CODEWITHSUNDEEP
pythonfiledirectory
ENJ ENJ
ENJ ENJ

Reputation: 1

Having issue writing to file

I am beginning to learn python and am having some trouble getting n output to print to txt file on the desktop. I want it to be Mac and windows comptible. I keep getting a syntax error at a line that doesn't exist or no such file directory on line 4. I am trying to create the text file.

import os
os.path.join("~","Desktop")
output_file = open(os.path.join("~","Desktop","PythoBLASTout.txt"),"w")
from Bio import SearchIO
E_VALUE_THRES = 0.01
with open('/Users/evanclark/conesnail.xml', 'rU') as input:
    for qresult in SearchIO.parse(input, "blast-xml"):
        hits = qresult.hits
        query_id = qresult.id
        if len(hits) > 0:
            target_id = hits[0].id
            evalue = hits[0].hsps[0].evalue
            if evalue < E_VALUE_THRES:
                print("%s\t%s" % (query_id, target_id))


        #output_file.write("%s\t%s" % (query_id, target_id)

Upvotes: 0

Views: 35

Answers (1)

Turn
Turn

Reputation: 7030

If you want to do tilde expansion you need to tell Python to do this explicitly:

output_file = open(os.path.expanduser(os.path.join("~", ...)), "w")

Upvotes: 1

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