intermediate files to be removed

[thkuo]

The dictionaries used by different files may be redundant Review:

• collect_rpg_data.R (for the expression table)

  mutation_table.py \
  -f dict.txt \
  -a /data3/reference_sequences/Pseudomonas_aeruginosa_PA14_annotation_with_ncRNAs_07_2011_12genes.tab \
  -o DNA-Pool1.tab

• dict.txt: prefix of ".flt.vcf" (the file some_line+".flt.vcf") [to be deprecated]
• .flt.vcf: generated above, which contains only snps [to be simplified]
• Pseudomonas_aeruginosa_PA14_annotation_with_ncRNAs_07_2011_12genes.tab: gene locus information [to be deprecated]

  @Pseudomonas_aeruginosa_PA14|NC_008463|6537649
  @Strain Refseq_Accession        Replicon        Locus_Tag       Feature_Type    Start   Stop    Strand  Gene_Name       Product_Name
  Pseudomonas_aeruginosa_PA14     NC_008463       Chromosome      PA14_00010      CDS     483     2027    +       dnaA    chromosomal_replication_initiation_protein
  Pseudomonas_aeruginosa_PA14     NC_008463       Chromosome      PA14_00020      CDS     2056    3159    +       dnaN    DNA_polymerase_III_subunit_beta

  ---

  Snp2Amino.py \
  -f DNA-Pool1.tab \
  -g /data3/reference_sequences/Pseudomonas_aeruginosa_PA14_ncRNA.gbk \
  -o DNA_Pool1_final.tab

  It doesn't generate syn table but an all table... to be rewritten with pandas

• DNA-Pool1.tab: created by mutation_table.py; containing four columns: "gene, pos, ref, alt"

[thkuo]

Best option: making them not required Second best option: automatically creating them without additional data from the users

[thkuo]

The required software, such as bcftools, are too old...

[thkuo]

software versions controlled using conda