def signalp_task(path_orfs,out_dir,tasks): out_name = os.path.basename(path_orfs).split('.')[0] trgs = ['{0!s}/{1!s}.signalp'.format(out_dir,out_name)] cmd = '{0!s} -f short -n {1!s} {2!s}'.format(fg.tool_path_check(TOOLS_DICT['signalp'].full_exe[0]),trgs[-1],path_orfs) name = 'signalp_' + out_name out,err = fg.GEN_LOGS(name) return Task(command=cmd,dependencies=tasks,targets=trgs,name=name,stdout=out,stderr=err)
def salmon_unpaired_task(index,unpaired,out_name,gene_map,out_dir,cpu_cap,tasks): trgs = [] cmd = '{0!s} quant -i {1!s} -l U -r {2!s} -o {3!s}/{4!s} --geneMap {5!s} -p {6!s} --extraSensitive'.format( fg.tool_path_check(TOOLS_DICT['salmon'].full_exe[0]),index,unpaired,out_dir,out_name,gene_map,cpu_cap) name = 'salmon_unpaired_' + os.path.basename(index) out,err = fg.GEN_LOGS(name) return Task(command=cmd,dependencies=tasks,targets=trgs,name=name,stdout=out,stderr=err,cpu=cpu_cap)
def signalp_task(opc, path_orfs, out_dir, tasks): out_name = os.path.basename(path_orfs).split('.')[0] trgs = ['{0!s}/{1!s}.signalp'.format(out_dir, out_name)] cmd = '{0!s} -f short -n {1!s} {2!s}'.format(tool_path_check(TOOLS_DICT['signalp'].full_exe[0]), trgs[-1], path_orfs) name = 'signalp_' + out_name out, err = gen_logs(opc.path_logs, name) return Task(command=cmd, dependencies=tasks, targets=trgs, name=name, stdout=out, stderr=err)
def prinseq_task(opc, out_dir, input_1, input_2, basename, opts, tasks): ''' Defines prinseq task. Uses GEN_PATH_DIR(), PATH_PRINSEQ Params : input_1 - a list of 1/left fastq files input_2 - a list of 2/right fastq files basename - the basename for all output files opts - optional params for trinity task. tasks = the tasks that this task is dependent on ''' trgs = [ '{0!s}/{1!s}_1_{2!s}'.format(out_dir, basename, os.path.basename(input_1)), '{0!s}/{1!s}_2_{2!s}'.format(out_dir, basename, os.path.basename(input_2)) ] pseudo_trgs = [ '{0!s}/{1!s}_{2!s}.fastq'.format(out_dir, basename, x) for x in range(1, 3) ] cmd = ( 'perl {0!s} -fastq {1!s} -fastq2 {2!s} --out_format 3 --out_good {3!s}/{4!s} ' '--out_bad null --trim_qual_left 20 --trim_qual_right 20 --trim_qual_type min ' '--min_len 55 --trim_tail_left 8 --trim_tail_right 8 {5!s} -log; mv {6!s} {7!s};' ' mv {8!s} {9!s};').format( tool_path_check(TOOLS_DICT['prinseq'].full_exe[0]), input_1, input_2, out_dir, basename, opts, pseudo_trgs[0], trgs[0], pseudo_trgs[1], trgs[1]) name = basename out, err = gen_logs(opc.path_logs, name) return Task(command=cmd, dependencies=tasks, name=name, stdout=out, stderr=err, targets=trgs)
def salmon_unpaired_task(opc, index, unpaired, out_name, gene_map, out_dir, cpu_cap, tasks): trgs = [ '{0!s}/{1!s}_quant.sf'.format(out_dir, out_name), '{0!s}/{1!s}_quant.genes.sf'.format(out_dir, out_name) ] if len(gene_map) > 0: trans_gene_map = ' --geneMap {0!s}'.format(gene_map) cmd = ( '{0!s} quant -i {1!s} -l U -r {2!s} -o {3!s}/{4!s} {5!s} ' #'-p {6!s} --extraSensitive; cp {3!s}/{4!s}/quant.sf ' '-p {6!s} --dumpEq --extraSensitive; cp {3!s}/{4!s}/quant.sf ' '{3!s}/{4!s}_quant.sf; cp {3!s}/{4!s}/quant.genes.sf ' '{3!s}/{4!s}_quant.genes.sf').format( tool_path_check(TOOLS_DICT['salmon'].full_exe[0]), index, unpaired, out_dir, out_name, trans_gene_map, cpu_cap) name = 'salmon_unpaired_' + os.path.basename( index) + '_' + os.path.basename(unpaired) out, err = gen_logs(opc.path_logs, name) return Task(command=cmd, dependencies=tasks, targets=trgs, name=name, stdout=out, stderr=err, cpu=cpu_cap)
def kallisto_task(index,out_dir,out_name,left,right,tasks): trgs = [] cmd = '{0!s} quant -i {1!s} -o {2!s}/{3!s} {4!s} {5!s}'.format( fg.tool_path_check(TOOLS_DICT['kallisto'].full_exe[0]),index,out_dir,out_name,left,right) name = 'kallisto' out,err = fg.GEN_LOGS(name) return Task(command=cmd,dependencies=tasks,targets=trgs,name=name,stdout=out,stderr=err)
def busco_task(opc, dbs, assembly_path, assembly_name, out_dir, reference_name, cpu_cap, tasks): ''' Defines the busco task. Uses PATH_DIR, PATH_BUSCO, PATH_BUSCO_REFERENCE Params : reference_name - Name of the reference file to be used by busco cpu_cap - the cpu limit to be gicen to busco. tasks - a list of tasks that this task is dependant on. ''' trgs = [ '{0!s}/run_busco_{1!s}_{2!s}'.format(out_dir, assembly_name, reference_name) ] busco_db = dbs['busco_' + reference_name] cmd = ('cd {0!s}; python {1!s} ' '-o busco_{3!s}_{2!s} -i {4!s} -l {5!s}/{2!s}_odb9 -m ' 'tran -f -c {6!s}').format( out_dir, tool_path_check(TOOLS_DICT['busco'].full_exe[0]), reference_name, assembly_name, assembly_path, busco_db.call_path, cpu_cap) name = 'busco_' + reference_name + '_' + assembly_name out, err = gen_logs(opc.path_logs, name) return Task(command=cmd, dependencies=tasks, targets=trgs, name=name, cpu=cpu_cap, stdout=out, stderr=err)
def trimmomatic_task(opc, out_dir, left, right, cpu_cap, basename, tasks): base_str = '{0!s}/{1!s}'.format(out_dir, basename) trgs = [ base_str + '_1_' + os.path.basename(left), base_str + '_2_' + os.path.basename(right) ] orphans = [ base_str + '_1s_' + os.path.basename(left), base_str + '_2s_' + os.path.basename(right) ] cmd = ('java -jar {0!s} PE -threads {3!s} {1!s} {2!s} {5!s} {4!s} {7!s} ' '{6!s} ILLUMINACLIP:{8!s}:2:30:10 LEADING:3 TRAILING:3 ' 'SLIDINGWINDOW:4:15 MINLEN:35').format( tool_path_check(TOOLS_DICT['trimmomatic'].full_exe[0]), left, right, cpu_cap, orphans[0], trgs[0], orphans[1], trgs[1], TOOLS_DICT['trimmomatic'].full_exe[1]) name = basename out, err = gen_logs(opc.path_logs, name) return Task(command=cmd, dependencies=tasks, name=name, stdout=out, stderr=err, targets=trgs, cpu=cpu_cap)
