python多个输入和多个输出

Question

I have written a script in python, which works on a single file. I couldn't find an answer to make it run on multiple files and to give output for each file separately.

out = open('/home/directory/a.out','w')
infile = open('/home/directory/a.sam','r')

for line in infile:
    if not line.startswith('@'):
        samlist = line.strip().split()
        if 'I' or 'D' in samlist[5]:
            match = re.findall(r'(\d+)I', samlist[5]) # remember to chang I and D here aswell
            intlist = [int(x) for x in match]
##            if len(intlist) < 10:
            for indel in intlist:
                if indel >= 10:
##                    print indel
            ###intlist contains lengths of insertions in for each read
            #print intlist
                    read_aln_start = int(samlist[3])
                    indel_positions = []
                    for num1, i_or_d, num2, m in re.findall('(\d+)([ID])(\d+)?([A-Za-z])?', samlist[5]):
                        if num1:
                            read_aln_start += int(num1)
                        if num2:
                            read_aln_start += int(num2)
                        indel_positions.append(read_aln_start)
                #print indel_positions
                    out.write(str(read_aln_start)+'\t'+str(i_or_d) + '\t'+str(samlist[2])+ '\t' + str(indel) +'\n')
out.close()

I would like my script to take multiple files with names like a.sam, b.sam, c.sam and for each file give me the output : aout.sam, bout.sam, cout.sam

Can you please pass me either a solution or a hint.

Regards, Irek

Answer 1

Loop over filenames.

input_filenames = ['a.sam', 'b.sam', 'c.sam']
output_filenames = ['aout.sam', 'bout.sam', 'cout.sam']
for infn, outfn in zip(input_filenames, output_filenames):
    out = open('/home/directory/{}'.format(outfn), 'w')
    infile = open('/home/directory/{}'.format(infn), 'r')
    ...

UPDATE

Following code generate output_filenames from given input_filenames.

import os

def get_output_filename(fn):
    filename, ext = os.path.splitext(fn)
    return filename + 'out' + ext

input_filenames = ['a.sam', 'b.sam', 'c.sam'] # or glob.glob('*.sam')
output_filenames = map(get_output_filename, input_filenames)

Answer 2

I'd recommend wrapping that script in a function, using the def keyword, and passing the names of the input and output files as parameters to that function.

def do_stuff_with_files(infile, outfile):
    out = open(infile,'w')
    infile = open(outfile,'r')
    # the rest of your script

Now you can call this function for any combination of input and output file names.

do_stuff_with_files('/home/directory/a.sam', '/home/directory/a.out')

If you want to do this for all files in a certain directory, use the glob library. To generate the output filenames, just replace the last three characters ("sam") with "out".

import glob
indir, outdir = '/home/directory/', '/home/directory/out/'
files = glob.glob1(indir, '*.sam')
infiles  = [indir  + f              for f in files]
outfiles = [outdir + f[:-3] + "out" for f in files]
for infile, outfile in zip(infiles, outfiles):
    do_stuff_with_files(infile, outfile)

Answer 3

The following script allows working with an input and output file. It will loop over all files in the given directory with the ".sam" extension, perform the specified operation on them, and output the results to a separate file.

Import os
# Define the directory containing the files you are working with
path = '/home/directory'
# Get all the files in that directory with the desired
# extension (in this case ".sam")
files = [f for f in os.listdir(path) if f.endswith('.sam')]
# Loop over the files with that extension
for file in files:
    # Open the input file
    with open(path + '/' + file, 'r') as infile:
        # Open the output file
        with open(path + '/' + file.split('.')[0] + 'out.' +
                               file.split('.')[1], 'a') as outfile:
            # Loop over the lines in the input file
            for line in infile:
                # If a line in the input file can be characterized in a
                # certain way, write a different line to the output file.
                # Otherwise write the original line (from the input file)
                # to the output file
                if line.startswith('Something'):
                    outfile.write('A different kind of something')
                else:
                    outfile.write(line)
    # Note the absence of either a infile.close() or an outfile.close()
    # statement. The with-statement handles that for you