This function written is python shortens the string of a .txt file on every other line and makes a copy in a new file. This is very useful in bioinformatics. My problem was I had a Phred file from Illumina sequencing where both ends of the sequence was N. If I map this using bowtie and allow two low quality reads per sequence a lot of the data would be thrown out.
Simple example:
+
Shorten
Keep
Shorten
Keep
----------------
Example output
+
horte
Keep
horte
Keep
------------------
def every_other_line_shorten(starting_file, ending_file):
# open the files
from_file = open(starting_file, 'r') # read from file
to_file = open(ending_file, 'w') # write to_file
line = from_file.readline()
while line != "":
# keeps line
to_file.write(line)
line = from_file.readline()
# cuts line
to_file.write(line[1:-2] + '\n')
line = from_file.readline()
print('done')
to_file.close()
from_file.close()