def build_salmon_task(path_assembly,assembly_name,out_dir,cpu_cap,tasks): trgs = ['{0!s}/{1!s}_salmon'.format(out_dir, assembly_name)] cmd = '{0!s} index --transcripts {1!s} --index {2!s}/{3!s}_salmon --threads {4!s} --type quasi'.format( fg.tool_path_check(TOOLS_DICT['salmon'].full_exe[0]),path_assembly, out_dir, assembly_name, cpu_cap) name = 'build_salmon_' + assembly_name out,err = fg.GEN_LOGS(name) return Task(command=cmd,dependencies=tasks,targets=trgs,name=name,stdout=out,stderr=err, cpu=cpu_cap)
def gene_trans_map_task(path_assembly,out_dir,tasks): assembly_name = os.path.basename(path_assembly).split('.fa')[0] trgs = ['{0!s}/{1!s}.gene_trans_map'.format(out_dir, assembly_name)] cmd = '{0!s} {1!s} > {2!s}'.format(fg.tool_path_check(TOOLS_DICT['trinity'].full_exe[1]),path_assembly,trgs[0]) name = 'gene_trans_map_' + assembly_name out,err = fg.GEN_LOGS(name) return Task(command=cmd,dependencies=tasks,targets=trgs,name=name,stdout=out,stderr=err)
def tmhmm_task(path_orfs,out_dir,tasks): out_name = os.path.basename(path_orfs).split('.')[0] trgs = ['{0!s}/{1!s}.tmhmm'.format(out_dir, out_name)] cmd = 'cd {0!s}; {1!s} --short < {2!s} > {3!s}'.format(out_dir,fg.tool_path_check(TOOLS_DICT['tmhmm'].full_exe[0]),path_orfs,trgs[0]) name = 'tmhmm_' + out_name out,err = fg.GEN_LOGS(name) return Task(command=cmd,dependencies=tasks,targets=trgs,name=name,stdout=out,stderr=err)
def ret(): for t in other_dependencies: try: if( not d.finished()): return False except Task.ExitCodeException: return False assembly_files = sorted(os.listdir(reads_dir)) assembly_files = [os.path.join(reads_dir, f) for f in assembly_files] new_lefts = [[g for g in assembly_files if(os.path.basename(f) in g)] for f in lefts] new_lefts = [k[0] for k in new_lefts if(len(k) > 0)] new_rights = [[g for g in assembly_files if(os.path.basename(f) in g)] for f in rights] new_rights = [k[0] for k in new_rights if(len(k) > 0)] new_singles = [[g for g in assembly_files if(os.path.basename(f) in g)] for f in singles] new_singles = [k[0] for k in new_singles if(len(k) > 0)] if(len(new_lefts) == len(lefts) and len(new_rights) == len(rights) and len(new_singles) == len(singles) and len(new_lefts)+len(new_singles) != 0): new_lefts = ','.join(new_lefts+new_singles) new_rights = ','.join(new_rights) new_lefts = '--left '+new_lefts if(len(new_lefts) > 0) else '' new_rights = '--right '+new_rights if(len(new_rights) > 0) else '' cmd = '{0!s} --assembly {1!s} {2!s} {3!s} --threads {4!s} {5!s} --output {6!s}'.format( fg.tool_path_check(TOOLS_DICT['transrate'].full_exe[0]), assembly_path, new_lefts, new_rights, cpu_cap, reference, transrate_dir) transrate_task.command = cmd else: print('Unable to match input files with trimmed output. Continuing transrate using input files instead.') return True
def build_kallisto_task(assembly_path, assembly_name,out_dir,tasks): trgs = [] cmd = '{0!s} index -i {1!s}/{2!s}_kallisto {3!s}'.format( fg.tool_path_check(TOOLS_DICT['kallisto'].full_exe[0]),out_dir,assembly_name,assembly_path) name = 'build_kallisto' out,err = fg.GEN_LOGS(name) return Task(command=cmd,dependencies=tasks,targets=trgs,name=name,stdout=out,stderr=err)
def salmon_task(opc, index, left, right, out_name, gene_map, out_dir, cpu_cap, tasks): trgs = [ '{0!s}/{1!s}/quant.sf'.format(out_dir, out_name), '{0!s}/{1!s}/quant.genes.sf'.format(out_dir, out_name) ] if len(gene_map) > 0: trans_gene_map = ' --geneMap {0!s}'.format(gene_map) cmd = ( '{0!s} quant -i {1!s} -l IU -1 {2!s} -2 {3!s} -o {4!s}/{5!s} ' #'--geneMap {6!s} -p {7!s} --extraSensitive; cp {4!s}/{5!s}/quant.sf ' '{6!s} -p {7!s} --dumpEq' ).format( #cmd = '{0!s} quant -i {1!s} -l IU -1 {2!s} -2 {3!s} -o {4!s}/{5!s} #--geneMap {6!s} -p {7!s} --extraSensitive --numBootstraps 30 --biasCorrect ; cp ' \ tool_path_check(TOOLS_DICT['salmon'].full_exe[0]), index, left, right, out_dir, out_name, trans_gene_map, cpu_cap) name = os.path.basename(index) + '_' + os.path.basename(left) out, err = gen_logs(opc.path_logs, name) return Task(command=cmd, dependencies=tasks, targets=trgs, name=name, stdout=out, stderr=err, cpu=cpu_cap)
def trinity_task(opc, path_assembly, out_dir, fastq, fastq2, unpaired, cpu_cap_trin, cpu_cap_bfly, mem_trin, mem_bfly, normalize_flag, tasks): ''' Defines the trinity task. Uses GEN_PATH_DIR(), PATH_TRINITY, NAME_ASSEMBLY Params : left - a 1/left fastq files right - a 2/right fastq files cpu_cap - number of threads used by trinity tasks - a list of tasks that this task is dependent on ''' normalize_flag = '--normalize_reads' if (normalize_flag) else '' input_str = '' if (unpaired != [] and fastq == []): input_str += '--single ' + ','.join(unpaired) if (fastq != []): input_str += '--left ' + ','.join(fastq + unpaired) input_str += ' --right ' + ','.join(fastq2) trgs = [path_assembly] cmd = ( '{0!s} --seqType fq {1!s} --CPU {2!s} --max_memory {3!s}G --bflyCalculateCPU {4!s} ' '--output {6!s}/trinity; cp {6!s}/trinity/Trinity.fasta {7!s};' ).format(tool_path_check(TOOLS_DICT['trinity'].full_exe[0]), input_str, cpu_cap_trin, mem_trin, normalize_flag, mem_bfly, out_dir, trgs[0]) name = 'trinity_assembly' out, err = gen_logs(opc.path_logs, name) cpu_cap = max(cpu_cap_trin, cpu_cap_bfly) return Task(command=cmd, dependencies=tasks, targets=trgs, name=name, cpu=cpu_cap, stdout=out, stderr=err)
