Question

I have a text file (bowtie alignment file) that looks like this:

read_1  +   345995|PACid:16033981   599 AGTAGTAATCAGTCACCCGCAAGGTAGACAAGG   qqqqqqqqqqqqqqqqqqqqq!!qqqqqqqqqq   0   
read_2  +   949205|PACid:16054220   338 TACCAGCACTAATGCACCGGATCCCATCAGATC   qqqqqqqqqqqqqqqqqqqqqqqqqqqqqq!!q   0   31:A>T
read_3  +   932004|PACid:16034380   1226    GGCACCTTATGAGAAATCAAAGTTTTTGGGTTC   qqqqqqqqqqqqqqq!!qqqqqqqqqqqqq!!q   3   

I want to subtract one from Column #4 (the position), and print each line with the updated value.

I can read the file, then separated the fields based on tab, and also identify Column #4 as data[3], but then I am stuck with subtracting one from each value in Column #4 and printing all the fields in each line with updated value for Column #4.

How can I do this using Python?

I tried something like this:

in_file = open(sys.argv[1],'r')
out_file = open(sys.argv[2], 'w')
for line in in_file: 
    data = line.rstrip().split('\t') 
    position = int(float(data[3]) -1)

but I am not sure about how to proceed with printing the lines with updated position.

Answer 1

Use the csv module, informing it your field delimiter is a tab:

from io import StringIO

indata = StringIO(u"""read_1    +   345995|PACid:16033981   599 AGTAGTAATCAGTCACCCGCAAGGTAGACAAGG   qqqqqqqqqqqqqqqqqqqqq!!qqqqqqqqqq   0
read_2  +   949205|PACid:16054220   338 TACCAGCACTAATGCACCGGATCCCATCAGATC   qqqqqqqqqqqqqqqqqqqqqqqqqqqqqq!!q   0   31:A>T
read_3  +   932004|PACid:16034380   1226    GGCACCTTATGAGAAATCAAAGTTTTTGGGTTC   qqqqqqqqqqqqqqq!!qqqqqqqqqqqqq!!q   3
""")

# that StringIO stuff is just for testing, you should do
# with open('your_file_name', 'r') as indata:
# before the 'for' loop, and then indent the rest one level.

from csv import reader

for line in reader(indata, delimiter='\t'):
    if len(line) > 3:
        line[3] = str(int(line[3]) - 1)
    print '\t'.join(line)

Then just convert the position to a number, subtract one, convert it back, and print the line.