Mercurial > repos > oinizan > demultiplex
diff demultiplex.py.save2 @ 0:da4101033e10 draft default tip
planemo upload
| author | oinizan |
|---|---|
| date | Wed, 18 Oct 2017 05:30:40 -0400 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/demultiplex.py.save2 Wed Oct 18 05:30:40 2017 -0400 @@ -0,0 +1,425 @@ +#!/usr/bin/env python2.7 +# +# Copyright (C) 2014 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. +# + +__author__ = 'Plateforme bioinformatique Toulouse and SIGENAE' +__copyright__ = 'Copyright (C) 2015 INRA' +__license__ = 'GNU General Public License' +__version__ = '1.2.0' +__email__ = 'frogs@inra.fr' +__status__ = 'prod' + +import os +import sys +import gzip +import time +import tarfile +import argparse + +CURRENT_DIR = os.path.dirname(os.path.abspath(__file__)) +# PATH +BIN_DIR = os.path.abspath(os.path.join(os.path.dirname(CURRENT_DIR), "libexec")) +os.environ['PATH'] = BIN_DIR + os.pathsep + os.environ['PATH'] +# PYTHONPATH +LIB_DIR = os.path.abspath(os.path.join(os.path.dirname(CURRENT_DIR), "lib")) +sys.path.append(LIB_DIR) +if os.getenv('PYTHONPATH') is None: os.environ['PYTHONPATH'] = LIB_DIR +else: os.environ['PYTHONPATH'] = os.environ['PYTHONPATH'] + os.pathsep + LIB_DIR + +from frogsUtils import * + + +################################################################################################################################################## +# +# COMMAND LINES +# +################################################################################################################################################## +class Demultiplex(Cmd): + """ + @summary : Demultiplex samples. + """ + def __init__(self, R1_input_file, R2_input_file, barcode_file, mismatches, end, global_tmp_files, R1_output_files, R2_output_files, demultiplex_err_files1, demultiplex_err_files2, demultiplex_log): + """ + @param R1_input_file : [str] Path to the R1 fastq file. + @param R2_input_file : [str] Path to the R2 fastq file. + @param barcode_file : [str] Path to barcodes and samples (one line by sample) description file. Line format : SAMPLE_NAME<TAB>BARCODE. + @param mismatches : [int] Number of mismatches allowed + @param end : [str] barcode ends ? forward : bol or reverse : eol (def bol) + @param global_tmp_files : [str] Path for R1 and R2 files. + @param R1_output_files : [list] Paths to the R1 fastq files (one by sample). User provides an empty list. + @param R2_output_files : [list] Paths to the R2 fastq files (one by sample). User provides an empty list. + @param demultiplex_err_files : [list] Paths to the files with ambiguous and unmatched reads. User provides an empty list. + """ + + tmp_files = TmpFiles( global_tmp_files.tmp_dir ) + + tmp_folder = os.path.join( global_tmp_files.tmp_dir, global_tmp_files.prefix + "_tmp", tmp_files.prefix ) + global_tmp_files.dirs.append(tmp_folder) + if not os.path.exists(tmp_folder): + os.mkdir(tmp_folder) + self.samples_names = list() + # Update output data + FH_barcode = open( barcode_file ) + for line in FH_barcode: + sample_name, barcode = line.strip().rsplit(None, 1) + # OI DEBUG + print "Line is " + line + print "Sample name is " + sample_name + print "Barcode is " + barcode + print "Append to R1_output_files file: " + tmp_folder + " " + sample_name + " " + '_R1.fastq' + R1_output_files.append( os.path.join(tmp_folder, sample_name + '_R1.fastq') ) + + global_tmp_files.files.append(os.path.join(tmp_folder, sample_name + '_R1.fastq') ) + if R2_input_file != None: + R2_output_files.append( os.path.join(tmp_folder, sample_name + '_R2.fastq') ) + global_tmp_files.files.append(os.path.join(tmp_folder, sample_name + '_R2.fastq')) + self.samples_names.append( sample_name.replace(' ', '_') ) + FH_barcode.close() + self.R1_input_file = R1_input_file + self.ambiguous = os.path.join(tmp_folder, 'ambiguous_R1.fastq') + self.unmatched = os.path.join(tmp_folder, 'unmatched_R1.fastq') + demultiplex_err_files1.extend( [self.ambiguous,self.unmatched] ) + global_tmp_files.files.extend( [self.ambiguous,self.unmatched] ) + if R2_input_file != None: + demultiplex_err_files2.extend( [os.path.join(tmp_folder, 'ambiguous_R2.fastq'),os.path.join(tmp_folder, 'unmatched_R2.fastq') ]) + global_tmp_files.files.extend( [os.path.join(tmp_folder, 'ambiguous_R2.fastq'),os.path.join(tmp_folder, 'unmatched_R2.fastq') ]) + + # Set class + if R2_input_file != None: + Cmd.__init__( self, + 'perl ' + os.environ['TOOL_DIRECTORY'] + '/splitbc.pl', + 'Demultiplex reads.', + R1_input_file + ' ' + R2_input_file + ' --' + end + ' --bcfile ' + barcode_file + ' --mismatches ' + `mismatches` + ' --trim --no_adapt --prefix-r1 ' + os.path.join(tmp_folder, '%_R1.fastq') +\ + ' --prefix-r2 ' + os.path.join(tmp_folder, '%_R2.fastq') + ' >> ' + demultiplex_log, + None ) + else: + Cmd.__init__( self, + 'perl '+ os.environ['TOOL_DIRECTORY'] + '/splitbc.pl', + 'Demultiplex reads.', + R1_input_file + ' --' + end + ' --bcfile ' + barcode_file + ' --mismatches ' + `mismatches` + ' --trim --no_adapt --prefix-r1 ' + os.path.join(tmp_folder, '%_R1.fastq') +\ + ' >> ' + demultiplex_log, + None ) + + def parser(self, log_file): + """ + @summary : Parse the command results to add information in log_file. + @log_file : [str] Path to the sample process log file. + """ + # Parse output + nb_seq_before = get_fastq_nb_seq(self.R1_input_file) + nb_seq_unmatched = get_fastq_nb_seq(self.unmatched) + nb_seq_ambiguous = get_fastq_nb_seq(self.ambiguous) + # Write result + FH_log = Logger( log_file ) + FH_log.write( 'Results :\n' ) + FH_log.write( '\tnb seq before demultiplexing : ' + str(nb_seq_before) + '\n' ) + FH_log.write( '\tnb seq after process matched : ' + str(nb_seq_before - nb_seq_unmatched) + '\n' ) + FH_log.write( '\tnb seq after process non-ambiguous : ' + str(nb_seq_before - nb_seq_unmatched - nb_seq_ambiguous) + '\n' ) + FH_log.close() + + def get_version(self): + """ + @summary : Returns the program version number. + @return : version number if this is possible, otherwise this method return 'unknown'. + """ + return Cmd.get_version(self, 'stdout') + + +class Archive(Cmd): + """ + @summary : Creates an archive with files. + """ + def __init__(self, archived_files, archive_path): + """ + @param archived_files: [list] Files added in final archive. + @param archive_path: [str] Path to the new archive. + """ + + tmp_files=TmpFiles( os.path.dirname(archive_path) ) + tmp_folder = os.path.join( tmp_files.tmp_dir, tmp_files.prefix) + tmp_files.dirs.append(tmp_folder) + if not os.path.exists(tmp_folder): + os.makedirs(tmp_folder) + + if len(archived_files) == 0: + raise Exception( "At least one file must be add to the archive '" + archive_path + "'." ) + + archived_basenames = list() + for current in archived_files: + if not os.path.dirname(current) == tmp_folder: + os.rename(current, os.path.join(tmp_folder,os.path.basename(current))) + tmp_files.files.append(os.path.join(tmp_folder,os.path.basename(current))) + archived_basenames.append(os.path.basename(current)) + # OI DEBUG + archive_path_present = "archive_path is file or directory: " + str(os.path.isfile(archive_path)) + " or " + str(os.path.isdir(archive_path)) + print archive_path_present + tmp_folder_present = "tmp_folder is file or directory: " + str(os.path.isfile(tmp_folder)) + " or " + str(os.path.isdir(tmp_folder)) + print tmp_folder_present + for files in archived_basenames: + print "archived basename is " + files + files_present = "archived basename is file or directory: " + str(os.path.isfile(files)) + " or " + str(os.path.isdir(files)) + print files_present + # END OI DEBUG + + + + Cmd.