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For Users: Command line Interface

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billzt edited this page Aug 29, 2017 · 7 revisions

Installation

Before installation, make sure you meet these requirements.

Clone or download the source code. Add the script directory to your system PATH.

WARNING: Don't copy any script out of the directory to run it.

Design & Check

The script pipeline_design_check.pl corresponds to this module. See perldoc pipeline_design_check.pl to get full documents.

Parameters

Most parameters corresponds to the web interface and can be self-explained in the POD. Here are several parameters needed to be explained.

  • --template
  • --checkingdb
    • They are database names (in fact FASTA file names) with path. For example, if your database is /path/to/reference.fa, there should be five files in the database directory: /path/to/reference.fa, /path/to/reference.fa.fai, /path/to/reference.fa.nhr, /path/to/reference.fa.nin, /path/to/reference.fa.nsq. Then you should use /path/to/reference.fa as the parameter value
    • --checkingdb allows multiple databases separated by comma. The first is regarded as the main database.
  • --debug
    • Turn on this would keep some tmp files.

Test and Results

In the test_data directory, create a file query.dat:

seq1 200 10
seq1 400 10

Run:

pipeline_design_check.pl --input=query.dat --template=example.fa

After finished, it would create an output directory PrimerServerOutput including all results:

PrimerServerOutput
  |
  |-- primer3output.txt (The results produced by Primer3)
  |-- primer3output.simple.table.txt (A file deduced from primer3output.txt. 
  |                                   It can be used as the input of specificity-checking)
  |-- specificity.check.result.txt (similar as primer3output.simple.table.txt, but adding amplicon numbers)
  |-- specificity.check.result.amplicon (list all the amplicons for each primer)
  |-- primer.final.result.txt (** Final data integration results **)
  |-- result.specificity.check/ (List the raw alignments of primers and templates)

Usually, users can get their needed primers in the file primer.final.result.txt

Check Only

The script pipeline_check.pl corresponds to this module. See perldoc pipeline_check.pl to get full documents.

Parameters

Most parameters corresponds to the web interface and can be self-explained in the POD.

Test and Results

In the test_data directory, create a file query.dat:

P1 CTTCTGCAATGCCAAGTCCAG   GTGGTGAAGGGTCGGTTGAA
P2 ACCAAACCCCAGAGTCAATTAA  TCTATCTATTGCACTGCCTGTTG

Run:

pipeline_check.pl --input=query.dat --db=example.fa

After finished, it would create an output directory PrimerServerOutput including all results:

PrimerServerOutput
  |
  |-- specificity.check.result.txt (similar as query.dat, but adding amplicon numbers)
  |-- specificity.check.result.amplicon (list all the amplicons for each primer)
  |-- result.specificity.check/ (List the raw alignments of primers and templates)

Usually, users can get the specificity-checking results in the file specificity.check.result.txt

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