def pfam_seq_task(path_orfs,out_dir, cpu_cap, tasks): out_name = os.path.basename(path_orfs).split('.')[0] trgs = ['{0!s}/{1!s}.pfam_tblout'.format(out_dir,out_name)] cmd = '{0!s} --cpu {1!s} --tblout {2!s} {3!s} {4!s}'.format( fg.tool_path_check(TOOLS_DICT['hmmer'].full_exe[0]),cpu_cap,trgs[0],PATH_PFAM_DATABASE, path_orfs) name = 'pfam_tblout_' + out_name out,err = fg.GEN_LOGS(name) return Task(command=cmd,dependencies=tasks,targets=trgs,name=name,stdout=out,stderr=err,cpu=cpu_cap)
def salmon_task(index,left,right,out_name,gene_map,out_dir,cpu_cap,tasks): trgs = ['{0!s}/{1!s}_quant.sf'.format(out_dir,out_name),'{0!s}/{1!s}_quant.genes.sf'.format(out_dir,out_name)] cmd = '{0!s} quant -i {1!s} -l IU -1 {2!s} -2 {3!s} -o {4!s}/{5!s} --geneMap {6!s} -p {7!s} --extraSensitive; cp ' \ '{4!s}/{5!s}/quant.sf {4!s}/{5!s}_quant.sf; cp {4!s}/{5!s}/quant.genes.sf {4!s}/{5!s}_quant.genes.sf'.format( fg.tool_path_check(TOOLS_DICT['salmon'].full_exe[0]),index,left,right,out_dir,out_name,gene_map,cpu_cap) name = 'salmon_' + os.path.basename(index) + '_' + os.path.basename(left) out,err = fg.GEN_LOGS(name) return Task(command=cmd,dependencies=tasks,targets=trgs,name=name,stdout=out,stderr=err,cpu=cpu_cap)
def tmhmm_task(opc, path_orfs, out_dir, tasks): out_name = os.path.basename(path_orfs).split('.')[0] trgs = ['{0!s}/{1!s}.tmhmm'.format(out_dir, out_name)] cmd = 'cd {0!s}; {1!s} --short < {2!s} > {3!s}'.format( out_dir, tool_path_check(TOOLS_DICT['tmhmm'].full_exe[0]), path_orfs, trgs[0]) name = 'tmhmm_' + out_name out, err = gen_logs(opc.path_logs, name) return Task(command=cmd, dependencies=tasks, targets=trgs, name=name, stdout=out, stderr=err)
def pfam_seq_task(opc, dbs, path_orfs, out_dir, cpu_cap, tasks): out_name = os.path.basename(path_orfs).split('.')[0] trgs = ['{0!s}/{1!s}.pfam_tblout'.format(out_dir, out_name)] cmd = '{0!s} --cpu {1!s} --tblout {2!s} {3!s} {4!s}'.format( tool_path_check(TOOLS_DICT['hmmer'].full_exe[0]), cpu_cap, trgs[0], dbs['pfam'].call_path, path_orfs) name = 'pfam_tblout_' + out_name out, err = gen_logs(opc.path_logs, name) return Task(command=cmd, dependencies=tasks, targets=trgs, name=name, stdout=out, stderr=err, cpu=cpu_cap)
def gene_trans_map_task(opc, path_assembly, out_dir, tasks): assembly_name = os.path.basename(path_assembly).split('.fa')[0] trgs = ['{0!s}/{1!s}.gene_trans_map'.format(out_dir, assembly_name)] cmd = 'perl {0!s} {1!s} > {2!s}'.format( tool_path_check(TOOLS_DICT['trinity'].full_exe[1]), path_assembly, trgs[0]) name = 'gene_trans_map_' + assembly_name out, err = gen_logs(opc.path_logs, name) return Task(command=cmd, dependencies=tasks, targets=trgs, name=name, stdout=out, stderr=err)
def build_blast_task(path_db,out_dir,dbtype,tasks,log_flag=True): trgs = [] #title doesn't seem to change the out name .. it's still xx.gz.psq, etc? CHECK. title = os.path.basename(path_assembly).split('.')[0] cmd = 'gunzip -c {0!s} | {1!s} -in - -dbtype {2!s} -title {3!s} -out {4!s}'.format( path_assembly, fg.tool_path_check(TOOLS_DICT['blast'].full_exe[0]),dbtype,title,out_dir) name = 'build_blastplus_db_' + title out, err = fg.GEN_LOGS(name) if(log_flag) else (None, None) return Task(command=cmd,dependencies=tasks,targets=trgs,name=name,stdout=out,stderr=err)
def intersect_bed_task(out_dir,bam_file,bed_reference,output_name,tasks): ''' ''' trgs = ['{0!s}/{1!s}.bed'.format(out_dir,output_name)] cmd = '{0!s} intersect -abam {1!s} -b {2!s} -wb -bed > {3!s}'.format( fg.tool_path_check(TOOLS_DICT['bedtools'].full_exe[0]),bam_file,bed_reference,trgs[0]) name = 'intersect_bed_'+output_name out,err = fg.GEN_LOGS(name) return Task(command=cmd,dependencies=tasks,targets=trgs,name=name,stdout=out,stderr=err)
def build_bowtie_task(path_assembly, assembly_name, out_dir, tasks): ''' ''' trgs = ['{0!s}/{1!s}.1.bt2'.format(out_dir,assembly_name)] cmd = '{0!s} --offrate 1 -f {1!s} {2!s}/{3!s}'.format( fg.tool_path_check(TOOLS_DICT['bowtie2'].full_exe[0]), path_assembly, out_dir, assembly_name) name = 'build_bowtie_' + assembly_name out,err = fg.GEN_LOGS(name) return Task(command=cmd,dependencies=tasks,targets=trgs,name=name,stdout=out,stderr=err)
def express_task(assembly_path,out_dir,out_name,bam_input,tasks): ''' ''' trgs = ['{0!s}/{1!s}.xprs'.format(out_dir,out_name)] cmd = ('mkdir {1!s}/{2!s}; {0!s} --output-dir {1!s}/{2!s} {3!s} {4!s}; mv ' '{1!s}/{2!s}/results.xprs {5!s}; rm -rf {1!s}/{2!s};').format( fg.tool_path_check(TOOLS_DICT['express'].full_exe[0]),out_dir,out_name,assembly_path,bam_input,trgs[0]) name = 'express_'+out_name out,err = fg.GEN_LOGS(name) return Task(command=cmd,dependencies=tasks,targets=trgs,name=name,stdout=out,stderr=err)
def rnammer_task(path_assembly, out_dir, tasks): assembly_name = os.path.basename(path_assembly).split('.fa')[0] path_to_rnammer = os.path.dirname(TOOLS_DICT['rnammer'].folder_name) trgs = ['{0!s}/{1!s}.fasta.rnammer.gff'.format(out_dir,assembly_name)] cmd = ("cd {0!s}; {1!s} --transcriptome {2!s} --path_to_rnammer {4!s} " "--org_type euk; cd -").format(out_dir,fg.tool_path_check(TOOLS_DICT['rnammer'].full_exe[0]), path_assembly,path_to_rnammer) name = 'rnammer_' + assembly_name out,err = GEN_LOGS(name) return Task(command=cmd,dependencies=tasks,targets=trgs,name=name,stdout=out,stderr=err)
