<div dir="ltr">Hi,<div><br></div><div>I think you would like to use function "tostring()":</div><div>For example:<br></div><div>contigs = SeqIO.parse(open(sys.argv[1]), 'fasta')<br></div><div>for contig in contigs:</div>
<div> seq = contig.seq.tostring()</div><div> print seq</div><div><br></div><div><br></div><div>Regards.</div><div>Ju</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Sun, Jun 29, 2014 at 6:43 AM, Ismail Uddin <span dir="ltr"><<a href="mailto:ismail.sameeuddin@gmail.com" target="_blank">ismail.sameeuddin@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small;color:rgb(51,51,51)">
<div class="gmail_default">Dear Sir or Madam,</div><div class="gmail_default"><br></div><div class="gmail_default">
I would like to post a question regarding FASTA file parsing using the BioPython module. The current tutorial online indicates how to parse a FASTA file, but the output is in the format Seq('<<sequence here>>', SingleLetterAlphabet())</div>
<div class="gmail_default"><br></div><div class="gmail_default">I would like to know how one may simply print out the entire sequence without any adjoining text i.e. 'ACTACGGCGAT'</div><div class="gmail_default">
<br>
</div><div class="gmail_default">I ask this question, as I am trying to write a script that will read each entry in the FASTA file and produce a dictionary of key being the ID and the value being the raw sequence.</div><div class="gmail_default">
<br></div><div style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:13px"><div dir="ltr"><div><font face="arial, helvetica, sans-serif" color="#999999"><div class="gmail_default" style="font-size:small;color:rgb(51,51,51);display:inline">
Thank you in advance for your help and cooperation,<br></div></font></div><div><font face="arial, helvetica, sans-serif" color="#999999"><div class="gmail_default" style="font-size:small;color:rgb(51,51,51);display:inline">
Ismail Uddin</div></font></div></div></div></div>
</div>
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