title: File permissions lost after unzipping with zipfile
body: <p>I have extracted a zip file (<code>hisat2-2.2.0-Linux_x86_64.zip</code> from <a href="https://cloud.biohpc.swmed.edu/index.php/s/hisat2-220-Linux_x86_64/download" rel="nofollow noreferrer">https://cloud.biohpc.swmed.edu/index.php/s/hisat2-220-Linux_x86_64/download</a>) in Ubuntu (by right-clicking the file and choose extract here) and this gives me the following file permissions:</p>
  <pre><code>total 91M
  -rw-r--r-- 1 user user  584 Jul  9  2019 NEWS
  -rw-r--r-- 1 user user  78K Jul  9  2019 MANUAL.markdown
  -rw-r--r-- 1 user user  35K Jul  9  2019 LICENSE
  -rwxr-xr-x 1 user user 2.8K Jul  9  2019 hisat2-build
  -rw-r--r-- 1 user user 1.3K Jul  9  2019 AUTHORS
  -rw-r--r-- 1 user user  202 Jan 23  2020 TUTORIAL
  -rw-r--r-- 1 user user  64K Jan 23  2020 MANUAL
  -rw-r--r-- 1 user user    6 Dec  2  2020 VERSION
  -rwxr-xr-x 1 user user  35K Dec  2  2020 hisat2_simulate_reads.py
  -rwxr-xr-x 1 user user 5.6K Dec  2  2020 hisat2_read_statistics.py
  -rwxr-xr-x 1 user user 2.7K Dec  2  2020 hisat2-inspect
  -rwxr-xr-x 1 user user 5.0K Dec  2  2020 hisat2_extract_splice_sites.py
  -rwxr-xr-x 1 user user  35K Dec  2  2020 hisat2_extract_snps_haplotypes_VCF.py
  -rwxr-xr-x 1 user user  19K Dec  2  2020 hisat2_extract_snps_haplotypes_UCSC.py
  -rwxr-xr-x 1 user user 5.5K Dec  2  2020 hisat2_extract_exons.py
  -rwxr-xr-x 1 user user  20K Dec  2  2020 hisat2
  -rwxr-xr-x 1 user user 5.0K Dec  2  2020 extract_splice_sites.py
  -rwxr-xr-x 1 user user 5.5K Dec  2  2020 extract_exons.py
  -rwxr-xr-x 1 user user 5.3M Dec  2  2020 hisat2-build-s
  -rwxr-xr-x 1 user user 5.3M Dec  2  2020 hisat2-build-l
  -rwxr-xr-x 1 user user  15M Dec  2  2020 hisat2-align-s
  -rwxr-xr-x 1 user user  15M Dec  2  2020 hisat2-align-l
  -rwxr-xr-x 1 user user 3.5M Dec  2  2020 hisat2-inspect-s
  -rwxr-xr-x 1 user user 3.5M Dec  2  2020 hisat2-inspect-l
  -rwxr-xr-x 1 user user 6.7M Dec  2  2020 hisat2-repeat
  -rwxr-xr-x 1 user user 3.7M Dec  2  2020 hisat2-build-s-debug
  -rwxr-xr-x 1 user user 3.6M Dec  2  2020 hisat2-build-l-debug
  -rwxr-xr-x 1 user user  11M Dec  2  2020 hisat2-align-s-debug
  -rwxr-xr-x 1 user user  11M Dec  2  2020 hisat2-align-l-debug
  -rwxr-xr-x 1 user user 1.8M Dec  2  2020 hisat2-inspect-s-debug
  -rwxr-xr-x 1 user user 1.7M Dec  2  2020 hisat2-inspect-l-debug
  -rwxr-xr-x 1 user user 5.2M Dec  2  2020 hisat2-repeat-debug
  drwxr-xr-x 2 user user 4.0K Dec  2  2020 scripts
  drwxr-xr-x 5 user user 4.0K Dec  2  2020 example
  </code></pre>
  <p>When I unzip this file with Python:</p>
  <pre><code>from zipfile import ZipFile
  
  download_file = &quot;hisat2-2.2.0-Linux_x86_64.zip&quot;
  
  with ZipFile(download_file, 'r') as zip_ref:
                  zip_ref.extractall(script_dir)
  </code></pre>
