Fixed and updated file writing

[KasperThystrup]

Made some updates to file writing which should improve when writing results:

• Moved module imports to top of script to avoid missing modules like cPickle (since py3.5+) which only comes up with the -f pickle argument
• Updated pandas.to_csv calls to use destionation string, rather than open() write handler
• Replaced open() with with(open, ...) as fh:
• Restructured file writing directly into the write function to improve readability (IMHO) and save a few lines

[KasperThystrup]

Note, this has been tested locally using conda 26.1.1 to install with following instructions:
sistr_cmd.yaml:

name: sistr_cmd
dependencies:
  - bioconda::sistr_cmd
  - conda-forge::numpy>=1.11.1,<2.0
  - conda-forge::setuptools<82.0.0

Executed with the following (and succeeding):

sistr -f tab --qc -t 4 -l /paht/2/Senterica_serovar.txt --cgmlst-profiles /path/2/shovill_cgmlst_profiles.csv --alleles-output /outdir/shovill_allele-results.json --output-prediction /outdir/shovill_sistr.tab /path/2/shovill.fasta

sistr -f csv --qc -t 4 -l /paht/2/Senterica_serovar.txt --cgmlst-profiles /path/2/shovill_cgmlst_profiles.csv --alleles-output /outdir/shovill_allele-results.json --output-prediction /outdir/shovill_sistr.csv /path/2/shovill.fasta

sistr -f json --qc -t 4 -l /paht/2/Senterica_serovar.txt --cgmlst-profiles /path/2/shovill_cgmlst_profiles.csv --alleles-output /outdir/shovill_allele-results.json --output-prediction /outdir/shovill_sistr.json /path/2/shovill.fasta

sistr -f pickle --qc -t 4 -l /paht/2/Senterica_serovar.txt --cgmlst-profiles /path/2/shovill_cgmlst_profiles.csv --alleles-output /outdir/shovill_allele-results.json --output-prediction /outdir/shovill_sistr.pickle /path/2/shovill.fasta