Scripts used to analyze Acinetobacter baumannii CRISPR-Cas systems

Perl scripts

• bindConting2ab.pl - bind contigs of phage-plasmids from a Blast report
• bindConting2ab_phageplasmid.pl - bind contigs from a Blast report
• convertffn2referencesFromRoary.pl - search for CDS sequences correspondig to pangenome references
• countVirusVariantsBySpacers.pl - count the number of viral variants targeted by the spacers
• createFileForPeaks1.pl - create a distribution plot of protospacers
• createFileForPeaks1_genes.pl - create a distribution plot of protospacers (by genes)
• createGroupsOfRedundantSequences.pl - cluster redundant sequences
• extractCancunSequences.pl - extract genomic islands
• extractSpacerTypes.pl - classify spacers by CRISPR-Cas type
• extractSpacerTypes_withDirections.pl - classify spacers by CRISPR-Cas type (oriented based on the repeat sequences)
• getPamSequences.pl - extract PAM sequences
• maskCRISPRinViruses.pl - mask CRISPR arrays with Ns
• typeSpacersFromFasta.pl
• typeSpacersFromFasta_frequency.pl - extract and classify spacers (adding frequencies)

R scripts (figure script: input files)

• fig2.R: all.gggenes
• fig3.R: islands.xlsx, p1virus.ab, p1virus_incomplete.ab, ../types/ifa.ab, ../types/ifb.ab
• fig4.R: metadata_ab_def_caudovirus.tsv, tree.tree, metadata_st79.tsv, ppcrispr/data/CP087336/polymorphisms_move.phy_phyml_tree.txt, metadata_ppcrispr.tsv, pp_completos/data/CP087336/polymorphisms_move.phy_phyml_tree.txt, metadata_pp.tsv
• fig5.R: nspacers3.tsv, nspacers_types.tsv, rp_ifa1.seq, rp_ifa2.seq, rp_ifb.seq
• fig6.R: variants_spacers2.tsv
• fig7.R: pam_p1virus_ifa1_12.seq, pam_p1virus_ifa2_12.seq, pam_p1virus_ifb_12.seq, spacers_vs_ab00002_80_80_2.tsv, spacers_vs_p1virusffn_ditribution.tsv, ../gggenes/p1virus.gggenes, pam_freq_p1virus_cds.tsv
• supplfigs2.R: ../../spacers_new/virus_100_phage.id, ../../strains.ab, phage_matrix_p1virus.tsv, metadata_ab_phigaro.tsv

Additional files

• ref_phigaro_ab.fasta: prophages (references)
• all_ab_phigaro_out_sup8kb.fasta: prophages (all)
• ab_phigaro.asoc: prophages (prophage clusters)
• spacers_ab_uniq.fasta: non-redundant spacers
• spacers_ab_uniq_types2.tsv: spacer types