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<DIV><FONT face="News Gothic" color=#0000ff size=2><SPAN
class=230212406-02042003>Dear all,</SPAN></FONT></DIV>
<DIV><FONT face="News Gothic" color=#0000ff size=2><SPAN
class=230212406-02042003></SPAN></FONT> </DIV>
<DIV><FONT face="News Gothic" color=#0000ff size=2><SPAN
class=230212406-02042003>thanks for the quick replies and help with the fasta
conversion problem. I already started fiddling around in perl to convert the
fasta files into files acceptable to tgicl for EST assembly. </SPAN></FONT><FONT
face="News Gothic" color=#0000ff size=2><SPAN class=230212406-02042003>But Eitan
provided the most simpel solution in his one line perl 'script' that exactly did
what I needed. BIG THANKS. The script just gets rid of all stuff after the
filename (as long as no spaces are in the filename) and preserves all sequence
or quality info behind it. </SPAN></FONT><FONT face="News Gothic" color=#0000ff
size=2><SPAN class=230212406-02042003>His solution is below.</SPAN></FONT></DIV>
<DIV><FONT face="News Gothic" color=#0000ff size=2><SPAN
class=230212406-02042003></SPAN></FONT> </DIV>
<DIV><FONT face="News Gothic" color=#0000ff size=2><SPAN
class=230212406-02042003>I still don't get why tgicl does't accept files in
allowed fastA format. But I don't bother anymore. My EST assembly is one step
further.</SPAN></FONT></DIV>
<DIV><FONT face="News Gothic" color=#0000ff size=2><SPAN
class=230212406-02042003></SPAN></FONT> </DIV>
<DIV><FONT face="News Gothic" color=#0000ff size=2><SPAN
class=230212406-02042003>Thanks again to all people sending me perl
solutions!</SPAN></FONT></DIV>
<DIV><FONT face="News Gothic" color=#0000ff size=2><SPAN
class=230212406-02042003></SPAN></FONT> </DIV>
<DIV><FONT face="News Gothic" color=#0000ff size=2><SPAN
class=230212406-02042003>Alex</SPAN></FONT></DIV>
<DIV><FONT face="News Gothic" color=#0000ff size=2><SPAN
class=230212406-02042003></SPAN></FONT> </DIV>
<DIV><FONT face="News Gothic" color=#0000ff size=2><SPAN
class=230212406-02042003></SPAN></FONT> </DIV>
<DIV></DIV>
<DIV class=OutlookMessageHeader lang=nl dir=ltr align=left><FONT face=Tahoma
size=2>-----Oorspronkelijk bericht-----<BR><B>Van:</B> Eitan Rubin
[mailto:Eitan.Rubin@weizmann.ac.il] <BR><B>Verzonden:</B> dinsdag 1 april 2003
20:28<BR><B>Aan:</B> A.Bossers@ID.DLO.NL<BR><B>Onderwerp:</B> Fasta
convertion<BR><BR></FONT></DIV>
<DIV><FONT face=Arial size=2>Hi,</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2> If I am not mistaken, you question is "how
do I convert format A below to format B". If this indeed what you need, the
following should do the trick:</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>perl -pe 's/^>(\S+).*/>$1/;' old_format_file
> new_format_file</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Format A:</FONT></DIV>
<DIV><FONT face=Arial size=2>==========</FONT></DIV>
<DIV><FONT face=Arial size=2>>seqname1 some text with spaces</FONT></DIV>
<DIV><FONT face=Arial size=2>ACGTAGACTGACT..</FONT></DIV>
<DIV><FONT face=Arial size=2>>seqname2 some other text etc</FONT></DIV>
<DIV><FONT face=Arial size=2>ACGATCGATAGCT</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Format B:</FONT></DIV>
<DIV><FONT face=Arial size=2>========</FONT></DIV>
<DIV><FONT face=Arial size=2>
<DIV><FONT face=Arial size=2>>seqname1</FONT></DIV>
<DIV><FONT face=Arial size=2>ACGTAGACTGACT..</FONT></DIV>
<DIV><FONT face=Arial size=2>>seqname2</FONT></DIV>
<DIV><FONT face=Arial size=2>ACGATCGATAGCT</FONT></DIV></FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2> Eitan</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial
size=2>------------------------------------------------------------------------<BR>Eitan
Rubin, PhD<BR>Head of Bioinformatics and Biological Computing<BR>Dept.
Biological Services<BR>Weizmann Institute of Science<BR>Tel:
+972-8-9343456<BR>Fax: +972-8-9346006</FONT></DIV></BODY></HTML>