make_telomere_bed

Input:

• Single .fasta file of contigs/scaffolds
• Unit sequence of telomeres (cf. http://telomerase.asu.edu/sequences_telomere.html)

Output:

• Single .bed file each line of which is as follows:

<contig_name> <start_position> <end_position> <copy_number>

• (TRF's original output file for the fasta file and filtered TRF output file containing only the telomere-related lines)

Dependencies:

• Tandem Repeat Finder
• Python 3

How to install

$ git clone https://github.com/yoshihikosuzuki/make_telomere_bed
$ cd make_telomere_bed
$ python setup.py install

After this, a command make_telomere_bed should be available.

How to run

1. Main program

usage: make_telomere_bed [-h] [-t TRF_PATH] [-s] [-I]
                         contig_fasta unit_sequence

positional arguments:
  contig_fasta          A fasta file name.
  unit_sequence         Unit sqeuence like `TTAGGG`. Both capital and small
                        are OK.

optional arguments:
  -h, --help            show this help message and exit
  -t TRF_PATH, --trf_path TRF_PATH
                        Path to TRF's executable. [trf]
  -s, --split_contigs   Use this option if TRF takes forever. TRF sometimes
                        freezes for long contigs, and if this is specified,
                        then split contigs in `contig_fasta` into 1 Mbp
                        substrings. [False]
  -I, --ignore_exist    Ignore existing files and generate them again. The
                        final .bed file is always generated anyway. [False]

NOTES:

• Results are written to files, not stdout.
• This program does not run TRF if the result file already exists. Therefore, you can try different telomere unit sequences without running TRF every time. If you wish to ignore the current TRF result and re-generate it, then use the -I option.
• This program can be actually used for any tandem repeats other than telomeres. What this program does is to extract outputs of TRF whose consensus unit sequence is exactly same as the given unit sequence while permitting reverse complement sequence and cyclic alignment. Therefore, this program is suitable for tandem repeats with short units (e.g. <10 bp) but not for those with long units (e.g. >50 bp) because longer units are less likely to have exact matches with other units in the same tandem repeat array.

2. Filter BED file by score (= # of telomere motifs)

usage: filter_bed [-h] [-l MAX_GAP_LEN] [-m MIN_SCORE] in_bed

positional arguments:
  in_bed                Input .bed file (of telomere motifs).

optional arguments:
  -h, --help            show this help message and exit
  -l MAX_GAP_LEN, --max_gap_len MAX_GAP_LEN
                        Max distance between two adjacent positions to be
                        merged. [3000]
  -m MIN_SCORE, --min_score MIN_SCORE
                        Threshold of the score. Every adjacent positions
                        within <`max_gap_len` bp are merged and the total
                        score among them is used. [100]

NOTES:

• Results are written to stdout.