$sSequence = $sSequenceSpliced;
$nCDSstartNC -= $lCut;
$nCDSendNC -= $lCut;
}
$aNMCache[$sNCFileID . ':' . $sRefSeqID] = array($nCDSstartNC, $nCDSendNC, $sSequence);
}
list($nCDSstart, $nCDSend, $sSequence) = $aNMCache[$sNCFileID . ':' . $sRefSeqID];
// Get Motif or upstream sequence.
if ($sType == 'peak_classification') {
// Fetch motif.
$aTIS['Motif'] = substr($sSequence, 0, 3);
} else {
// For 5'UTR (all we see here), get the whole upstream sequence.
$aTIS['DNASeqToAUG'] = substr($sSequence, 0, -3);
// Now, get it translated.
$sProteinSequence = RPF_translateDNA($aTIS['DNASeqToAUG']);
$aTIS['ProtSeqToAUG'] = $sProteinSequence;
}
}
}
fputs($aSample['file_out'][$sType]['handle'], implode("\t", $aTIS) . "\n");
// Only for 5'UTR classification, we show all. Otherwise, just the first will do.
if ($sType != 'peak_classification_5UTR') {
break;
}
}
if (!($nLine % 50)) {
$nPercentageRead = round($nLine / $aSample['peak_count'], 2);
$nAvailableWidth = $_SETT['terminal_width'] - 8 - strlen($nLine);
$lDone = round($nPercentageRead * $nAvailableWidth);
print str_repeat(chr(8), $_SETT['terminal_width']) . '[' . str_repeat('=', $lDone) . str_repeat(' ', $nAvailableWidth - $lDone) . '] ' . $nLine . ' ' . str_pad(round($nPercentageRead * 100), 3, ' ', STR_PAD_LEFT) . '%';
// 0-based position.
if ($nPositionInString < 0) {
// We don't have the start of the sequence.
$bTranslatable = false;
if ($nCDSstart == 1) {
$sSequenceProtein = 'no_5UTR';
} else {
// No upstream sequence, or not enough upstream sequence available.
$sSequenceProtein = 'unannotated_5UTR';
}
}
}
$sSequenceToTranslate = $sSequenceToTranslateToStop = '';
if ($bTranslatable) {
$sSequenceToTranslate = substr($sSequence, $nPositionInString);
$sSequenceProtein = RPF_translateDNA($sSequenceToTranslate);
// Shorten sequence, only show until the first stop.
$sSequenceProtein = substr($sSequenceProtein, 0, strpos($sSequenceProtein . '*', '*') + 1);
// Then create a short mRNA sequence, up and until the first stop.
$sSequenceToTranslateToStop = substr($sSequenceToTranslate, 0, strlen($sSequenceProtein) * 3);
}
// Output...
fputs($fFileOut, $sChr . ':' . $nPosition . "\t" . $sTranscript . "\t" . $nPositionOnTranscript . "\t" . $sSequenceToTranslateToStop . "\t" . $sSequenceToTranslate . "\t" . $sSequenceProtein . "\n");
}
// Clean up...
$sLabel = '';
// Print the progress.
if (!($nLine % 5)) {
$nPercentageRead = round($nLine / $nLines, 2);
$nAvailableWidth = $_SETT['terminal_width'] - 8 - strlen($nLine);
$lDone = round($nPercentageRead * $nAvailableWidth);
