/tools/ngs_simulation/ngs_simulation.py
https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 280 lines · 266 code · 3 blank · 11 comment · 5 complexity · 62277c41e2e5ef606145b376fbd802e0 MD5 · raw file
- #!/usr/bin/env python
- """
- Runs Ben's simulation.
- usage: %prog [options]
- -i, --input=i: Input genome (FASTA format)
- -g, --genome=g: If built-in, the genome being used
- -l, --read_len=l: Read length
- -c, --avg_coverage=c: Average coverage
- -e, --error_rate=e: Error rate (0-1)
- -n, --num_sims=n: Number of simulations to run
- -p, --polymorphism=p: Frequency/ies for minor allele (comma-separate list of 0-1)
- -d, --detection_thresh=d: Detection thresholds (comma-separate list of 0-1)
- -p, --output_png=p: Plot output
- -s, --summary_out=s: Whether or not to output a file with summary of all simulations
- -m, --output_summary=m: File name for output summary of all simulations
- -f, --new_file_path=f: Directory for summary output files
- """
- # removed output of all simulation results on request (not working)
- # -r, --sim_results=r: Output all tabular simulation results (number of polymorphisms times number of detection thresholds)
- # -o, --output=o: Base name for summary output for each run
- from rpy import *
- import os
- import random, sys, tempfile
- from galaxy import eggs
- import pkg_resources; pkg_resources.require( "bx-python" )
- from bx.cookbook import doc_optparse
- def stop_err( msg ):
- sys.stderr.write( '%s\n' % msg )
- sys.exit()
- def __main__():
- #Parse Command Line
- options, args = doc_optparse.parse( __doc__ )
- # validate parameters
- error = ''
- try:
- read_len = int( options.read_len )
- if read_len <= 0:
- raise Exception, ' greater than 0'
- except TypeError, e:
- error = ': %s' % str( e )
- if error:
- stop_err( 'Make sure your number of reads is an integer value%s' % error )
- error = ''
- try:
- avg_coverage = int( options.avg_coverage )
- if avg_coverage <= 0:
- raise Exception, ' greater than 0'
- except Exception, e:
- error = ': %s' % str( e )
- if error:
- stop_err( 'Make sure your average coverage is an integer value%s' % error )
- error = ''
- try:
- error_rate = float( options.error_rate )
- if error_rate >= 1.0:
- error_rate = 10 ** ( -error_rate / 10.0 )
- elif error_rate < 0:
- raise Exception, ' between 0 and 1'
- except Exception, e:
- error = ': %s' % str( e )
- if error:
- stop_err( 'Make sure the error rate is a decimal value%s or the quality score is at least 1' % error )
- try:
- num_sims = int( options.num_sims )
- except TypeError, e:
- stop_err( 'Make sure the number of simulations is an integer value: %s' % str( e ) )
- if options.polymorphism != 'None':
- polymorphisms = [ float( p ) for p in options.polymorphism.split( ',' ) ]
- else:
- stop_err( 'Select at least one polymorphism value to use' )
- if options.detection_thresh != 'None':
- detection_threshes = [ float( dt ) for dt in options.detection_thresh.split( ',' ) ]
- else:
- stop_err( 'Select at least one detection threshold to use' )
- # mutation dictionaries
- hp_dict = { 'A':'G', 'G':'A', 'C':'T', 'T':'C', 'N':'N' } # heteroplasmy dictionary
- mt_dict = { 'A':'C', 'C':'A', 'G':'T', 'T':'G', 'N':'N'} # misread dictionary
- # read fasta file to seq string
- all_lines = open( options.input, 'rb' ).readlines()
- seq = ''
- for line in all_lines:
- line = line.rstrip()
- if line.startswith('>'):
- pass
- else:
- seq += line.upper()
- seq_len = len( seq )
- # output file name template
