29,49 @@ def __init__(self,
 			else:
 				self._fai_index=None
 
-		self._reg_block=re.compile(r"(\(([0-9]+),[0-9]+,[FRN],([0-9]+),([0-9]+)\))")
+		self._reg_block=re.compile(r"(\(([0-9]+),([0-9]+),[FRN],([0-9]+),([0-9]+)\))")
 
-	def lift_rnf_name(self,rnf_name):
+	def lift_rnf_name(self,rnf_name, genome_id):
 		if self._chain is None:
 			return rnf_name
 		for occur in self._reg_block.finditer(rnf_name):
 			groups=occur.groups()
-			chrom_id=int(groups[1])
-			chrom=self._fai_index.dict_ids_chr[chrom_id]
-			o_left=groups[2]
-			o_right=groups[3]
-			left=int(o_left)
-			right=int(o_right)
-			if left!=0:
-				n_left=self._chain.one_based_transl(chrom,left)
-				f_new_left=str(n_left).zfill(len(o_left))
-				rnf_name=rnf_name.replace(",{},".format(o_left),",{},".format(f_new_left))
-			if right!=0:
-				new_right=self._chain.one_based_transl(chrom,right)
-				f_new_right=str(n_right).zfill(len(o_right))
-				rnf_name=rnf_name.replace(",{})".format(o_right),",{})".format(f_new_right))
+			p_genome_id=int(groups[1])
+			chrom_id=int(groups[2])
+
+			# is this segment from a genome to be transformed?1
+			if int(genome_id)==int(p_genome_id):
+				#print("going to transform",file=sys.stderr)
+				chrom=self._fai_index.dict_ids_chr[chrom_id]
+				o_left=groups[3]
+				o_right=groups[4]
+				left=int(o_left)
+				right=int(o_right)
+				if left!=0:
+					n_left=self._chain.one_based_transl(chrom,left)
+					f_new_left=str(n_left).zfill(len(o_left))
+					rnf_name=rnf_name.replace(",{},".format(o_left),",{},".format(f_new_left))
+					#print("left",o_left,"=>",f_new_left,file=sys.stderr)
+				if right!=0:
+					new_right=self._chain.one_based_transl(chrom,right)
+					f_new_right=str(n_right).zfill(len(o_right))
+					rnf_name=rnf_name.replace(",{})".format(o_right),",{})".format(f_new_right))
+					#print(o_right,"=>",f_new_right,file=sys.stderr)
 		return rnf_name
 
 	def lift_fastq(self,
 				fastq_in_fo,
-				fastq_out_fo
+				fastq_out_fo,
+				genome_id,
 			):
 		for i, line in enumerate(fastq_in_fo,start=0):
 			if i%4==0:
-				fastq_out_fo.write(self.lift_rnf_name(line))
+				fastq_out_fo.write(self.lift_rnf_name(line,genome_id=int(genome_id)))
 			else:
 				fastq_out_fo.write(line)
 
 	def lift_sam(self,
+				genome_id,
 				sam_in_fn=None,
 				bam_in_fn=None,
 				sam_out_fn=None,
@@ -90,5 +99,5 @@ def lift_sam(self,
 		infile = pysam.AlignmentFile(in_fn, in_mode)
 		outfile = pysam.AlignmentFile(out_fn, out_mode, template=infile)
 		for s in infile:
-			s.qname=self.lift_rnf_name(s.qname)
+			s.qname=self.lift_rnf_name(s.qname,genome_id=int(genome_id))
 			outfile.write(s)

rnftools/scripts.py

@@ -623,11 +623,13 @@ def liftover(args):
 					rnf_lifter.lift_fastq(
 							fastq_in_fo=fastq_in_fo,
 							fastq_out_fo=fastq_out_fo,
+							genome_id=args.genome_id,
 						)
 	else:
 		rnf_lifter.lift_sam(
 				sam_in_fn=args.input_fn,
 				sam_out_fn=args.output_fn,
+				genome_id=args.genome_id,
 			)
 
 def add_liftover_parser(subparsers,subcommand,help,description):
@@ -639,6 +641,14 @@ def add_liftover_parser(subparsers,subcommand,help,description):
 			dest='chain_fn',
 			help='Chain liftover file for coordinates transformation. [no transformation]',
 		)
+	parser_liftover.add_argument(
+			'-g','--genome-id',
+			type=str,
+			metavar='int',
+			dest='genome_id',
+			help='ID of genome to be transformed.',
+			required=True,
+		)
 	parser_liftover.add_argument(
 			'-x','--faidx',
 			type=str,

setup.cfg

@@ -2,9 +2,9 @@
 name = RNFtools
 author = Karel Brinda
 author-email = karel.brinda@gmail.com
-summary = A package for Read Naming Format (RNF).
+summary = RNF framework for NGS: simulation of reads, evaluation of mappers, conversion of RNF-compliant data..
 description-file = README.rst
-home-page = http://github.com/karel-brinda/rnftools
+home-page = http://karel-brinda.github.io/rnftools/
 requires-python = >=3.2
 license = MIT
 keywords = Bioinformatics, Computational Biology, Next-Generation Sequencing, Read Simulation, Mappers Evaluation, Snakemake
@@ -14,7 +14,7 @@ supported-platform =
 	MacOS
 	CygWin
 classifier = 
-	Development Status :: 3 - Alpha
+	Development Status :: 4 - Beta
 	Environment :: Console
 	Intended Audience :: Science/Research
 	License :: OSI Approved :: MIT License

tests/command_line/rnftools_liftover.sh

@@ -5,15 +5,14 @@ set -o pipefail
 
 cd "$(dirname "$0")"
 
-rnftools liftover -c liftover.chain liftover_orig.bam - > _liftover_new1.sam
-rnftools liftover -c liftover.chain --output-format bam liftover_orig.bam - > _liftover_new1.bam
+rnftools liftover --genome-id 1 -c liftover.chain liftover_orig.bam - > _liftover_new1.sam
+rnftools liftover --genome-id 1 -c liftover.chain --output-format bam liftover_orig.bam - > _liftover_new1.bam
 
-rnftools liftover liftover_orig.bam _liftover_orig.sam
+rnftools liftover --genome-id 1 liftover_orig.bam _liftover_orig.sam
 
-rnftools liftover -c liftover.chain liftover_orig.bam _liftover_new2.sam
-rnftools liftover -c liftover.chain liftover_orig.bam _liftover_new2.bam
-rnftools liftover -c liftover.chain _liftover_orig.sam _liftover_new3.sam
-rnftools liftover -c liftover.chain _liftover_orig.sam _liftover_new3.bam
-
-rnftools liftover --invert -c liftover.chain _liftover_new1.bam _liftover_pseudoorig.sam
+rnftools liftover --genome-id 1 -c liftover.chain liftover_orig.bam _liftover_new2.sam
+rnftools liftover --genome-id 1 -c liftover.chain liftover_orig.bam _liftover_new2.bam
+rnftools liftover --genome-id 1 -c liftover.chain _liftover_orig.sam _liftover_new3.sam
+rnftools liftover --genome-id 1 -c liftover.chain _liftover_orig.sam _liftover_new3.bam
 
+rnftools liftover --genome-id 1 --invert -c liftover.chain _liftover_new1.bam _liftover_pseudoorig.sam