<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div>You can use gff3_merge to collect them into a single file, or to keep them as separate files but in the same directory just use the standard linux copy command. Similarly you can use fasta_merge to collect the fasta files.</div><div><br></div><div>Example:</div><blockquote style="margin:0 0 0 40px; border:none; padding:0px;"><div>mkdir results</div></blockquote><blockquote style="margin:0 0 0 40px; border:none; padding:0px;"><div>cp *.maker.output/*_datastore/*/*/*.gff results/</div></blockquote><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> Hung-Wei Hsu <<a href="mailto:ares711122@gmail.com">ares711122@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Thursday, 21 March, 2013 8:08 PM<br><span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] Directory structure is too deep!<br></div><div><br></div><div dir="ltr"><span style="font-size: 14px; font-family: arial, sans-serif; ">Hi MAKER developers,</span><br><div><span style="font-size: 14px; font-family: arial, sans-serif; "><br></span></div><div style=""><font face="arial,sans-serif"><span style="font-size:14px">I found that the MAKER outputs of each contigs were located in separate deep directory.</span></font></div><div style=""><font face="arial,sans-serif"><span style="font-size:14px">Can MAKER collect these outputs in one simple directory so that these results can be easily examined?</span></font></div><div style=""><font face="arial,sans-serif"><span style="font-size:14px">Thanks a lot in advance.</span></font></div><div style=""><font face="arial,sans-serif"><span style="font-size:14px"><br></span></font></div><div style=""><font face="arial,sans-serif"><span style="font-size:14px">Warmest regards,</span></font></div><div style=""><font face="arial,sans-serif"><span style="font-size:14px">Hung-Wei</span></font></div></div>
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