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Asked: 2026-05-31T02:14:48+00:00

I want to read in a non text file. It has an extension .map

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I want to read in a non text file. It has an extension “.map” but can be opened by notepad. How should I open this file through python?

file = open("path-to-file","r") doesn’t work for me. It returns No such file or directory: error.

Here’s what my file looks like:

111 + gi|89106884|ref|AC_000091.1| 725803 TCGAGATCGACCATGTTGCCCGCCT IIIIIIIIIIIIIIIIIIIIIIIII 0 14:A>G
457 + gi|89106884|ref|AC_000091.1| 32629 CCGTGTCCACCGACTACGACACCTC IIIIIIIIIIIIIIIIIIIIIIIII 0 4:C>G,22:T>C
779 + gi|89106884|ref|AC_000091.1| 483582 GATCACCCACGCAAAGATGGGGCGA IIIIIIIIIIIIIIIIIIIIIIIII 0 15:A>G,18:C>G
784 + gi|89106884|ref|AC_000091.1| 226200 ACCGATAGTGAACCAGTACCGTGAG IIIIIIIIIIIIIIIIIIIIIIIII 1

If I do the follwing:

file = open("D:\bowtie-0.12.7-win32\bowtie-0.12.7\output_635\results_NC_000117.fna.1.ebwt.map","rb")

It still gives me No such file or directory: 'D:\x08owtie-0.12.7-win32\x08owtie-0.12.7\\output_635\results_NC_000117.fna.1.ebwt.map' error. Is this because the file isn’t binary or I don’t have some permissions?

Would apppreciate help with this!

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1 Answer

  1. Editorial Team

    Binary files should use a binary mode.

    f = open("path-to-file","rb")

    But that won’t help if you don’t have the appropriate permissions or don’t know the format of the file itself.

    EDIT:

    Obviously you didn’t bother reading the error message, or you would have noticed that the filename it is using is not the one you expected.

    f = open("D:\\bowtie-0.12.7-win32\\bowtie-0.12.7\\output_635\\results_NC_000117.fna.1.ebwt.map","rb")
f = open(r"D:\bowtie-0.12.7-win32\bowtie-0.12.7\output_635\results_NC_000117.fna.1.ebwt.map","rb")
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