As of now this project is not set up to work with setuptools/distribute. Instead, it is a self-contained directory that can be directly executed with python, i.e.
python 4c
Global help text can be displayed with
python 4c -h
The tools are setup as subcommands
python 4c {make-index,align,fragcount,bin}
and help for each can be obtained with
python 4c subcommand -h
Subcommands listed in order relevant for analyzing paired end solexa 4C experiments:
| make-index | Create bowtie index of restriction fragments (with flanking region) |
| align | Align 4c pairs to restriction fragment index |
| fragcount | Summarize the number of reads per detected fragment |
| bin | test help text |
###Python libraries:
- argparse (either python >= 2.7 or backported separate library)
- Biopython
- pybedtools
- pysam
- numpy
###External executables on path:
- bowtie and bowtie-build
- samtools