GTsegments 0.21

Compute Genomic & Transcriptomic segments

This program is designed to work with python 2.7, python 3.2+ and pypy. It needs the following libraries:

• Biopython

• NetworkX

• numpy (pypy users, please follow the numpypy install process)

• progressbar2

• UFx

Parameters

gts.py [-h] [--genome_type {gbk,tsv,seq}] [--graph_type {gexf,list}]
              [-min INT] [-max INT] [-d THRESHOLD] [--no_filter] [-o FILE]
              [-no_dom] [-m | --no_gene_list] [-q]
              COEXP_GRAPH [GENOME [GENOME ...]]

Compute the list of GTsegments from a genome and a coexpression network.

example:
gts.py -min 2 -max 50 -d 0.6 coexp_graph.gexf genome.gbk

positional arguments:
  COEXP_GRAPH           Coexpression graph
  GENOME                genome file(s) containing genomic organization of
                        chromosomes

optional arguments:
  -h, --help            show this help message and exit
  -q, --quiet           Quiet mode: display only critical errors

File type:
  --genome_type {gbk,tsv,seq}
                        Type of the genome file(s) (default: gbk)
  --graph_type {gexf,list}
                        Type of the coexpression graph file (default: gexf)

GTsegments size:
  -min INT, --min_size INT
                        Minimum length of a GTsegment (default: 2)
  -max INT, --max_size INT
                        Maximum length of a GTsegment (default: maximum
                        possible)

Density option:
  -d THRESHOLD, --density THRESHOLD
                        Select GTsegments with a genomic density ≥ THRESHOLD
                        in ]0,1] (default: 0.6)
  --no_filter           Do not apply density filtering

Output options:
  -o FILE, --output FILE
                        Output file name
  -no_dom, --no_domination
                        Keep all the GTsegments instead of the dominant ones
  -m, --matrix          Output the density matrix instead of the listing of
                        GTsegments
  --no_gene_list        Do not add the gene list column in the listing of
                        GTsegments

Example

From the following graph.txt and seq.txt files,

• seq.txt

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
#26

• graph.txt

2       4
4       5
7       8
6       9
6       10
9       10
12      16
14      15
14      16
14      18
11      17
17      23
25      1
# The node 26 does not exist in the genome (commented) and will ignored
25      26

the following command …

gts.py graph.txt seq.txt --graph_type list --genome_type seq

will produce the following output:

chromosome  start   end     length  active_genes    density list_of_active_genes
seq.txt     2       5       4       3       0.75    2 4 5
seq.txt     4       5       2       2       1.0     4 5
seq.txt     6       10      5       3       0.6     6 9 10
seq.txt     7       8       2       2       1.0     7 8
seq.txt     9       10      2       2       1.0     9 10
seq.txt     12      16      5       4       0.8     12 14 15 16
seq.txt     12      18      7       5       0.714285714286  12 14 15 16 18
seq.txt     14      16      3       3       1.0     14 15 16
seq.txt     14      18      5       4       0.8     14 15 16 18
seq.txt     25      1       2       2       1.0     25 1

Acknowledgement

This work was supported by grants Fondap 15090007, Basal program PFB-03 CMM, IntegrativeBioChile INRIA Assoc. Team and CIRIC-INRIA Chile (line Natural Resources).