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config.txt
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config.txt
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# Directory where scripts resides. This is needed so that you can call the pipeline from any other directory
scripts_dir=/home/kviljoen/scripts_dir/
python_base=/opt/exp_soft/python-2.7.3/bin/python
blast_base=/opt/exp_soft/ncbi-blast-2.2.28+/bin
in_dir=/researchdata/fhgfs/clinton.moodley/JCVI_data_correct/strep_assemblies
tmp_dir=/researchdata/fhgfs/clinton.moodley/JCVI_results_KL/tmp_dir
out_dir=/researchdata/fhgfs/clinton.moodley/JCVI_results_KL/out_dir
log_dir=/researchdata/fhgfs/clinton.moodley/JCVI_results_KL/logs
query_list=/home/kviljoen/strep_pbp_project/query.list
file_list=/home/kviljoen/strep_pbp_project/round2_missing_files_found_file.list
pid_list=/home/kviljoen/strep_pbp_project/Strep_PID_table_v2.txt
pbp_refs=/home/kviljoen/strep_pbp_project/KL_Strep_pneumoniae_NCBI_random_reference_pbp_seqs.fasta
#BLAST configs
num_threads='2'
evalue='10e-05'
num_output='100'
min_len='1500' #minimum sequence length to filter out partial pbp hits, i.e. the aligned part of the contig must be at least minlen