__init__( self, + 'tar', + 'Archives files.', + '-zcf ' + archive_path + ' -C ' + tmp_folder + " " + " ".join(archived_basenames), + None ) + + self.Files=tmp_files + + + def parser(self,log_file): + self.Files.deleteAll() + + +################################################################################################################################################## +# +# FUNCTIONS +# +################################################################################################################################################## +def is_gzip( file ): + """ + @return: [bool] True if the file is gziped. + @param file : [str] Path to processed file. + """ + is_gzip = None + FH_input = gzip.open( file ) + try: + FH_input.readline() + is_gzip = True + except: + is_gzip = False + finally: + FH_input.close() + return is_gzip + +def split_barcode_file( barcode_file, barcodes_file_list, global_tmp_files ): + """ + @summary: In case of double multiplexe, split barcode file in one forward and multiple reverse barcode files + @param barcode_file: [str] Path to the input barcode file + @param barcodes_file_list: [list] List of path to the ouput barcode files + @param out_dir: [str] path to the output directory to write barcode files + """ + out_dir = global_tmp_files.tmp_dir + barcode_input = open(barcode_file,"r") + barcode_dict={} + for l in barcode_input.readlines(): + [s,f,r]=l.strip().split() + if not "forward_bc" in barcode_dict: + barcode_dict["forward_bc"] = [f+"\t"+f] + elif not f+"\t"+f in barcode_dict["forward_bc"]: + barcode_dict["forward_bc"].append( f+"\t"+f) + if not f+"_reverse_bc" in barcode_dict: + barcode_dict[f+"_reverse_bc"] = [s+"\t"+r] + else : + barcode_dict[f+"_reverse_bc"].append(s+"\t"+r) + + f=barcode_dict.pop("forward_bc") + barcodes_file_list.append(os.path.join(out_dir,"forward_bc")) + global_tmp_files.files.append(os.path.join(out_dir,"forward_bc")) + FH_out = open(os.path.join(out_dir,"forward_bc"),"w") + FH_out.write("\n".join(f)+"\n") + FH_out.close() + + for bc_file in barcode_dict: + barcodes_file_list.append(os.path.join(out_dir,bc_file)) + global_tmp_files.files.append(os.path.join(out_dir,bc_file)) + FH_out = open(os.path.join(out_dir,bc_file),"w") + FH_out.write("\n".join(barcode_dict[bc_file])+"\n") + FH_out.close() + +def get_fastq_nb_seq( fastq_file ): + """ + @summary: Returns the number of sequences in fastq_file. + @param fastq_file: [str] Path to the fastq file processed. + @return: [int] The number of sequences. + """ + FH_input = None + if not is_gzip(fastq_file): + FH_input = open( fastq_file ) + else: + FH_input = gzip.open( fastq_file ) + nb_line = 0 + for line in FH_input: + nb_line += 1 + FH_input.close() + nb_seq = nb_line/4 + return nb_seq + +def concat_files(list_input, output_file): + + FH_out=open(output_file,"w") + for f in list_input : + FH_in = open(f) + string="" + i=0 + for line in FH_in: + string+= line + i+=1 + if i==2000 : + FH_out.write(string) + string="" + i=0 + if i != 0: + FH_out.write(string) + FH_in.close() + FH_out.close() + +def summarise_results( summary_file, barcode_file, log_file ): + """ + @summary: Writes one summary of results from several logs. + @param summary_file: [str] The output file. + @param log_files: [list] The list of path to log files (one log file by sample). + """ + sample_dict=dict() + FH_barcode= open(barcode_file) + for line in FH_barcode: + sample_dict[line.split()[0]]=0 + + FH_summary = open(summary_file, "w") + FH_summary.write( "#sample\tcount\n") + FH_log = open(log_file,"r") + sample_dict["unmatched"]=0 + sample_dict["ambiguous"]=0 + + for line in FH_log.readlines(): + if line.startswith("Barcode") or line.startswith("total") : + pass + else : + l=line.replace('(','\t').split() + if l[0] in sample_dict: + sample_dict[l[0]] += int(l[1]) + + for s in sample_dict: + FH_summary.write(s + '\t' + str(sample_dict[s]) + '\n') + FH_summary.close() + + +################################################################################################################################################## +# +# MAIN +# +################################################################################################################################################## +if __name__ == "__main__": + # Manage parameters + parser = argparse.ArgumentParser( + description='Split by samples the reads in function of inner barcode.' + ) + parser.add_argument('-m', '--mismatches', type=int, default=0, help="Number of mismatches allowed in barcode. [Default: %(default)s]") + parser.add_argument('-e', '--end', type=str, default="bol", help="barcode is at the begining of the forward end (bol) or of the reverse (eol) or both (both). [Default: %(default)s]") + parser.add_argument( '--debug', default=False, action='store_true', help="Keep temporary files to debug program." ) + parser.add_argument( '-v', '--version', action='version', version=__version__ ) + # Inputs + group_input = parser.add_argument_group( 'Inputs' ) + group_input.add_argument( '--input-R1', required=True, help='The R1 sequence file with all samples (format: fastq).' ) + group_input.add_argument( '--input-R2', default=None, help='The R2 sequence file with all samples (format: fastq).' ) + group_input.add_argument( '--input-barcode', help='This file describes barcodes and samples (one line by sample). Line format : SAMPLE_NAME<TAB>BARCODE or SAMPLE_NAME<TAB>BARCODE_FW<TAB>BARCODE_RV.' ) + group_output = parser.add_argument_group( 'Outputs' ) + # Outputs + group_output.add_argument( '--output-demultiplexed', default="demultiplexed_read.tar.gz", help='The tar file containing R1 files and R2 files for each sample (format: tar). [Default: %(default)s]' ) + group_output.add_argument( '--output-excluded', default="undemultiplexed_read.tar.gz", help='The tar file containing R1 files and R2 files not demultiplexed (format: tar). [Default: %(default)s]' ) + group_output.add_argument( '-s', '--summary', default='summary.tsv', help='TSV file with summary of filters results (format: TSV). [Default: %(default)s]') + group_output.add_argument( '-l', '--log-file', default=sys.stdout, help='This output file will contain several information on executed commands.') + args = parser.parse_args() + prevent_shell_injections(args) + + Logger.static_write(args.log_file, "## Application\nSoftware :" + sys.argv[0] + " (version : " + str(__version__) + ")\nCommand : " + " ".join(sys.argv) + "\n\n") + + # Process + R1_files = list() + R2_files = list() + tmp_barcode_files = list() + tmp_R1_files = list() + tmp_R2_files = list() + demultiplex_err_files1 = list() + demultiplex_err_files2 = list() + excluded_R1_file = os.path.join(os.path.split(args.output_demultiplexed)[0],os.path.basename(args.input_R1)+"_excluded_demult") + if args.input_R2 != None : + excluded_R2_file = os.path.join(os.path.split(args.output_demultiplexed)[0],os.path.basename(args.input_R2)+"_excluded_demult") + uniq_id = str(time.time()) + "_" + str(os.getpid()) + + tmp_files = TmpFiles( os.path.split(args.output_demultiplexed)[0] ) + demultiplex_log = tmp_files.add("Demult.log") + tmp_folder=tmp_files.add_dir("tmp") + os.mkdir(tmp_folder) + + sample_list=[] + try: + # Process + if args.end == "bol" or args.end == "eol" : + + info="\n#Demultiplexing " + os.path.basename(args.input_R1) + if args.input_R2 != None: + info+= " and " + os.path.basename(args.input_R2) + info += " with " + os.path.basename(args.input_barcode) + " in " + args.end + " strand\n" + Logger.static_write(args.log_file,info) + Demultiplex(args.input_R1, args.input_R2, args.input_barcode, args.mismatches, args.end, tmp_files, R1_files, R2_files, demultiplex_err_files1,demultiplex_err_files2, demultiplex_log).submit( args.log_file ) + # OI DEBUG + for r1file in R1_files: + Logger.static_write(args.log_file,"\n\t#Archive demultiplexed files is " + r1file + " \n") + + else: + split_barcode_file(args.input_barcode, tmp_barcode_files, tmp_files) + info="\n#Demultiplexing " + os.path.basename(args.input_R1) + if args.input_R2 != None: + info+= " and " + os.path.basename(args.input_R2) + info += " with " + os.path.basename(tmp_barcode_files[0]) + " in bol strand\n" + Logger.static_write(args.log_file,info) + Demultiplex(args.input_R1, args.input_R2, tmp_barcode_files[0], args.mismatches, "bol", tmp_files, tmp_R1_files, tmp_R2_files, demultiplex_err_files1,demultiplex_err_files2, demultiplex_log).submit( args.log_file ) + for idx,read1_file in enumerate(tmp_R1_files): + bc = os.path.basename(read1_file).replace("_R1.fastq","") + if os.path.join(tmp_files.tmp_dir,bc+"_reverse_bc") in tmp_barcode_files: + if os.stat(tmp_R1_files[idx]).st_size != 0 : + info="\n#Demultiplexing " + os.path.basename(tmp_R1_files[idx]) + if args.input_R2 != None: + info+= " and " + os.path.basename(tmp_R2_files[idx]) + info += " with " + bc+"_reverse_bc" + " in eol strand\n" + Logger.static_write(args.log_file,info) + if args.input_R2 != None: + Demultiplex(tmp_R1_files[idx], tmp_R2_files[idx], os.path.join(tmp_files.tmp_dir,bc+"_reverse_bc"), args.mismatches, "eol", tmp_files, R1_files, R2_files, demultiplex_err_files1, demultiplex_err_files2, demultiplex_log).submit( args.log_file ) + else: + Demultiplex(tmp_R1_files[idx], None, os.path.join(tmp_files.tmp_dir,bc+"_reverse_bc"), args.mismatches, "eol", tmp_files, R1_files, R2_files, demultiplex_err_files1, demultiplex_err_files2, demultiplex_log).submit( args.log_file ) + + Logger.static_write(args.log_file,"\n#Summarising result\n") + summarise_results( args.summary, args.input_barcode, demultiplex_log ) + Logger.static_write(args.log_file,"\n#Concatenation of undemultiplexed files 1\n") + concat_files(demultiplex_err_files1, excluded_R1_file ) + if len(R2_files) > 0: + Logger.static_write(args.log_file,"\n#Concatenation of undemultiplexed files 2\n") + concat_files(demultiplex_err_files2, excluded_R2_file ) + Logger.static_write(args.log_file,"\n#Archive demultiplexed R1 and R2 files\n") + Archive(R1_files + R2_files, args.output_demultiplexed).submit( args.log_file ) + Logger.static_write(args.log_file,"\n#Archive undemultiplexed R1 and R2 files\n") + Archive([excluded_R1_file,excluded_R2_file], args.output_excluded).submit( args.log_file ) + else: + Logger.static_write(args.log_file,"\n#Archive demultiplexed files\n") + Archive(R1_files, args.output_demultiplexed).submit( args.log_file ) + Logger.static_write(args.log_file,"\n#Archive undemultiplexed files\n") + Logger.static_write(args.log_file,"\n#Excluded_R1_file is " + excluded_R1_file + "\n") + Archive([excluded_R1_file], args.output_excluded).submit( args.log_file ) + + # Remove temporary files + finally: + #OI DEBUG + if not args.debug: + pass + #Logger.static_write(args.log_file,"\n#Removing temporary files\n") + #tmp_files.deleteAll()