def transdecoder_longorfs_task(path_assembly, path_transdecoder_output, cpu_cap, tasks): assembly_name = os.path.basename(path_assembly).split('.fa')[0] longorf_outbase = os.path.join(path_transdecoder_output, assembly_name + '.fasta.transdecoder_dir') trgs = ['{0!s}/longest_orfs.pep'.format(longorf_outbase),'{0!s}/longest_orfs.gff3'.format(longorf_outbase), '{0!s}/longest_orfs.cds'.format(longorf_outbase)] cmd = ("mkdir -p {0!s}; cd {0!s}; {1!s} -t {2!s}").format(path_transdecoder_output, fg.tool_path_check(TOOLS_DICT['transdecoder'].full_exe[0]),path_assembly,cpu_cap) name = 'TransDecoder_LongORFs_' + assembly_name out,err = fg.GEN_LOGS(name) return Task(command=cmd,dependencies=tasks,targets=trgs,name=name,stdout=out,stderr=err,cpu=cpu_cap)
def rnammer_task(opc, path_assembly, out_dir, tasks): assembly_name = os.path.basename(path_assembly).split('.fa')[0] path_to_rnammer = os.path.dirname(TOOLS_DICT['rnammer'].folder_name) trgs = ['{0!s}/{1!s}.fasta.rnammer.gff'.format(out_dir, assembly_name)] cmd = ("cd {0!s}; {1!s} --transcriptome {2!s} --path_to_rnammer {4!s} " "--org_type euk; cd -").format( out_dir, tool_path_check(TOOLS_DICT['rnammer'].full_exe[0]), path_assembly, path_to_rnammer) name = 'rnammer_' + assembly_name out, err = gen_logs(opc.path_logs, name) return Task(command=cmd, dependencies=tasks, targets=trgs, name=name, stdout=out, stderr=err)
def trimmomatic_unpaired_task(out_dir,input1, cpu_cap, basename, tasks): form = lambda s, i : s.format(out_dir, basename, os.path.basename(i)) trgs = [form('{0!s}/{1!s}_{2!s}', input1)] orphans = [form('{0!s}/{1!s}_orphans_{2!s}', input1)] cmd = ('java -jar {0!s} SE -threads {4!s} {1!s} {2!s} {3!s} ILLUMINACLIP:' '{5!s}:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:35' ).format(fg.tool_path_check(TOOLS_DICT['trimmomatic'].full_exe[0]), input1, trgs[0], orphans[0],cpu_cap, TOOLS_DICT['trimmomatic'].full_exe[2]) #PATH_TRIMMOMATIC_ADAPTERS_SINGLE) name = basename out, err = fg.GEN_LOGS(name) return Task(command=cmd, dependencies=tasks, name=name, stdout=out, stderr=err, targets=trgs, cpu=cpu_cap)
def transdecoder_longorfs_task(opc, path_assembly, path_transdecoder_output, cpu_cap, tasks): assembly_name = os.path.basename(path_assembly).split('.fa')[0] longorf_outbase = os.path.join(path_transdecoder_output, opc.assembly_name + '.fasta.transdecoder_dir') trgs = ['{0!s}/longest_orfs.pep'.format(longorf_outbase), '{0!s}/longest_orfs.gff3'.format(longorf_outbase), '{0!s}/longest_orfs.cds'.format(longorf_outbase)] cmd = ("mkdir -p {0!s}; cd {0!s}; {1!s} -t {2!s}").format(path_transdecoder_output, tool_path_check(TOOLS_DICT['transdecoder'].full_exe[0]), path_assembly, cpu_cap) name = 'TransDecoder_LongORFs_' + assembly_name out, err = gen_logs(opc.path_logs, name) return Task(command=cmd, dependencies=tasks, targets=trgs, name=name, stdout=out, stderr=err, cpu=cpu_cap)
def bowtie2_task(bowtie2_index,out_dir,fastq1,fastq2,out_name,opt,cpu_cap,tasks): ''' ''' opts = ['-a -t --end-to-end', '-t --local'] trgs = ['{0!s}/{1!s}.bam'.format(out_dir,out_name)] cmd = ('{0!s} {1!s} -L {2!s} -N 1 --maxins 800 --threads {3!s} -x {4!s} -1 ' '{5!s} -2 {6!s} | samtools view -Sb - > {7!s} ').format(fg.tool_path_check(TOOLS_DICT['bowtie2'].full_exe[1]), opts[opt],22,cpu_cap,bowtie2_index,fastq1,fastq2,trgs[0]) name = 'bowtie2_'+out_name out,err = fg.GEN_LOGS(name) return Task(command=cmd,dependencies=tasks,targets=trgs,name=name,stdout=out,stderr=err,cpu=cpu_cap)
def prinseq_unpaired_task(out_dir,input1, basename, opts, tasks): ''' ''' trgs = ['{0!s}/{1!s}_{2!s}'.format(out_dir, basename, os.path.basename(input1))] cmd = ('perl {0!s} -fastq {1!s} --out_format 3 --out_good {2!s}/{3!s} --out_bad null ' '--trim_qual_left 20 --trim_qual_right 20 --trim_qual_type min --min_len 35 ' '--trim_tail_left 8 --trim_tail_right 8 {4!s} -log; mv {2!s}/{3!s}.fastq {5!s}' ).format(fg.tool_path_check(TOOLS_DICT['prinseq'].full_exe[0]), input1, out_dir, basename, opts, trgs[0]) name = basename out, err = fg.GEN_LOGS(name) return Task(command = cmd, dependencies=tasks, name=name, stdout=out, stderr=err, targets=trgs)
def build_bowtie_task(opc, path_assembly, assembly_name, out_dir, tasks): trgs = ['{0!s}/{1!s}.1.bt2'.format(out_dir, assembly_name)] cmd = '{0!s} --offrate 1 -f {1!s} {2!s}/{3!s}'.format( tool_path_check(TOOLS_DICT['bowtie2'].full_exe[0]), path_assembly, out_dir, assembly_name) name = 'build_bowtie_' + assembly_name out, err = gen_logs(opc.path_logs, name) return Task(command=cmd, dependencies=tasks, targets=trgs, name=name, stdout=out, stderr=err)
def cegma_task(out_dir,assembly,cpu_cap, tasks): ''' Defines the cegma task. Uses PATH_DIR, PATH_CEGMA, NAME_ASSEMBLY. Params : cpu_cap - number of threads to be used by cegma tasks - a list of tasks that this task is dependant on (trinity_task) ''' assembly_name = os.path.basename(assembly).split('.fa')[0] trgs = ['{0!s}/{1!s}.completeness_report'.format(out_dir,assembly_name)] cmd = '{0!s} -g {1!s} -v -o {3!s}/{2!s} -T {4!s}'.format(fg.tool_path_check(TOOLS_DICT['cegma'].full_exe[0]), assembly,assembly_name,out_dir,cpu_cap) name = 'cegma' out,err = fg.GEN_LOGS(name) return Task(command=cmd,dependencies=tasks,targets=trgs,name=name,cpu=cpu_cap,stdout=out,stderr=err)
