ReadME

Description:
anticonv.pl is a perl script to create a new antisenseML file from certain format input file.

Usage:

perl anticonv.pl -i inputfile -r reviser -d date -o outfile

the option -i must be specified.

Documentation:

1) Format of input file:There are four top1 level element:target,reference,antiseq,antiassay.
the top1 level format:
<element(column1 title;column2 title;...)\n
column1\t comlumn \t ... column \n
>\n

element stand for :target,reference,antiseq
column title in the '(' and ')' is optional, but '(' and ')' is absolutely necessarily.
\t means tab key,\n means newline key.
note: when element is antiassay, the format is different:
<antiassay:AssayType:SeriesID:RefIDs:Transfection_Method\n

top2 level element: efficacy,control,figure,comments, format is as followed:
{element(column1 title;column2 title;...)\n
column1 \t column2 \t ... column \n
}

Example:

<target(TargetType;GenbankID;miRBaseAccessionNumber;Description;Sequence;Information)


>
<reference(ReferenceID;PubMedID;Author;Title;Journal;Book;Date;Volumn;Issue;Pages;Path)
>
<antiseq(AntiID;AntiType;SeqType;Seq;Strand;Source;Postion;shRNAseq;Modification;RefIDs)
>
<antiassay:InVitro:sid200634:ref000001:Lipofectin
{efficacy(AntiID;RefID;CtrlIDs;CellLine;AssayLevel;AssayMethod;Conc;Efficacy)
}
{control(CtrlID;CtrlType;CtrlSeq;AssayLevel;AssayMethod;Conc;Eff)
}
{figure(FigID;FigName;FigURL;FigPath;AntiIDs;CtrlIDs;Title;Annotation)
}
{comments()

}
>

Hint:We can use the Microsoft Excel to create input file, an template antisenml.xls are provide on the FTP site
http://ftp.bioinformatics.org/pub/antiml/



