"""

Read insert length distribution.

"""

insert_dist_file = open(insert_dist_filename, "r")

insert_dist = array([int(line.strip()) \

for line in insert_dist_file])

return insert_dist

# insert_filename = glob.glob(os.path.join(insert_dir, "*.insert_dist"))

# if len(insert_filename) == 0:

min_exon_size):

"""

Compute insert length distribution and output it to the given

directory.

"""

print "Computing insert length distribution of %s" %(bam_filename)

print " - Using gene models from: %s" %(gff_filename)

print " - Outputting to: %s" %(output_dir)

print " - Minimum exon size used: %d" %(min_exon_size)

if not os.path.isdir(output_dir):

print "Making directory: %s" %(output_dir)

os.makedirs(output_dir)

output_filename = os.path.join(output_dir,

"%s.insert_len" %(os.path.basename(bam_filename)))

# Load BAM file with reads

bamfile = sam_utils.load_bam_reads(bam_filename)

# Load the genes from the GFF

print "Loading genes from GFF..."

t1 = time.time()

gff_genes = gene_utils.load_genes_from_gff(gff_filename)

t2 = time.time()

print " - Loading genes from GFF took %.2f seconds" %(t2 - t1)

insert_lengths = []

t1 = time.time()

relevant_region = 0

for gene_id, gene_info in gff_genes.iteritems():

gene_obj = gene_info["gene_object"]

# Get all the constitutive parts

const_parts = gene_obj.get_const_parts()

chrom = gene_obj.chrom

# Consider only the large constitutive parts

for part in const_parts:

if part.len >= min_exon_size:

# Get all the reads that land in the coordinates of the exon

try:

exon_reads = bamfile.fetch(chrom, part.start, part.end)

except ValueError:

print "Could not fetch from region: ", chrom, part.start, part.end

continue

# Pair all the paired-end reads that land there

paired_reads = sam_utils.pair_sam_reads(exon_reads)

num_paired_reads = len(paired_reads)

if num_paired_reads == 0:

continue

print "Found %d region" %(relevant_region)

relevant_region += 1

# Compute the insert length of each read

for read_pair_id, read_pair in paired_reads.iteritems():

if len(read_pair) != 2:

# Skip non-paired reads

continue

left_read, right_read = read_pair

insert_len = right_read.pos - left_read.pos + 1

if insert_len > 0:

insert_lengths.append(insert_len)

else:

print "Negative or zero insert length ignored..."

# Output results to file

output_file = open(output_filename, 'w')

insert_length_str = "\n".join(map(str, insert_lengths))

output_file.write(insert_length_str)

output_file.close()

t2 = time.time()

from optparse import OptionParser

parser = OptionParser()

parser.add_option("--compute-insert-len", dest="compute_insert_len", nargs=3, default=None,

help="Compute insert length for given sample. Takes as input "

"a sorted, indexed BAM file with headers, a GFF file with gene models, "

"and an output directory.")

parser.add_option("--min-exon-size", dest="min_exon_size", nargs=1, type="int", default=500,

help="Minimum size of constitutive exon (in nucleotides) that should be used "

"in the computation. Default is 500 bp.")

(options, args) = parser.parse_args()

if options.compute_insert_len != None:

bam_filename = os.path.abspath(os.path.expanduser(options.compute_insert_len[0]))

gff_filename = os.path.abspath(os.path.expanduser(options.compute_insert_len[1]))

output_dir = os.path.abspath(os.path.expanduser(options.compute_insert_len[2]))