def diamond_task(blast_type, out_dir, path_query, ref, cpu_cap, tasks): ''' valid blast_types: "blastx", "blastp" ''' base_ref = os.path.basename(ref) query_name = os.path.basename(path_query).split('.')[0] trgs = ['{0!s}/{1!s}_{2!s}.diamond_{3!s}'.format(out_dir, query_name, base_ref, blast_type)] pseudo_trgs = ['{0!s}/diamond_{1!s}_{2!s}'.format(out_dir, base_ref, blast_type)] cmd = ('{0!s} {1!s} --db {2!s} --query {3!s} --daa {4!s} --tmpdir {5!s} ' '--max-target-seqs 20 --sensitive --threads {6!s} --evalue 0.001; {0!s} view ' '--daa {4!s}.daa --out {7!s};').format( fg.tool_path_check(TOOLS_DICT['diamond'].full_exe[0]), blast_type, ref, path_query, pseudo_trgs[0], out_dir, cpu_cap, trgs[0]) name = 'diamond_{0!s}_{1!s}_{2!s}'.format(blast_type, base_ref, query_name) out, err = fg.GEN_LOGS(name) return Task(command=cmd, dependencies=tasks, cpu=cpu_cap, targets=trgs, name=name, stdout=out, stderr=err)
def trimmomatic_task(out_dir,left, right, cpu_cap, basename, tasks): form = lambda s, i : s.format(out_dir, basename, os.path.basename(i)) trgs = [form('{0!s}/{1!s}_1_{2!s}', left), form('{0!s}/{1!s}_2_{2!s}', right)] orphans = [form('{0!s}/{1!s}_1s_{2!s}', left), form('{0!s}/{1!s}_2s_{2!s}', right)] cmd = ('java -jar {0!s} PE -threads {3!s} {1!s} {2!s} {5!s} {4!s} {7!s} ' '{6!s} ILLUMINACLIP:{8!s}:2:30:10 LEADING:3 TRAILING:3 ' 'SLIDINGWINDOW:4:15 MINLEN:35').format( fg.tool_path_check(TOOLS_DICT['trimmomatic'].full_exe[0]), left, right, cpu_cap, orphans[0], trgs[0], orphans[1], trgs[1], TOOLS_DICT['trimmomatic'].full_exe[1]) #PATH_TRIMMOMATIC_ADAPTERS_PAIRED) name = basename out, err = fg.GEN_LOGS(name) return Task(command=cmd, dependencies=tasks, name=name, stdout=out, stderr=err, targets=trgs, cpu=cpu_cap)
def diamond_task(opc, blast_type, out_dir, path_query, ref, cpu_cap, tasks): ''' valid blast_types: "blastx", "blastp" ''' base_ref = os.path.basename(ref) query_name = os.path.basename(path_query).split('.')[0] trgs = ['{0!s}/{1!s}_{2!s}.diamond_{3!s}'.format(out_dir, query_name, base_ref, blast_type)] pseudo_trgs = ['{0!s}/diamond_{1!s}_{2!s}'.format(out_dir, base_ref, blast_type)] cmd = ('{0!s} {1!s} --db {2!s} --query {3!s} --daa {4!s} --tmpdir {5!s} ' '--max-target-seqs 20 --sensitive --threads {6!s} --evalue 0.001; {0!s} view ' '--daa {4!s}.daa --out {7!s};').format( tool_path_check(TOOLS_DICT['diamond'].full_exe[0]), blast_type, ref, path_query, pseudo_trgs[0], out_dir, cpu_cap, trgs[0]) name = 'diamond_{0!s}_{1!s}_{2!s}'.format(blast_type, base_ref, query_name) out, err = gen_logs(opc.path_logs, name) return Task(command=cmd, dependencies=tasks, cpu=cpu_cap, targets=trgs, name=name, stdout=out, stderr=err)
def kallisto_task(opc, index, out_dir, out_name, left, right, tasks): # NO TARGETS trgs = [] cmd = '{0!s} quant -i {1!s} -o {2!s}/{3!s} {4!s} {5!s}'.format( tool_path_check(TOOLS_DICT['kallisto'].full_exe[0]), index, out_dir, out_name, left, right) name = 'kallisto' out, err = gen_logs(opc.path_logs, name) return Task(command=cmd, dependencies=tasks, targets=trgs, name=name, stdout=out, stderr=err)
def build_kallisto_task(opc, assembly_path, assembly_name, out_dir, tasks): # NO TARGETS trgs = [] cmd = '{0!s} index -i {1!s}/{2!s}_kallisto {3!s}'.format( tool_path_check(TOOLS_DICT['kallisto'].full_exe[0]), out_dir, assembly_name, assembly_path) name = 'build_kallisto' out, err = gen_logs(opc.path_logs, name) return Task(command=cmd, dependencies=tasks, targets=trgs, name=name, stdout=out, stderr=err)
def build_blast_task(path_db, out_dir, dbtype, tasks): trgs = [] # title doesn't seem to change the out name .. it's still xx.gz.psq, etc? CHECK. title = os.path.basename(path_db).split('.')[0] cmd = 'gunzip -c {0!s} | {1!s} -in - -dbtype {2!s} -title {3!s} -out {4!s}'.format( path_db, tool_path_check(TOOLS_DICT['blast'].full_exe[0]), dbtype, title, out_dir) name = 'build_blastplus_db_' + title out, err = gen_db_logs(name) return Task(command=cmd, dependencies=tasks, targets=trgs, name=name, stdout=out, stderr=err)
def express_task(opc, bowtie2_index, assembly_path, out_dir, out_name, bam_input, tasks): trgs = ['{0!s}/{1!s}.xprs'.format(out_dir, out_name)] cmd = ('mkdir {1!s}/{2!s}; {0!s} --output-dir {1!s}/{2!s} {3!s} {4!s}; mv ' '{1!s}/{2!s}/results.xprs {5!s}; rm -rf {1!s}/{2!s};').format( tool_path_check(TOOLS_DICT['express'].full_exe[0]), out_dir, out_name, assembly_path, bam_input, trgs[0]) name = 'express_' + os.path.basename(bowtie2_index) + '_' + out_name out, err = gen_logs(opc.path_logs, name) return Task(command=cmd, dependencies=tasks, targets=trgs, name=name, stdout=out, stderr=err)
def busco_task(assembly_path, assembly_name, out_dir,reference_name, cpu_cap, tasks): ''' Defines the busco task. Uses PATH_DIR, PATH_BUSCO, PATH_BUSCO_REFERENCE Params : reference_name - Name of the reference file to be used by busco cpu_cap - the cpu limit to be gicen to busco. tasks - a list of tasks that this task is dependant on. ''' trgs = ['{0!s}/run_busco_{1!s}_{2!s}'.format(out_dir,assembly_name,reference_name)] cmd = ('cd {0!s}; /matta1/biotools/anaconda/envs/py3k/bin/python {1!s} ' '-o busco_{3!s}_{2!s} -in {4!s} -l {5!s}/{2!s}_buscos/{2!s} -m trans -f -c {6!s}' ).format(out_dir,fg.tool_path_check(TOOLS_DICT['busco_plant'].full_exe[0]),reference_name,assembly_name,assembly_path, PATH_BUSCO_REFERENCE,cpu_cap) name = 'busco_'+ reference_name + '_' + assembly_name out,err = fg.GEN_LOGS(name) return Task(command=cmd,dependencies=tasks,targets=trgs,name=name,cpu=cpu_cap,stdout=out,stderr=err)