- # removed output of all simulation results on request (not working)
- # if options.sim_results == "true":
- # out_name_template = os.path.join( options.new_file_path, 'primary_output%s_' + options.output + '_visible_tabular' )
- # else:
- # out_name_template = tempfile.NamedTemporaryFile().name + '_%s'
- out_name_template = tempfile.NamedTemporaryFile().name + '_%s'
- print 'out_name_template:', out_name_template
- # set up output files
- outputs = {}
- i = 1
- for p in polymorphisms:
- outputs[ p ] = {}
- for d in detection_threshes:
- outputs[ p ][ d ] = out_name_template % i
- i += 1
- # run sims
- for polymorphism in polymorphisms:
- for detection_thresh in detection_threshes:
- output = open( outputs[ polymorphism ][ detection_thresh ], 'wb' )
- output.write( 'FP\tFN\tGENOMESIZE=%s\n' % seq_len )
- sim_count = 0
- while sim_count < num_sims:
- # randomly pick heteroplasmic base index
- hbase = random.choice( range( 0, seq_len ) )
- #hbase = seq_len/2#random.randrange( 0, seq_len )
- # create 2D quasispecies list
- qspec = map( lambda x: [], [0] * seq_len )
- # simulate read indices and assign to quasispecies
- i = 0
- while i < ( avg_coverage * ( seq_len / read_len ) ): # number of reads (approximates coverage)
- start = random.choice( range( 0, seq_len ) )
- #start = seq_len/2#random.randrange( 0, seq_len ) # assign read start
- if random.random() < 0.5: # positive sense read
- end = start + read_len # assign read end
- if end > seq_len: # overshooting origin
- read = range( start, seq_len ) + range( 0, ( end - seq_len ) )
- else: # regular read
- read = range( start, end )
- else: # negative sense read
- end = start - read_len # assign read end
- if end < -1: # overshooting origin
- read = range( start, -1, -1) + range( ( seq_len - 1 ), ( seq_len + end ), -1 )
- else: # regular read
- read = range( start, end, -1 )
- # assign read to quasispecies list by index
- for j in read:
- if j == hbase and random.random() < polymorphism: # heteroplasmic base is variant with p = het
- ref = hp_dict[ seq[ j ] ]
- else: # ref is the verbatim reference nucleotide (all positions)
- ref = seq[ j ]
- if random.random() < error_rate: # base in read is misread with p = err
- qspec[ j ].append( mt_dict[ ref ] )
- else: # otherwise we carry ref through to the end
- qspec[ j ].append(ref)
- # last but not least
- i += 1
- bases, fpos, fneg = {}, 0, 0 # last two will be outputted to summary file later
- for i, nuc in enumerate( seq ):
- cov = len( qspec[ i ] )
- bases[ 'A' ] = qspec[ i ].count( 'A' )
- bases[ 'C' ] = qspec[ i ].count( 'C' )
- bases[ 'G' ] = qspec[ i ].count( 'G' )
- bases[ 'T' ] = qspec[ i ].count( 'T' )
- # calculate max NON-REF deviation
- del bases[ nuc ]
- maxdev = float( max( bases.values() ) ) / cov
- # deal with non-het sites
- if i != hbase:
- if maxdev >= detection_thresh: # greater than detection threshold = false positive
- fpos += 1
- # deal with het sites
- if i == hbase:
- hnuc = hp_dict[ nuc ] # let's recover het variant
- if ( float( bases[ hnuc ] ) / cov ) < detection_thresh: # less than detection threshold = false negative
- fneg += 1
- del bases[ hnuc ] # ignore het variant
- maxdev = float( max( bases.values() ) ) / cov # check other non-ref bases at het site
- if maxdev >= detection_thresh: # greater than detection threshold = false positive (possible)
- fpos += 1
- # output error sums and genome size to summary file
- output.write( '%d\t%d\n' % ( fpos, fneg ) )
- sim_count += 1
- # close output up
- output.close()
