comparison metagene_readthrough.py @ 13:7c944fd9907e draft

release 2

12:ee3a3435ce43

        file_extension.close()
    except Exception,e:
        stop_err( 'Error during computing analysis : ' + str( e ) ) 


def cleaning_bam(bam):
    '''
        Remove reads unmapped, non uniquely mapped and reads with length lower than 25 and upper than 32, and mapping quality upper than 12
    '''
    try :
        header = subprocess.check_output(['samtools', 'view', '-H', bam], stderr= subprocess.PIPE)
        #header = results.split('\n')
        
        # check mapper for define multiple tag
        if re.search('bowtie', header):
            multi_tag = "XS:i:"
        elif re.search('bwa', header):
            multi_tag = "XT:A:M"
        else :
            stop_err("No PG tag find in"+bam+". Please use bowtie or bwa for mapping")
        
        tmp_sam = tempfile.mktemp()
        cmd = "samtools view %s > %s" % (bam, tmp_sam) 
        proc = subprocess.Popen( args=cmd, shell=True, stderr = subprocess.PIPE)
        returncode = proc.wait()
        
        
        with open(tempfile.mktemp(),'w') as out :
            out.write(header)
            with open(tmp_sam,'r') as sam :
                for line in sam :
                    if multi_tag not in line and line.split('\t')[1] != '4' and int(line.split('\t')[4]) > 12 :
                        if len(line.split('\t')[9]) < 32 and len(line.split('\t')[9]) > 25 :
                            out.write(line)
        bamfile = tempfile.mktemp()+'.bam'   
        cmd = "samtools view -hSb %s > %s" % (out.name,bamfile)
        proc = subprocess.Popen( args=cmd, shell=True, stderr = subprocess.PIPE)
        returncode = proc.wait()
        
        return bamfile
    
    except Exception,e:
        stop_err( 'Error during cleaning bam : ' + str( e ) ) 
    
def write_html_page(html,subfolder) :
        
        
    try :

            
        #GFF = store_gff(options.gff)
        #GFF = ribo_functions.store_gtf(options.gff)
        ## check gff reading
        if not GFF['order'] :
            stop_err( 'Incorrect GFF file' + str( e ) )
        clean_file = cleaning_bam(options.bamfile)
        compute_analysis(clean_file, GFF, options.fasta, options.gff, subfolder, options.extend)
        if os.path.exists( clean_file ):
            os.remove( clean_file )
        
        write_html_page(html_file,subfolder)

13:7c944fd9907e

        file_extension.close()
    except Exception,e:
        stop_err( 'Error during computing analysis : ' + str( e ) ) 


    
def write_html_page(html,subfolder) :
        
        
    try :

            
        #GFF = store_gff(options.gff)
        #GFF = ribo_functions.store_gtf(options.gff)
        ## check gff reading
        if not GFF['order'] :
            stop_err( 'Incorrect GFF file' )
        clean_file = ribo_functions.cleaning_bam(options.bamfile)
        compute_analysis(clean_file, GFF, options.fasta, options.gff, subfolder, options.extend)
        if os.path.exists( clean_file ):
            os.remove( clean_file )
        
        write_html_page(html_file,subfolder)