9. Amend program_z_script where it states << Add new programs here >>. Example:
echo "script_step=\">> executing program_z\"" >> $script_dir/
script$chr_no
echo "program_z $required_input $out_dir" >> $script_dir/
script$chr_no || error_exit
where $required_input is the input as determined in step
2.
10. A generic Perl script called “get_evidence.pl” (located in install_dir/vacceed/new_species/pipeline/common_programs) can be
amended accordingly to extract the relevant evidence from the
program_z output file (see Note 20). Alternatively, any programming language can be used to write a program to extract evidence. In such a case, the program name would need to replace
“get_evidence.pl” in program_z_script. Regardless of the extraction program, evidence needs to be saved in a user-named file
with the suffix “_evd” (e.g., programz_evd in the directory
install_dir/vacceed/new_species/pipeline/evidence/output).
4 Notes
1. The bioinformatics programs are third-party and are not part of
the Vacceed package. Furthermore, installation steps for the
third-party programs are not described in this chapter. Most
of the programs provide a ReadMe file with instructions. Even
so, these installations are still a challenging aspect to preparing
Vacceed ready for use. It is highly recommended to seek the
help of an administrator or an experienced Linux user.
2. Vacceed checks to see if a protein sequence contains invalid
letters (e.g., characters other than [ACDEFGHIKLMNP
QRSTVWY]).
3. Vacceed collates relevant, predicted protein characteristics (typically in the form of numerical values) into one file called
evidence_profiles, that is, contents of all files with the extension
“_evd” in the evidence/output directory are combined as columns into evidence_profiles.
4. Ensure that each third-party program runs successfully before
testing Vacceed.
5. The computation takes less than a few minutes depending on
the computer environment to run the test when both MHCI
and MHCII are removed. Furthermore, MHCI and MHCII
predictions on the whole are not accurate [16] (particularly
MHCII [17]) and only marginally contributed to the Vacceed
end result when tested with the T. gondii sample data [8].
Eukaryotic Pathogen Antigen Discovery Using Vacceed
39
echo "script_step=\">> executing program_z\"" >> $script_dir/
script$chr_no
echo "program_z $required_input $out_dir" >> $script_dir/
script$chr_no || error_exit
where $required_input is the input as determined in step
2.
10. A generic Perl script called “get_evidence.pl” (located in install_dir/vacceed/new_species/pipeline/common_programs) can be
amended accordingly to extract the relevant evidence from the
program_z output file (see Note 20). Alternatively, any programming language can be used to write a program to extract evidence. In such a case, the program name would need to replace
“get_evidence.pl” in program_z_script. Regardless of the extraction program, evidence needs to be saved in a user-named file
with the suffix “_evd” (e.g., programz_evd in the directory
install_dir/vacceed/new_species/pipeline/evidence/output).
4 Notes
1. The bioinformatics programs are third-party and are not part of
the Vacceed package. Furthermore, installation steps for the
third-party programs are not described in this chapter. Most
of the programs provide a ReadMe file with instructions. Even
so, these installations are still a challenging aspect to preparing
Vacceed ready for use. It is highly recommended to seek the
help of an administrator or an experienced Linux user.
2. Vacceed checks to see if a protein sequence contains invalid
letters (e.g., characters other than [ACDEFGHIKLMNP
QRSTVWY]).
3. Vacceed collates relevant, predicted protein characteristics (typically in the form of numerical values) into one file called
evidence_profiles, that is, contents of all files with the extension
“_evd” in the evidence/output directory are combined as columns into evidence_profiles.
4. Ensure that each third-party program runs successfully before
testing Vacceed.
5. The computation takes less than a few minutes depending on
the computer environment to run the test when both MHCI
and MHCII are removed. Furthermore, MHCI and MHCII
predictions on the whole are not accurate [16] (particularly
MHCII [17]) and only marginally contributed to the Vacceed
end result when tested with the T. gondii sample data [8].
Eukaryotic Pathogen Antigen Discovery Using Vacceed
39