[Biophp-dev] (no subject)

biophp-dev@bioinformatics.org biophp-dev@bioinformatics.org
Mon, 18 Oct 2004 10:50:43 +0200 

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Hi all,

Here is a little update of my suggestion for =
CVS/biophp/genephp/parsers/fasta.inc.php

regards,

Fred


function fetchNext()
    {
        $record=3DArray(); //for returning results
        if($this->next_label) {
            list($id,$sequence)=3D$this->findNextLabel();
            //treat the Defline used at NCBI
            //>gi|42794768|ref|NM_002576.3| Homo sapiens =
p21/Cdc42/Rac1-activated kinase 1 (STE20 homolog, yeast) (PAK1), mRNA
            if(ereg("^gi", $id)) {
                $id =3D substr($id, 3); //take off gi|
                list($id, $db, $accession_version, $definition) =3D =
explode("|", $id);
                list($accession, $version) =3D explode(".", =
$accession_version);
                $record['ncbi_gi_id']   =3D$id;
                $record['id']           =3D$accession;
                $record['accession']    =3D$accession;
                $record['version']      =3D$accession_version;
                $record['definition']   =3D$definition;
                if (ereg("mRNA", $definition)) $record['moltype'] =3D =
"mRNA";
                if (ereg("Homo sapiens", $definition)) {
                    $record['source']   =3D "Homo sapiens (human)";
                    $record['organism'] =3D "Homo sapiens";
                }
            }
            else {
            $record['id']=3D$id;
            }
            $record['sequence']=3D$sequence;
            return $record;
        }
        else {
            //no more records in file
            return false;
        }
    }

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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
<HTML>
<HEAD>
<META HTTP-EQUIV=3D"Content-Type" CONTENT=3D"text/html; =
charset=3Diso-8859-1">
<META NAME=3D"Generator" CONTENT=3D"MS Exchange Server version =
6.0.6556.0">
<TITLE></TITLE>
</HEAD>
<BODY>
<!-- Converted from text/rtf format -->

<P><FONT SIZE=3D2 FACE=3D"Arial">Hi all,</FONT>
</P>

<P><FONT SIZE=3D2 FACE=3D"Arial">Here is a little update of my =
suggestion for CVS/biophp/genephp/parsers/fasta.inc.php</FONT>
</P>

<P><FONT SIZE=3D2 FACE=3D"Arial">regards,</FONT>
</P>

<P><FONT SIZE=3D2 FACE=3D"Arial">Fred</FONT>
</P>
<BR>

<P><FONT SIZE=3D2 FACE=3D"Arial">function fetchNext()</FONT>

<BR><FONT SIZE=3D2 FACE=3D"Arial">&nbsp;&nbsp;&nbsp; {</FONT>

<BR><FONT SIZE=3D2 =
FACE=3D"Arial">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
$record=3DArray(); //for returning results</FONT>

<BR><FONT SIZE=3D2 =
FACE=3D"Arial">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
if($this-&gt;next_label) {</FONT>

<BR><FONT SIZE=3D2 =
FACE=3D"Arial">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp; list($id,$sequence)=3D$this-&gt;findNextLabel();</FONT>

<BR><FONT SIZE=3D2 =
FACE=3D"Arial">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp; //treat the Defline used at NCBI</FONT>

<BR><FONT SIZE=3D2 =
FACE=3D"Arial">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp; //&gt;gi|42794768|ref|NM_002576.3| Homo sapiens =
p21/Cdc42/Rac1-activated kinase 1 (STE20 homolog, yeast) (PAK1), =
mRNA</FONT></P>

<P><FONT SIZE=3D2 =
FACE=3D"Arial">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp; if(ereg(&quot;^gi&quot;, $id)) {</FONT>

<BR><FONT SIZE=3D2 =
FACE=3D"Arial">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; $id =3D substr($id, 3); //take off =
gi|</FONT>

<BR><FONT SIZE=3D2 =
FACE=3D"Arial">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; list($id, $db, $accession_version, =
$definition) =3D explode(&quot;|&quot;, $id);</FONT>

<BR><FONT SIZE=3D2 =
FACE=3D"Arial">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; list($accession, $version) =3D =
explode(&quot;.&quot;, $accession_version);</FONT>

<BR><FONT SIZE=3D2 =
FACE=3D"Arial">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; $record['ncbi_gi_id']&nbsp;&nbsp; =
=3D$id;</FONT>

<BR><FONT SIZE=3D2 =
FACE=3D"Arial">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
$record['id']&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=
 =3D$accession;</FONT>

<BR><FONT SIZE=3D2 =
FACE=3D"Arial">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; $record['accession']&nbsp;&nbsp;&nbsp; =
=3D$accession;</FONT>

<BR><FONT SIZE=3D2 =
FACE=3D"Arial">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
$record['version']&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
=3D$accession_version;</FONT>

<BR><FONT SIZE=3D2 =
FACE=3D"Arial">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; $record['definition']&nbsp;&nbsp; =
=3D$definition;</FONT>

<BR><FONT SIZE=3D2 =
FACE=3D"Arial">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; if (ereg(&quot;mRNA&quot;, =
$definition)) $record['moltype'] =3D &quot;mRNA&quot;;</FONT>

<BR><FONT SIZE=3D2 =
FACE=3D"Arial">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; if (ereg(&quot;Homo sapiens&quot;, =
$definition)) {</FONT>

<BR><FONT SIZE=3D2 =
FACE=3D"Arial">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
$record['source']&nbsp;&nbsp; =3D &quot;Homo sapiens =
(human)&quot;;</FONT>

<BR><FONT SIZE=3D2 =
FACE=3D"Arial">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
$record['organism'] =3D &quot;Homo sapiens&quot;;</FONT>

<BR><FONT SIZE=3D2 =
FACE=3D"Arial">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; }</FONT>

<BR><FONT SIZE=3D2 =
FACE=3D"Arial">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp; }</FONT>

<BR><FONT SIZE=3D2 =
FACE=3D"Arial">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp; else {</FONT>

<BR><FONT SIZE=3D2 =
FACE=3D"Arial">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp; $record['id']=3D$id;</FONT>

<BR><FONT SIZE=3D2 =
FACE=3D"Arial">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp; }</FONT>

<BR><FONT SIZE=3D2 =
FACE=3D"Arial">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp; $record['sequence']=3D$sequence;</FONT>

<BR><FONT SIZE=3D2 =
FACE=3D"Arial">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp; return $record;</FONT>

<BR><FONT SIZE=3D2 =
FACE=3D"Arial">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; }</FONT>

<BR><FONT SIZE=3D2 =
FACE=3D"Arial">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; else {</FONT>

<BR><FONT SIZE=3D2 =
FACE=3D"Arial">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp; //no more records in file</FONT>

<BR><FONT SIZE=3D2 =
FACE=3D"Arial">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp; return false;</FONT>

<BR><FONT SIZE=3D2 =
FACE=3D"Arial">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; }</FONT>

<BR><FONT SIZE=3D2 FACE=3D"Arial">&nbsp;&nbsp;&nbsp; }</FONT>
</P>

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