def rnaspades_task(path_assembly, out_dir, left, right, unpaired, cpu_cap, tasks): ''' ''' virtual_target = '{0!s}/rna_spades_out_dir'.format(out_dir) trgs = [path_assembly] input_strings = [] if(left!=[]): input_strings.append('-1 '+left[0]) input_strings.append('-2 '+right[0]) if(unpaired!=[]): input_strings.append('-s '+unpaired[0]) cmd = '{0!s} {1!s} --threads {2!s} -o {3!s}; cp {3!s}/contigs.fasta {4!s};'.format( fg.tool_path_check(TOOLS_DICT['rnaspades'].full_exe[0]),' '.join(input_strings),cpu_cap,virtual_target,trgs[0]) name = 'rnaSPAdes_assembly' out,err = fg.GEN_LOGS(name) return Task(command=cmd,dependencies=tasks,targets=trgs,name=name,stdout=out,stderr=err,cpu=cpu_cap)
def intersect_bed_task(opc, out_dir, bam_file, bed_reference, output_name, tasks): trgs = ['{0!s}/{1!s}.bed'.format(out_dir, output_name)] # cmd = '{0!s} intersect -abam {1!s} -b {2!s} -wb -bed > {3!s}'.format( cmd = '{0!s} -abam {1!s} -b {2!s} -wb -bed > {3!s}'.format( tool_path_check(TOOLS_DICT['bedtools'].full_exe[0]), bam_file, bed_reference, trgs[0]) name = 'intersect_bed_' + os.path.basename( bed_reference) + '_' + output_name out, err = gen_logs(opc.path_logs, name) return Task(command=cmd, dependencies=tasks, targets=trgs, name=name, stdout=out, stderr=err)
def build_salmon_task(opc, path_assembly, assembly_name, out_dir, cpu_cap, tasks): trgs = ['{0!s}/{1!s}_salmon'.format(out_dir, assembly_name)] cmd = ('{0!s} index --transcripts {1!s} --index {2!s}/{3!s}_salmon ' '--threads {4!s} --type quasi').format( tool_path_check(TOOLS_DICT['salmon'].full_exe[0]), path_assembly, out_dir, assembly_name, cpu_cap) name = 'build_salmon_' + assembly_name out, err = gen_logs(opc.path_logs, name) return Task(command=cmd, dependencies=tasks, targets=trgs, name=name, stdout=out, stderr=err, cpu=cpu_cap)
def build_diamond_task(path_db_fasta, out_path, tasks): ''' Is there a reason that we aren't checking for the installation of daimond? ''' title = os.path.basename(out_path) trgs = ['{0!s}'.format(out_path + '.dmnd')] cmd = '{0!s} makedb --in {1!s} --db {2!s}'.format( tool_path_check(TOOLS_DICT['diamond'].full_exe[0]), path_db_fasta, out_path) name = 'build_diamond_' + title out, err = gen_db_logs(name) return Task(command=cmd, dependencies=tasks, targets=trgs, name=name, stdout=out, stderr=err)
def blast_task(blast_type, out_dir, path_query, path_db, cpu_cap, tasks): exe_index = 1 if blast_type == 'blastx': exe_index = 1 elif blast_type == 'blastp': exe_index = 2 assembly_name = os.path.basename(path_query).split('.')[0] db_name = os.path.basename(path_db).split('.')[0] trgs = ["{0!s}/{1!s}_{2!s}.{3!s}".format(out_dir, assembly_name, db_name, blast_type)] cmd = ('{0!s} -query {1!s} -db {2!s} -num_threads {3!s} -max_target_seqs 1 ' '-outfmt "6 qseqid sseqid pident length mismatch gapopen qstart qend sstart ' 'send evalue bitscore stitle slen" -evalue 0.0001 > {4!s}' ).format(fg.tool_path_check(TOOLS_DICT['blast'].full_exe[exe_index]), path_query, path_db, cpu_cap, trgs[0]) name = '{0!s}_{1!s}_{2!s}'.format(assembly_name, blast_type, db_name) out,err = fg.GEN_LOGS(name) return Task(command=cmd,dependencies=tasks,targets=trgs,name=name,cpu=cpu_cap,stdout=out,stderr=err)
def blast_task(opc, blast_type, out_dir, path_query, path_db, cpu_cap, tasks): exe_index = 1 if(blast_type == 'blastx'): exe_index = 1 elif(blast_type == 'blastp'): exe_index = 2 assembly_name = os.path.basename(path_query).split('.')[0] db_name = os.path.basename(path_db).split('.')[0] trgs = ["{0!s}/{1!s}_{2!s}.{3!s}".format(out_dir, assembly_name, db_name, blast_type)] cmd = ('{0!s} -query {1!s} -db {2!s} -num_threads {3!s} -max_target_seqs 1 ' '-outfmt "6 qseqid sseqid pident length mismatch gapopen qstart qend sstart ' 'send evalue bitscore stitle slen" -evalue 0.0001 > {4!s}' ).format(tool_path_check(TOOLS_DICT['blast'].full_exe[exe_index]), path_query, path_db, cpu_cap, trgs[0]) name = '{0!s}_{1!s}_{2!s}'.format(assembly_name, blast_type, db_name) out, err = gen_logs(opc.path_logs, name) return Task(command=cmd, dependencies=tasks, targets=trgs, name=name, cpu=cpu_cap, stdout=out, stderr=err)
def bowtie2_unpaired_task(opc, bowtie2_index, out_dir, fastq, out_name, opt, cpu_cap, tasks): opts = ['-a -t --end-to-end', '-t --local', '-k 200 --end-to-end'] trgs = ['{0!s}/{1!s}.bam'.format(out_dir, out_name)] cmd = ('{0!s} {1!s} -L {2!s} -N 1 --threads {3!s} -x {4!s} -U ' '{5!s} | samtools view -Sb - > {6!s} ').format( tool_path_check(TOOLS_DICT['bowtie2'].full_exe[1]), opts[opt], 22, cpu_cap, bowtie2_index, fastq, trgs[0]) name = 'bowtie2_' + os.path.basename(bowtie2_index) + '_' + out_name out, err = gen_logs(opc.path_logs, name) return Task(command=cmd, dependencies=tasks, targets=trgs, name=name, stdout=out, stderr=err, cpu=cpu_cap)
def pfam_build_task(source, out_root_path, tasks): ''' Trgs seem to be declared without respect to input. ''' trgs = [ os.path.join(statics.PATH_PFAM_DIR, os.path.basename(source)) + '.h3f' ] cmd = 'cd {0!s} ; {1!s} -f {2!s};'.format( statics.PATH_DATABASES, tool_path_check(TOOLS_DICT['hmmer'].full_exe[1]), source) name = 'hmmpress_' + os.path.basename(source) out, err = gen_db_logs(name) return Task(command=cmd, dependencies=tasks, targets=trgs, name=name, stdout=out, stderr=err)
def rcorrector_task(opc, out_dir, left, right, cpu_cap, basename, tasks): trgs = [ '{0!s}/{1!s}.cor.fq'.format(out_dir, os.path.basename(left)), '{0!s}/{1!s}.corr.fq'.format(out_dir, os.path.basename(right)) ] cmd = 'perl {0!s} -1 {1!s} -2 {2!s} -t {3!s}'.format( tool_path_check(TOOLS_DICT['rcorrector'].full_exe[0]), left, right, cpu_cap) name = 'Rcorrector_' + basename out, err = gen_logs(opc.path_logs, name) return Task(command=cmd, dependencies=tasks, name=name, stdout=out, stderr=err, targets=trgs, cpu=cpu_cap)
def trimmomatic_unpaired_task(opc, out_dir, input1, cpu_cap, basename, tasks): trgs = [ '{0!s}/{1!s}_{2!s}'.format(out_dir, basename, os.path.basename(input1)) ] cmd = ('java -jar {0!s} SE -threads {3!s} {1!s} {2!s} ILLUMINACLIP:' '{4!s}:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:35' ).format(tool_path_check(TOOLS_DICT['trimmomatic'].full_exe[0]), input1, trgs[0], cpu_cap, TOOLS_DICT['trimmomatic']. full_exe[2]) # PATH_TRIMMOMATIC_ADAPTERS_SINGLE) name = basename out, err = gen_logs(opc.path_logs, name) return Task(command=cmd, dependencies=tasks, name=name, stdout=out, stderr=err, targets=trgs, cpu=cpu_cap)
def prinseq_unpaired_task(opc, out_dir, input1, basename, opts, tasks): trgs = [ '{0!s}/{1!s}_{2!s}'.format(out_dir, basename, os.path.basename(input1)) ] cmd = ( 'perl {0!s} -fastq {1!s} --out_format 3 --out_good {2!s}/{3!s} --out_bad null ' '--trim_qual_left 20 --trim_qual_right 20 --trim_qual_type min --min_len 35 ' '--trim_tail_left 8 --trim_tail_right 8 {4!s} -log; mv {2!s}/{3!s}.fastq {5!s}' ).format(tool_path_check(TOOLS_DICT['prinseq'].full_exe[0]), input1, out_dir, basename, opts, trgs[0]) name = basename out, err = gen_logs(opc.path_logs, name) return Task(command=cmd, dependencies=tasks, name=name, stdout=out, stderr=err, targets=trgs)
def transrate_task(reads_dir, assembly_path, assembly_name,lefts, rights, singles, out_dir, transrate_dir, cpu_cap, tasks, reference = ''): #, cpu_cap, tasks): trgs = ['{0!s}/assemblies.csv'.format(transrate_dir),'{0!s}/{1!s}/good.{1!s}.fasta'.format(transrate_dir,assembly_name),'{0!s}/{1!s}/{1!s}.fasta_quant.sf'.format(transrate_dir,assembly_name)] orig_lefts = lefts orig_rights = rights orig_singles = singles lefts = ','.join(lefts+singles) rights = ','.join(rights) lefts = '--left '+lefts if(len(lefts) > 0) else '' rights = '--right '+rights if(len(rights) > 0) else '' reference = '--reference ' + reference if(reference != '') else '' cmd = '{0!s} --assembly {1!s} {2!s} {3!s} --threads {4!s} {5!s} --output {6!s}'.format( fg.tool_path_check(TOOLS_DICT['transrate'].full_exe[0]), assembly_path, lefts, rights, cpu_cap, reference, transrate_dir) name = 'transrate_' + assembly_name out, err = fg.GEN_LOGS(name) temp_task = Task(command=cmd, dependencies=[], targets=trgs, name=name, cpu=cpu_cap, stdout=out, stderr=err, max_wall_time=720) deps = transrate_dep_generator(reads_dir, temp_task, orig_lefts, orig_rights, orig_singles, reference, assembly_path, cpu_cap, transrate_dir, tasks) temp_task.dependencies = [deps] return temp_task
def transdecoder_predict_orfs_task(path_assembly,path_transdecoder_output,tasks,pfam_input='',blastp_input=''): ''' Use transdecoder to predict ORF's from input fasta file. Required for downstream blastp, pfam, tmhmm, signalp. Targets: *transdecoder.* ''' pfam,blastp,retain_blastp, retain_pfam = '','','','' if len(pfam_input) > 0: pfam = '--retain_pfam_hits ' + pfam_input retain_pfam = '_retain_pfam' if len(blastp_input) > 0: blastp = '--retain_blastp_hits ' + blastp_input retain_blastp = '_retain_blastp' assembly_name = os.path.basename(path_assembly).split('.fa')[0] trgs = ['{0!s}/{1!s}.fasta.transdecoder.pep'.format(path_transdecoder_output,assembly_name),'{0!s}/{1!s}.fasta.transdecoder.bed'.format(path_transdecoder_output,assembly_name)] cmd = ("mkdir -p {0!s}; cd {0!s}; {1!s} -t {2!s} {3!s} {4!s}").format(path_transdecoder_output, fg.tool_path_check(TOOLS_DICT['transdecoder'].full_exe[1]),path_assembly,pfam, blastp) name = 'TransDecoder_Predict' + assembly_name + retain_pfam + retain_blastp out,err = fg.GEN_LOGS(name) return Task(command=cmd,dependencies=tasks,targets=trgs,name=name,stdout=out,stderr=err)
def transrate_task(opc, reads_dir, assembly_path, assembly_name, lefts, rights, out_dir, transrate_dir, cpu_cap, tasks, reference=''): #, cpu_cap, tasks): trgs = [ '{0!s}/assemblies.csv'.format(transrate_dir), '{0!s}/{1!s}/good.{1!s}.fasta'.format(transrate_dir, assembly_name), '{0!s}/{1!s}/{1!s}.fasta_quant.sf'.format(transrate_dir, assembly_name) ] orig_lefts = lefts orig_rights = rights lefts = ','.join(lefts) rights = ','.join(rights) lefts = '--left ' + lefts if (len(lefts) > 0) else '' rights = '--right ' + rights if (len(rights) > 0) else '' reference = '--reference ' + reference if (reference != '') else '' #cmd = '{0!s} --assembly {1!s} --threads {4!s} {5!s} --output {6!s}'.format( #no reads cmd = '{0!s} --assembly {1!s} {2!s} {3!s} --threads {4!s} {5!s} --output {6!s}'.format( tool_path_check(TOOLS_DICT['transrate'].full_exe[0]), assembly_path, lefts, rights, cpu_cap, reference, transrate_dir) name = 'transrate_' + assembly_name out, err = gen_logs(opc.path_logs, name) temp_task = Task(command=cmd, dependencies=[], targets=trgs, name=name, cpu=cpu_cap, stdout=out, stderr=err, max_wall_time=7200000) deps = transrate_dep_generator(reads_dir, temp_task, orig_lefts, orig_rights, reference, assembly_path, cpu_cap, transrate_dir, tasks) temp_task.dependencies = [deps] return temp_task
