Scripts useful for manipulation and basic analysis of common file types

-FastaManager.py: get_sequences, getseq2, get_group_seq, get_stretch2, get_gc, fasta_to_oneline, fasta_to_phylip, fasta_to_stockholm, oneline_to_fasta, parse_desc, simplify, prefix, size_filter, compare_lists, cleanup, get_sizes, divide, divide1seq, index_names, index_pairs, change_names, rename, rename_all, del_redun_names, del_redun_seq, check_redun, get_sp, parse_ensembl_fasta, convert_header, delete, concat, locate, indiv, mask, count, get_longest, format

-GFFUtil.py: Includes sort, merge, sort_merge, merge_depth, length, lengths, min_len, len_prcntl, compare_lens, prefix_id, loc_id, loc_id_keep, coords2gff, mask, overlap, and overlap+.

-Map_PWM_biopy.py: Map PWM or dictionary of PWMs to a sequence in a fasta file.

1. Load the following modules:

   module load GCC/7.3.0-2.30

   module load OpenMPI/3.1.1

   module load R/3.5.1-X11-20180604

2. Run the R script:

   R --vanilla --slave --args <arg 1> <arg 2> > script.R