UBCG2 - commands for example data

Run these lines to generate ucg files from fasta files.

java -jar UBCG2.jar -ucg_dir ucg -i fasta/CP012646_s_GCA_001281025.1_KCOM_1350.fasta -label "CP012646_s KCOM 1350" -acc "GCA_001281025.1" -taxon_name "CP012646_s" -strain_name "KCOM 1350" -hmm hmm/ubcg_v2.hmm

java -jar UBCG2.jar -ucg_dir ucg -i fasta/Streptococcus_constellatus_subsp._constellatus_GCA_000474075.1_SK53_TYPE.fasta -label "Streptococcus constellatus subsp. constellatus SK53_type" -acc "GCA_000474075.1" -taxon_name "Streptococcus constellatus subsp. constellatus" -strain_name "SK53" -type -hmm hmm/ubcg_v2.hmm 

java -jar UBCG2.jar -ucg_dir ucg -i fasta/Streptococcus_constellatus_subsp._pharyngis_GCA_000223295.2_SK1060_TYPE.fasta -label "Streptococcus constellatus subsp. pharyngis SK1060_type" -acc "GCA_000223295.2" -taxon_name "Streptococcus constellatus subsp. pharyngis" -strain_name "SK1060" -type -hmm hmm/ubcg_v2.hmm

java -jar UBCG2.jar -ucg_dir ucg -i fasta/CP014326_s_GCA_001560895.1_SVGS_061.fasta -label "CP014326_s SVGS_061" -acc "GCA_001560895.1" -taxon_name "CP014326_s" -strain_name "SVGS_061" -hmm hmm/ubcg_v2.hmm

java -jar UBCG2.jar -ucg_dir ucg -i fasta/Streptococcus_mitis_GCA_002014755.1_CCUG_31611_TYPE.fasta -label "Streptococcus mitis CCUG 31611_type" -acc "GCA_002014755.1" -taxon_name "Streptococcus mitis" -strain_name "CCUG 31611" -type -hmm hmm/ubcg_v2.hmm 

java -jar UBCG2.jar -ucg_dir ucg -i fasta/Streptococcus_pneumoniae_GCA_001457635.1_NCTC_7465_TYPE.fasta -label "Streptococcus pneumoniae NCTC 7465_type" -acc "GCA_001457635.1" -taxon_name "Streptococcus pneumoniae" -strain_name "NCTC 7465" -type -hmm hmm/ubcg_v2.hmm

java -jar UBCG2.jar -ucg_dir ucg -i fasta/Streptococcus_pseudopneumoniae_GCA_002087075.1_CCUG_49455_TYPE.fasta -label "Streptococcus pseudopneumoniae CCUG 49455_type" -acc "GCA_002087075.1" -taxon_name "Streptococcus pseudopneumoniae" -strain_name "CCUG 49455" -type -hmm hmm/ubcg_v2.hmm

java -jar UBCG2.jar -ucg_dir ucg -i fasta/Streptococcus_pneumoniae_GCA_000006885.1_TIGR4.fasta -label "Streptococcus pneumoniae TIGR4" -acc "GCA_000006885.1" -taxon_name "Streptococcus pneumoniae" -strain_name "TIGR4" -hmm hmm/ubcg_v2.hmm