I have a .csv with 3000 rows of data in 2 columns like this:
uc007ayl.1 ENSMUSG00000041439
uc009mkn.1 ENSMUSG00000031708
uc009mkn.1 ENSMUSG00000035491In another folder I have a graphs with name like this:
uc007csg.1_nt_counts.txt
uc007gjg.1_nt_counts.txtYou should notice those graphs have a name in the same format of my 1st column
I am trying to use python to identify those rows that have a graph and print the name of 2nd column in a new .txt file
These are the codes I have
import csv
with open("C:/*my dir*/UCSC to Ensembl.csv", "r") as f:
reader = csv.reader(f, delimiter = ',') for row in reader: print row[0]But this as far as I can get and I am stuck.
5 Answers
You're almost there:
import csv
import os.path
with open("C:/*my dir*/UCSC to Ensembl.csv", "rb") as f: reader = csv.reader(f, delimiter = ',') for row in reader: graph_filename = os.path.join("C:/folder", row[0] + "_nt_counts.txt") if os.path.exists(graph_filename): print (row[1])Note that the repeated calls to os.path.exists may slow down the process, especially if the directory lies on a remote filesystem and does not significantly more files than the number of lines in the CSV file. You may want to use os.listdir instead:
import csv
import os
graphs = set(os.listdir("C:/graph folder"))
with open("C:/*my dir*/UCSC to Ensembl.csv", "rb") as f: reader = csv.reader(f, delimiter = ',') for row in reader: if row[0] + "_nt_counts.txt" in graphs: print (row[1])First, try to see if print row[0] really gives the correct file identifier.
Second, concatenate the path to the files with row[0] and check if this full path exists (if the file exists, actually) with os.path.exists(path) (see ).
If it exits, you can write the row[1] (the second column) to a new file with f2.write("%s\n" % row[1] (first you have to open f2 for writing of course).
Well, the next step would be to check if the file exists? There are a few ways, but I like the EAFP approach.
try: with open(os.path.join(the_dir,row[0])) as f: pass
except IOError: print 'Oops no file'the_dir is the directory where the files are.
result = open('result.txt', 'w')
for line in open('C:/*my dir*/UCSC to Ensembl.csv', 'r'): line = line.split(',') try: open('/path/to/dir/' + line[0] + '_nt_counts.txt', 'r') except: continue else: result.write(line[1] + '\n')
result.close()import csv
import os
# get prefixes of all graphs in another directory
suff = '_nt_counts.txt'
graphs = set(fn[:-len(suff)] for fn in os.listdir('another dir') if fn.endswith(suff))
with open(r'c:\path to\file.csv', 'rb') as f: # extract 2nd column if the 1st one is a known graph prefix names = (row[1] for row in csv.reader(f, delimiter='\t') if row[0] in graphs) # write one name per line with open('output.txt', 'w') as output_file: for name in names: print >>output_file, name
