Scripts used for Acquisition and transmission of TB drug resistance in China

documents

Experiments of determinism
Experiments on sanity check

inputs

Beijing_lineage_list.txt: samples list for simulation
shuffle_test.txt: shuffled samples list for determinism check
RESI_SNPs: vcf file of resistant SNPs

reference

AL123456.2: H37Rv version AL123456.2
AL123456.3: H37Rv version AL123456.3 (used in this research)
TBSequence.fasta: H37Rv

results

Beijing_lineage_SNP.xlsx: 
SNP_count.txt		
data_infomation_Beijing.xlsx
determinism experiment.xlsx

simulation

TB_simulation.py: simulation

scripts

checkSNP.py: Python script for checking snp in reference
countSNPs.sh: Shell script for counting SNPs on all samples
callResiSnps.sh: Shell script for calling resistant SNPs on a single sample
FileDownload.pbs: PBS script for file downloading
FileDownload.py: Python script for file downloading
jobSubmission.py: Python script for job submitting
polyTB_Breezy.sh: Shell script for SNPs calling for one sample
unresi_SNP.sh: Shell script for calling unresistant SNPs on a single sample