- # Parameters (heteroplasmy, error threshold, colours)
- r( '''
- het=c(%s)
- err=c(%s)
- grade = (0:32)/32
- hues = rev(gray(grade))
- ''' % ( ','.join( [ str( p ) for p in polymorphisms ] ), ','.join( [ str( d ) for d in detection_threshes ] ) ) )
- # Suppress warnings
- r( 'options(warn=-1)' )
- # Create allsum (for FP) and allneg (for FN) objects
- r( 'allsum <- data.frame()' )
- for polymorphism in polymorphisms:
- for detection_thresh in detection_threshes:
- output = outputs[ polymorphism ][ detection_thresh ]
- cmd = '''
- ngsum = read.delim('%s', header=T)
- ngsum$fprate <- ngsum$FP/%s
- ngsum$hetcol <- %s
- ngsum$errcol <- %s
- allsum <- rbind(allsum, ngsum)
- ''' % ( output, seq_len, polymorphism, detection_thresh )
- r( cmd )
- if os.path.getsize( output ) == 0:
- for p in outputs.keys():
- for d in outputs[ p ].keys():
- sys.stderr.write(outputs[ p ][ d ] + ' '+str( os.path.getsize( outputs[ p ][ d ] ) )+'\n')
- if options.summary_out == "true":
- r( 'write.table(summary(ngsum), file="%s", quote=FALSE, sep="\t", row.names=FALSE)' % options.output_summary )
- # Summary objects (these could be printed)
- r( '''
- tr_pos <- tapply(allsum$fprate,list(allsum$hetcol,allsum$errcol), mean)
- tr_neg <- tapply(allsum$FN,list(allsum$hetcol,allsum$errcol), mean)
- cat('\nFalse Positive Rate Summary\n\t', file='%s', append=T, sep='\t')
- write.table(format(tr_pos, digits=4), file='%s', append=T, quote=F, sep='\t')
- cat('\nFalse Negative Rate Summary\n\t', file='%s', append=T, sep='\t')
- write.table(format(tr_neg, digits=4), file='%s', append=T, quote=F, sep='\t')
- ''' % tuple( [ options.output_summary ] * 4 ) )
- # Setup graphs
- #pdf(paste(prefix,'_jointgraph.pdf',sep=''), 15, 10)
- r( '''
- png('%s', width=800, height=500, units='px', res=250)
- layout(matrix(data=c(1,2,1,3,1,4), nrow=2, ncol=3), widths=c(4,6,2), heights=c(1,10,10))
- ''' % options.output_png )
- # Main title
- genome = ''
- if options.genome:
- genome = '%s: ' % options.genome
- r( '''
- par(mar=c(0,0,0,0))
- plot(1, type='n', axes=F, xlab='', ylab='')
- text(1,1,paste('%sVariation in False Positives and Negatives (', %s, ' simulations, coverage ', %s,')', sep=''), font=2, family='sans', cex=0.7)
- ''' % ( genome, options.num_sims, options.avg_coverage ) )
- # False positive boxplot
- r( '''
- par(mar=c(5,4,2,2), las=1, cex=0.35)
- boxplot(allsum$fprate ~ allsum$errcol, horizontal=T, ylim=rev(range(allsum$fprate)), cex.axis=0.85)
- title(main='False Positives', xlab='false positive rate', ylab='')
- ''' )
- # False negative heatmap (note zlim command!)
- num_polys = len( polymorphisms )
- num_dets = len( detection_threshes )
- r( '''
- par(mar=c(5,4,2,1), las=1, cex=0.35)
- image(1:%s, 1:%s, tr_neg, zlim=c(0,1), col=hues, xlab='', ylab='', axes=F, border=1)
- axis(1, at=1:%s, labels=rownames(tr_neg), lwd=1, cex.axis=0.85, axs='i')
- axis(2, at=1:%s, labels=colnames(tr_neg), lwd=1, cex.axis=0.85)
- title(main='False Negatives', xlab='minor allele frequency', ylab='detection threshold')
- ''' % ( num_polys, num_dets, num_polys, num_dets ) )
- # Scale alongside
- r( '''
- par(mar=c(2,2,2,3), las=1)
- image(1, grade, matrix(grade, ncol=length(grade), nrow=1), col=hues, xlab='', ylab='', xaxt='n', las=1, cex.axis=0.85)
- title(main='Key', cex=0.35)
- mtext('false negative rate', side=1, cex=0.35)
- ''' )
- # Close graphics
- r( '''
- layout(1)
- dev.off()
- ''' )
- # Tidy up
- # r( 'rm(folder,prefix,sim,cov,het,err,grade,hues,i,j,ngsum)' )
- if __name__ == "__main__" : __main__()