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I am trying to list all files within a directory that contain the string I specify as part of their names. I want to vary this string with each iteration of the loop. The code I am using is:

from subprocess import Popen
from subprocess import call

species_array = ["homo_sapiens", "pan_troglodytes", "pongo_abelii", "gorilla_gorilla", "macaca_mulatta", "callithrix_jacchus", "bos_taurus", "canis_familiaris", "equus_caballus", "felis_catus", "ovis_aries", "sus_scrofa", "oryctolagus_cuniculus", "rattus_norvegicus", "mus_caroli", "mus_pahari", "mus_musculus"]
run_length = (len(species_array) - 5)
path = "/homes/varshith/maf_files/1/testmafs/HAL_Files/"
for i in range (run_length):
    s = Popen("find", path, "-name", *species_array[i+1]*)
    print s.communicate()[0]

The file should contain species_array[i+1] as part of its name. Thanks in advance.

Varshith Chakrapani
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  • see http://stackoverflow.com/questions/3207219/how-to-list-all-files-of-a-directory-in-python – Urban48 Jan 21 '15 at 10:41
  • just use glob of fnmatch also why use `i+1` do you not want the first? – Padraic Cunningham Jan 21 '15 at 10:43
  • I dont want the first. And all of these glob functions only take into account a string that doesn't change over the entire program. I am looking for a code which enables me to find a variable substring in a filename. – Varshith Chakrapani Jan 21 '15 at 10:46

2 Answers2

2

If you want to use find you need to pass a list of args when shell=False. check_output will work for your case, you can slice the list instead of using range and you need str.format to wrap each specie/ele in *:

from subprocess import check_output

species_array = ["homo_sapiens", "pan_troglodytes", "pongo_abelii", "gorilla_gorilla", "macaca_mulatta", "callithrix_jacchus", "bos_taurus", "canis_familiaris", "equus_caballus", "felis_catus", "ovis_aries", "sus_scrofa", "oryctolagus_cuniculus", "rattus_norvegicus", "mus_caroli", "mus_pahari", "mus_musculus"]
path = "/homes/varshith/maf_files/1/testmafs/HAL_Files/"
for ele in species_array[1:-5]:
    s = check_output(["find", path, "-name", "*{0}*".format(ele)])
    print s

For python 2.6 use Popen:

from subprocess Popen,PIPE

species_array = ["homo_sapiens", "pan_troglodytes", "pongo_abelii", "gorilla_gorilla", "macaca_mulatta", "callithrix_jacchus", "bos_taurus", "canis_familiaris", "equus_caballus", "felis_catus", "ovis_aries", "sus_scrofa", "oryctolagus_cuniculus", "rattus_norvegicus", "mus_caroli", "mus_pahari", "mus_musculus"]
path = "/homes/varshith/maf_files/1/testmafs/HAL_Files/"
for ele in species_array[1:-5]:
    s = Popen(["find", path, "-name", "*{0}*".format(ele)],stdout=PIPE,stderr=PIPE)
    out,err = s.communicate()
    print(out,err)
Padraic Cunningham
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2

Your loop is all wrong. python is much more expressive than that:

1) You can skip the first element by starting the range at 1: 

for i in range(1, len(species_arr) - 4):

...then use i instead of i+1 inside your loop.

2) Even easier (and more idiomatic) is to use list slicing:

for species in species_arr[1:-4]:

3) You can format strings in python using the format() method.

Here is an example employing those concepts:

species_arr = [
    "homo_sapiens", 
    "pan_troglodytes", 
    "pongo_abelii", 
    "gorilla_gorilla", 
    "macaca_mulatta", 
    "callithrix_jacchus", 
    "bos_taurus", 
    "canis_familiaris", 
    "equus_caballus", 
    "felis_catus", 
    "ovis_aries", 
    "sus_scrofa", 
    "oryctolagus_cuniculus", 
    "rattus_norvegicus", 
    "mus_caroli", 
    "mus_pahari", 
    "mus_musculus"
]

chop_from_end = 4 

for species in species_arr[1:-chop_from_end]:
    fname = "*{0}*".format(species)
    print fname

--output:--
*pan_troglodytes*
*pongo_abelii*
*gorilla_gorilla*
*macaca_mulatta*
*callithrix_jacchus*
*bos_taurus*
*canis_familiaris*
*equus_caballus*
*felis_catus*
*ovis_aries*
*sus_scrofa*
*oryctolagus_cuniculus*

The format() method was introduced in python 3.0--but it was backported to python 2.6 (in a more limited form). If for some reason your install does not have the format() method, you can use the old way:

 fname = "*%s*" % species

See additional format() examples here:

https://docs.python.org/3/library/string.html#format-examples

4) Here's what you can do with the glob module:

import glob
import os.path
import pprint

base_dir = '/Users/7stud/python_programs/dir1'

names = ['a', 'b', 'c']

for name in names: 
    fname = "*{0}*".format(name)
    path = os.path.join(base_dir, fname)
    pprint.pprint(glob.glob(path))
    print '-' * 20

--output:--
['/Users/7stud/python_programs/dir1/__pycache__',
 '/Users/7stud/python_programs/dir1/a.txt',
 '/Users/7stud/python_programs/dir1/aa.txt',
 '/Users/7stud/python_programs/dir1/ab.txt',
 '/Users/7stud/python_programs/dir1/ba.txt']
--------------------
['/Users/7stud/python_programs/dir1/ab.txt',
 '/Users/7stud/python_programs/dir1/b.txt',
 '/Users/7stud/python_programs/dir1/ba.txt']
--------------------
['/Users/7stud/python_programs/dir1/__pycache__']
--------------------

Or, as a dict of name, matches pairs:

results = dict(
    (
      name,
      glob.iglob(os.path.join(base_dir, "*{0}*".format(name)))
    )
    for name in names
)

for name, _iter in results.items():
    print "{0}:".format(name)
    pprint.pprint(list(_iter))

--output:--
a:
['/Users/7stud/python_programs/dir1/__pycache__',
 '/Users/7stud/python_programs/dir1/a.txt',
 '/Users/7stud/python_programs/dir1/aa.txt',
 '/Users/7stud/python_programs/dir1/ab.txt',
 '/Users/7stud/python_programs/dir1/ba.txt']
c:
['/Users/7stud/python_programs/dir1/__pycache__']
b:
['/Users/7stud/python_programs/dir1/ab.txt',
 '/Users/7stud/python_programs/dir1/b.txt',
 '/Users/7stud/python_programs/dir1/ba.txt']
7stud
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