finding files in Python

find_file.py

#!/usr/bin/env python
# python 2.7

# various ways to try to find and return the files in a given directory
# some of these are ok, some are bad, some are real real bad

import os
import re
import glob

barcode = "my_file_prefix"
run_bam_dir = "/path/to/dir


# use this one; find the file in the dir with the matching prefix and file extension
res = glob.glob(run_bam_dir + '/{}*.bam'.format(barcode))

# check the length of the glob results
if len(res) != 1:
    print "Warning multiple files returned"

# check if file exists
os.path.isfile(res[0]) 

# OTHER WAYS:
# using a regex
res = [f for f in os.listdir(run_bam_dir) if re.search(r'{}.*\.bam$'.format(barcode), f)]
for f in res:
    print os.path.join(run_bam_dir, f)

# using a glob
res = [f for f in glob.glob(run_bam_dir + '/*.bam') if os.path.basename(f).startswith(barcode) ]


for file in os.listdir(run_bam_dir):
    # print file
    if ( file.endswith(".bam") and file.startswith(barcode) ):
        print(file)

# find the bam files 
for subdir, dirs, files in os.walk(run_bam_dir):
    # print subdir
    # print dirs
    # print files
    for file in files:
      if ( file.endswith(".bam") and file.startswith(barcode) ):
          print os.path.join(subdir,file)

print run_bam_dir
for path, subdirs, files in os.walk(run_bam_dir):
    print path
    print '\n'
    print subdirs
    print '\n'
    print files
    print '\n'
    for file in files:
        print os.path.abspath(file) # THIS GIVES THE WRONG PATH when the dir isnt a subdir of pwd
        print '\n'

for d in dirs:
    print d
    for f in glob.iglob(os.path.join(path, d, '*.bam')):
        print f


# find the VCF files in the input dir
raw_vcf_paths = []
for subdir, dirs, files in os.walk(input_dir):
    for file in files:
        if file.endswith('.vcf'):
            raw_vcf_paths.append((os.path.join(subdir,file)))

raw_vcf_paths.sort()