CPC2 standalone

• 2020-01-13 14:58, Yu-jian Kang
• This is a python 2 verison of CPC2 (same with the version of the original paper).
• Thanks for helps from HyperOdin, there is a python 3 version (the release of CPC2_standalone_python3 v1.0.1)

1 Pre-requisite:

a. Biopython package: a local version could be downloaded from http://biopython.org/wiki/Download

2 Install

a. Unpack the tarball:

tom@linux$ gzip -dc CPC2-beta.tar.gz | tar xf -

b. Build third-part packages:

tom@linux$ cd CPC2-beta
tom@linux$ export CPC_HOME="$PWD"
tom@linux$ cd libs/libsvm
tom@linux$ gzip -dc libsvm-3.18.tar.gz | tar xf -
tom@linux$ cd libsvm-3.18
tom@linux$ make clean && make

3 Run the predict

tom@linux$ cd $CPC_HOME
tom@linux$ bin/CPC2.py -i (input_seq) -o (result_in_table)

Example:

tom@linux$ bin/CPC2.py -i data/example.fa -o example_output

If you want to output predicted peptide sequence, use CPC2_output_peptide.py with “–ORF” option:

tom@linux$ bin/CPC2_output_peptide.py -i data/example.fa -o example_output --ORF

4 Output result

Result in table format (delimited by tab):
#ID peptide_length Fickett_score isoelectric_point ORF_integrity coding_probability coding_label

Contact

See the website for tutorial and more details. (http://cpc2.cbi.pku.edu.cn)

This is a beta version of CPC2, if have any questions please report to us.

Contact: cpc@mail.cbi.pku.edu.cn