CRI Tool

Calculate composite RIP index (CRI) score and generate box plots

Requirements

Python 2.7 and R

License

MIT

Repeat sequences (FASTA format)

• Neurospora_crassa.unmasked.fasta.seqs.txt.gz
• Saccharomyces_cerevisiae.EF4.66.dna.toplevel.fa.seqs.txt.gz
• Tuber_melanosporum_v1.0_unmasked.fa.seqs.txt.gz
• aspergillus_nidulans_fgsc_a4_1_contigs.fasta.seqs.txt.gz
• uncinocarpus_reesii_2_supercontigs.fasta.seqs.txt.gz

Calculate CRI score for each repeat

See other procedures in Methods for the CRI formula.

Example:

$ python CRI_fasta.py -f Tuber_melanosporum_v1.0_unmasked.fa.seqs.txt

Output files:

• CRI_CA_Tuber_melanosporum_v1_repeats.txt (CA->TA)
• CRI_CG_Tuber_melanosporum_v1_repeats.txt (CG->TG)

All outputs:

• CRI_CA_Neurospora_crassa_repeats.txt
• CRI_CA_aspergillus_nidulans_fgsc_a4_1_contigs_repeats.txt
• CRI_CA_Saccharomyces_cerevisiae_repeats.txt
• CRI_CA_Tuber_melanosporum_v1_repeats.txt
• CRI_CA_uncinocarpus_reesii_2_supercontigs_repeats.txt
• CRI_CG_aspergillus_nidulans_fgsc_a4_1_contigs_repeats.txt
• CRI_CG_Saccharomyces_cerevisiae_repeats.txt
• CRI_CG_Tuber_melanosporum_v1_repeats.txt
• CRI_CG_uncinocarpus_reesii_2_supercontigs_repeats.txt
• CRI_CG_Neurospora_crassa_repeats.txt

Generate box plots

Run R program:

Boxplot-CRI-Tuber-vs-other4.R

Output files: