def wig_pipe(infile, outfile):
''' (infile, outfile)
Reads in a .bedfile formatted alignment file and returns a .wig formatted data file.
'''
import wig_scripts
bedfile = wig_scripts.read_tab_data(infile)
read_pos = wig_scripts.bedfile_to_read_pos(bedfile)
data = wig_scripts.count_reads(read_pos)
wig_scripts.wig_out(outfile, data)
def process_bedfile_for_HMM(infile1, infile2, outfile1):
''' (total_TA_pos.wig, TnSeq_read_pos.bedfile, tnseq_data.wig) -> write to tnseq_data.wig
This program reads in a .wig file of the 'TA' positions in the Rlv3841 replicon in question,
a bedfile of all reads from a TnSeq alignment, and combines the positon data from the bedfile
with the .wig list. It then prints out a file with the TnSeq data in a format useable by
the
'''
import wig_scripts
output = []
processed = 0
total_ta_pos = []
total_tnseq_pos = []
TA_in = wig_scripts.read_space_data(infile1)
TnSeq_in = wig_scripts.read_tab_data(infile2)
read_counts = wig_scripts.bedfile_to_read_pos(TnSeq_in)
header = TA_in.pop(0)
### Takes the position of every 'TA' and pushes it into a list in int format
for pos in TA_in:
ta = int(pos[0])
total_ta_pos.append(ta)
for read in read_counts:
value = int(read)
total_tnseq_pos.append(value)
for ta_site in total_ta_pos:
read_number = total_tnseq_pos.count(ta_site)
items =[]
items = [ta_site, read_number]
output.append(items)
processed = processed+1
outfile1.write(header[0] + ' ' + header[1] + '\n')
for result in output:
position = str(result[0])
count = str(result[1])
outfile1.write(position)
outfile1.write(' ')
outfile1.write(count)
outfile1.write('\n')
outfile1.close()
infile1.close()
infile2.close()
def parse_bed(infile, directory):
''' (infile, directory) -> Print to parsed Output Files in directory
Reads a bedfile, parses the data based on the chrom identifier.
Prints reads to output files with the file name of chrom identifier "NC_0083XX.1.bed" onto
the desktop.
NOTE: This program is Rhizobium leguminosarum bv. viciae 3841 specific
Possible chrom identifiers are:
gi|116248676|ref|NC_008378.1|
gi|116249460|ref|NC_008379.1|
gi|116249766|ref|NC_008380.1|
gi|116254467|ref|NC_008381.1|
gi|116254910|ref|NC_008382.1|
gi|116255067|ref|NC_008383.1|
gi|116255200|ref|NC_008384.1|
'''
import wig_scripts
data = wig_scripts.read_tab_data(infile)
dir_out = directory
f78 = open(dir_out+'/NC_008378.1.bed', 'w')
f79 = open(dir_out+'/NC_008379.1.bed', 'w')
f80 = open(dir_out+'/NC_008380.1.bed', 'w')
f81 = open(dir_out+'/NC_008381.1.bed', 'w')
f82 = open(dir_out+'/NC_008382.1.bed', 'w')
f83 = open(dir_out+'/NC_008383.1.bed', 'w')
f84 = open(dir_out+'/NC_008384.1.bed', 'w')
err = open(dir_out+'/Errors.txt', 'w')
for line in data:
if str(line[0]) == 'gi|116248676|ref|NC_008378.1|':
for i in line:
f78.write(str(i)+'\t')
f78.write('\n')
elif str(line[0]) == 'gi|116249460|ref|NC_008379.1|':
for i in line:
f79.write(str(i)+'\t')
f79.write('\n')
elif str(line[0]) == 'gi|116249766|ref|NC_008380.1|':
for i in line:
f80.write(str(i)+'\t')
f80.write('\n')
elif str(line[0]) == 'gi|116254467|ref|NC_008381.1|':
for i in line:
f81.write(str(i)+'\t')
f81.write('\n')
elif str(line[0]) == 'gi|116254910|ref|NC_008382.1|':
for i in line:
f82.write(str(i)+'\t')
f82.write('\n')
elif str(line[0]) == 'gi|116255067|ref|NC_008383.1|':
for i in line:
f83.write(str(i)+'\t')
f83.write('\n')
elif str(line[0]) == 'gi|116255200|ref|NC_008384.1|':
for i in line:
f84.write(str(i)+'\t')
f84.write('\n')
else:
for i in line:
err.write(str(i)+'\t')
err.write('\n')
f78.close()
f79.close()
f80.close()
f81.close()
f82.close()
f83.close()
f84.close()
err.close()