  <p>The file permissions are different (I have lost the right to execute the file) when extracted from within Ubuntu:</p>
  <pre><code>total 91M
  drwxrwxr-x 2 user user 4.0K Aug 18 23:15 scripts
  drwxrwxr-x 2 user user 4.0K Aug 18 23:15 hisatgenotype_scripts
  drwxrwxr-x 2 user user 4.0K Aug 18 23:15 hisatgenotype_modules
  drwxrwxr-x 5 user user 4.0K Aug 18 23:15 example
  -rw-rw-r-- 1 user user 5.0K Aug 18 23:25 hisat2_extract_splice_sites.py
  -rw-rw-r-- 1 user user  35K Aug 18 23:25 hisat2_extract_snps_haplotypes_VCF.py
  -rw-rw-r-- 1 user user 122K Aug 18 23:25 hisatgenotype_locus.py
  -rw-rw-r-- 1 user user  21K Aug 18 23:25 hisatgenotype_build_genome.py
  -rw-rw-r-- 1 user user 4.8K Aug 18 23:25 hisat2_read_statistics.py
  -rw-rw-r-- 1 user user  19K Aug 18 23:25 hisat2_extract_snps_haplotypes_UCSC.py
  -rw-rw-r-- 1 user user 5.0K Aug 18 23:25 extract_splice_sites.py
  -rw-rw-r-- 1 user user  18K Aug 18 23:25 hisatgenotype.py
  -rw-rw-r-- 1 user user  73K Aug 18 23:25 hisatgenotype_hla_cyp.py
  -rw-rw-r-- 1 user user  52K Aug 18 23:25 hisatgenotype_extract_vars.py
  -rw-rw-r-- 1 user user  23K Aug 18 23:25 hisatgenotype_extract_reads.py
  -rw-rw-r-- 1 user user  34K Aug 18 23:25 hisat2_simulate_reads.py
  -rw-rw-r-- 1 user user 5.5K Aug 18 23:25 hisat2_extract_exons.py
  -rw-rw-r-- 1 user user 5.5K Aug 18 23:25 extract_exons.py
  -rw-rw-r-- 1 user user    6 Aug 18 23:25 VERSION
  -rw-rw-r-- 1 user user  202 Aug 18 23:25 TUTORIAL
  -rw-rw-r-- 1 user user  584 Aug 18 23:25 NEWS
  -rw-rw-r-- 1 user user  78K Aug 18 23:25 MANUAL.markdown
  -rw-rw-r-- 1 user user  64K Aug 18 23:25 MANUAL
  -rw-rw-r-- 1 user user  35K Aug 18 23:25 LICENSE
  -rw-rw-r-- 1 user user 2.7K Aug 18 23:25 hisat2-inspect
  -rw-rw-r-- 1 user user 2.8K Aug 18 23:25 hisat2-build
  -rwxrwxr-x 1 user user  20K Aug 18 23:25 hisat2
  -rw-rw-r-- 1 user user 1.3K Aug 18 23:25 AUTHORS
  -rw-rw-r-- 1 user user 5.5M Aug 18 23:25 hisat2-build-s
  -rw-rw-r-- 1 user user 5.5M Aug 18 23:25 hisat2-build-l
  -rw-rw-r-- 1 user user  15M Aug 18 23:25 hisat2-align-s
  -rw-rw-r-- 1 user user  15M Aug 18 23:25 hisat2-align-l
  -rw-rw-r-- 1 user user 3.4M Aug 18 23:25 hisat2-inspect-s
  -rw-rw-r-- 1 user user 3.4M Aug 18 23:25 hisat2-inspect-l
  -rw-rw-r-- 1 user user 6.8M Aug 18 23:25 hisat2-repeat
  -rw-rw-r-- 1 user user 3.5M Aug 18 23:25 hisat2-build-s-debug
  -rw-rw-r-- 1 user user 3.4M Aug 18 23:25 hisat2-build-l-debug
  -rw-rw-r-- 1 user user  11M Aug 18 23:25 hisat2-align-s-debug
  -rw-rw-r-- 1 user user  11M Aug 18 23:25 hisat2-align-l-debug
  -rw-rw-r-- 1 user user 1.7M Aug 18 23:25 hisat2-inspect-s-debug
  -rw-rw-r-- 1 user user 1.7M Aug 18 23:25 hisat2-inspect-l-debug
  -rw-rw-r-- 1 user user 5.1M Aug 18 23:25 hisat2-repeat-debug
  </code></pre>
  <p>How can I maintain the original file permissions with the Python command?</p>