def prinseq_task(out_dir,input_1, input_2, basename, opts, tasks): ''' Defines prinseq task. Uses GEN_PATH_DIR(), PATH_PRINSEQ Params : input_1 - a list of 1/left fastq files input_2 - a list of 2/right fastq files basename - the basename for all output files opts - optional params for trinity task. tasks = the tasks that this task is dependent on ''' trgs = ['{0!s}/{1!s}_1_{2!s}'.format(out_dir,basename,os.path.basename(input_1)), '{0!s}/{1!s}_2_{2!s}'.format(out_dir,basename,os.path.basename(input_2))] pseudo_trgs = ['{0!s}/{1!s}_{2!s}.fastq'.format(out_dir,basename,x) for x in range(1,3)] cmd = ('perl {0!s} -fastq {1!s} -fastq2 {2!s} --out_format 3 --out_good {3!s}/{4!s} ' '--out_bad null --trim_qual_left 20 --trim_qual_right 20 --trim_qual_type min ' '--min_len 55 --trim_tail_left 8 --trim_tail_right 8 {5!s} -log; mv {6!s} {7!s};' ' mv {8!s} {9!s};').format(fg.tool_path_check(TOOLS_DICT['prinseq'].full_exe[0]), input_1, input_2, out_dir, basename, opts,pseudo_trgs[0],trgs[0],pseudo_trgs[1],trgs[1]) name = basename out,err = fg.GEN_LOGS(name) return Task(command = cmd, dependencies=tasks, name=name, stdout=out, stderr=err, targets=trgs)
def cegma_task(opc, out_dir, assembly, cpu_cap, tasks): ''' Defines the cegma task. Uses PATH_DIR, PATH_CEGMA, NAME_ASSEMBLY. Params : cpu_cap - number of threads to be used by cegma tasks - a list of tasks that this task is dependant on (trinity_task) ''' assembly_name = os.path.basename(assembly).split('.fa')[0] trgs = ['{0!s}/{1!s}.completeness_report'.format(out_dir, assembly_name)] cmd = '{0!s} -g {1!s} -v -o {3!s}/{2!s} -T {4!s}'.format( tool_path_check(TOOLS_DICT['cegma'].full_exe[0]), assembly, assembly_name, out_dir, cpu_cap) name = 'cegma' out, err = gen_logs(opc.path_logs, name) return Task(command=cmd, dependencies=tasks, targets=trgs, name=name, cpu=cpu_cap, stdout=out, stderr=err)
def ret(): for t in other_dependencies: try: if (not t.finished()): return False except Task.ExitCodeException: return False assembly_files = sorted(os.listdir(reads_dir)) assembly_files = [os.path.join(reads_dir, f) for f in assembly_files] new_lefts = [[g for g in assembly_files if (os.path.basename(f) in g)] for f in lefts] new_lefts = [k[0] for k in new_lefts if (len(k) > 0)] new_rights = [[ g for g in assembly_files if (os.path.basename(f) in g) ] for f in rights] new_rights = [k[0] for k in new_rights if (len(k) > 0)] # new_singles = [[g for g in assembly_files if(os.path.basename(f) in g)] for f in singles] # new_singles = [k[0] for k in new_singles if(len(k) > 0)] if (len(new_lefts) == len(lefts) and len(new_rights) == len(rights)): # and len(new_singles) == len(singles) # and len(new_lefts)+len(new_singles) != 0): new_lefts = ','.join(new_lefts) # +new_singles) new_rights = ','.join(new_rights) new_lefts = '--left ' + new_lefts if (len(new_lefts) > 0) else '' new_rights = '--right ' + new_rights if ( len(new_rights) > 0) else '' cmd = '{0!s} --assembly {1!s} {2!s} {3!s} --threads {4!s} {5!s} --output {6!s}'.format( #cmd = '{0!s} --assembly {1!s} --threads {4!s} {5!s} --output {6!s}'.format( #no reads tool_path_check(TOOLS_DICT['transrate'].full_exe[0]), assembly_path, new_lefts, new_rights, cpu_cap, reference, transrate_dir) transrate_task.command = cmd else: warnings.warn( 'Unable to match input files with trimmed output. Continuing transrate using input files instead.' ) return True
def trinity_task(path_assembly, out_dir, fastq, fastq2, unpaired, cpu_cap_trin, cpu_cap_bfly, mem_trin, mem_bfly, normalize_flag, tasks): ''' Defines the trinity task. Uses GEN_PATH_DIR(), PATH_TRINITY, NAME_ASSEMBLY Params : left - a 1/left fastq files right - a 2/right fastq files cpu_cap - number of threads used by trinity tasks - a list of tasks that this task is dependent on ''' normalize_flag = '--normalize_reads' if(normalize_flag) else '' input_str = '' if(unpaired!=[] and fastq==[]): input_str+='--single '+','.join(unpaired) if(fastq!=[]): input_str+='--left '+','.join(fastq+unpaired) input_str+=' --right '+','.join(fastq2) trgs = [path_assembly] cmd = ('{0!s} --seqType fq {1!s} --CPU {2!s} --max_memory {3!s}G --bflyCalculateCPU {4!s} ' '--output {6!s}/trinity; cp {6!s}/trinity/Trinity.fasta {7!s};' ).format(fg.tool_path_check(TOOLS_DICT['trinity'].full_exe[0]), input_str, cpu_cap_trin, mem_trin, normalize_flag, mem_bfly, out_dir, trgs[0]) name = 'trinity_assembly' out,err = fg.GEN_LOGS(name) return Task(command=cmd,dependencies=tasks,targets=trgs,name=name,cpu=max(cpu_cap_trin,cpu_cap_bfly),stdout=out,stderr=err)
def pfam_build_task(source, tasks, log_flag=True): trgs = [PATH_PFAM_DATABASE+'.h3f'] cmd = 'cd {0!s} ; {1!s} -f {2!s};'.format(fg.PATH_DATABASES, fg.tool_path_check(TOOLS_DICT['hmmer'].full_exe[1]), source) name = 'hmmpress' out, err = fg.GEN_LOGS(name) if(log_flag) else (None, None) return Task(command=cmd, dependencies=tasks, targets=trgs, name=name, stdout=out, stderr=err)