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How to reproduce results:
Towards the Well-Tempered Chloroplast DNA Sequences

Research is implemented as a workflow named chloroplast_normalization with required parameters family and outgroup, and optional parameter max_update_date.

Step 1. main directory (optional)

Create a directory for a whole research. Make it working directory.

Step 2. family researches/directories

Create a research directory for each family. This creates research directories and initialize them with provided data.

zcit.py init Apiaceae -w chloroplast_normalization -p 'family=Apiaceae;outgroup=NC_041648;max_update_date=2020-12-31'
zcit.py init Asteraceae -w chloroplast_normalization -p 'family=Asteraceae;outgroup=NC_040857;max_update_date=2020-12-31'
zcit.py init Campanulaceae -w chloroplast_normalization -p 'family=Campanulaceae;outgroup=NC_046571;max_update_date=2020-12-31'
zcit.py init Lamiaceae -w chloroplast_normalization -p 'family=Lamiaceae;outgroup=NC_046852;max_update_date=2020-12-31'
zcit.py init Rosaceae -w chloroplast_normalization -p 'family=Rosaceae;outgroup=NC_046061;max_update_date=2020-12-31'

Step 3. For each family

Make family research directory working one. Run workflow in it with command zcit.py workflow run. This will run 3 steps:

  • fetch list of chloroplast accessions from NCBI (step 01_chloroplast_list),
  • fetch cpDNA sequences (step 02_seqs),
  • create step for GeSeq annotation of fetched sequences (step 03_GeSeq).

GeSeq (Annotation of Organellar Genomes) is web-based tool. Data has to be posted and results downloaded 'by the hand'. Follow printed instructions, or same one from the file 02_GeSeq/INSTRUCTIONS.txt.

After downloading GeSeq results, make zcit.py workflow run. Note: this runs steps so that demanding calculations have to be calculated on a dedicated server. In case of that, please consult demanding calculations. To sun steps locally run command zcit.py workflow run -r.

Notes:

  • In each stage of the calculation it is possible to visually research status with command zcit.py workflow graph.
  • Workflow uses external programs for alignment and phylogenetic analyses. There are 3 programs that have to be installed and the PATH on computer where calculations will be performed (locally or on dedicated server). In case some program is missing, calculation will stop with message what should be installed and set. Programs needed are:
    • MAFFT. Executable should be named mafft, or alternative name set with MAFFT_EXE environmnet variable.
    • RAxML. Executable should be named raxml_threads, or alternative name set with RAXML_EXE environmnet variable.
    • MrBayes. Executable should be named mr_bayes or mr_bayes_mpi in case of MPI version, or alternative names set with MR_BAYES_EXE and MR_BAYES_EXE environmnet variables.
      • Note: MrBayes hangs on some variation of input data (issue). Please use fixed version. Original version is here.