lukszafron / ctx-explorer

CTX-Explorer is an app for identification of inter- and intrachromosomal translocations developed in Python 3.

CTX-explorer

Welcome to the CTX-Explorer app.

This open-source Python 3 program was developed for identification of inter- and intrachromosomal translocations.

Additional Python libraries that need to be installed for this app to work correcly: subprocess, re, os, gzip, sys, getopt, statistics, itertools, termcolor

Additional software that needs to be installed for this app to work correctly: samtools, bamtools

The following options are available:

    -h, --help:             prints this help message.
    -t, --threads:          defines the number of CPU threads that are to be used (default: 1).
    -T, --tmpdir:           defines the directory where temporary files are to be stored (default: current dir).
    -q, --qual:             defines the minimal Phred quality score of mappings to be used (default: 20).
    -b, --bamfile:          the name of a BAM file to be used (MANDATORY).
    -I, --intractx:         indicates if intra-chromosomal translocations should be evaluated (default: 'no'). This option significantly increases memory usage.
    -1, --chrom1:           the name of the first chromosome (optional) involved in a translocation (e.g., 'chr1').
    -2, --chrom2:           the name of the second chromosome (optional) involved in a translocation (e.g., 'chr2').
    -l, --tlen:             minimal distance (in nucleotides) between the first and the second read forming a read pair (default: 1,000,000).
    -i, --insert:           the maximum insert size used for identification of CTX-supporting reads and hit pairs (default: median insert size * 2).
    -n, --nohits:           minimal number of hits for a translocation to be stored in the final report (default: 2).
    -N, --nohits_sec:       minimal number of hits per the second chromosome for a translocation to be stored in the final report (default: 2).
    -s, --min_size:         minimal size of a hit group for a translocation to be stored in the final report (default: 2).
    -d, --no_filter:        specifies whether the filtering by the number of supporting reads should be turned off (default: 'no').
    -p, --prefix:           specifies a prefix of a file in which the final report will be saved (default: 'output').
    -g, --gzipped:          indicates whether the final report file should be gzipped (default: 'no').
    -v, --version:          prints the version of this program.