<div dir="ltr">hi Lenna/Peter,<div><br></div><div>Yes sure ! I just figured out this after asking the question, thanks for clarifying this though</div><div><br></div><div>Rad</div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Nov 12, 2014 at 4:30 PM, Peter Cock <span dir="ltr"><<a href="mailto:p.j.a.cock@googlemail.com" target="_blank">p.j.a.cock@googlemail.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">Hi Rad,<div><br></div><div>Good question, but no.</div><div><br></div><div>It is Python syntax for a "raw" string meaning things like \n</div><div>and \t are left as they are and not turned into a newline<div>or tab. We need to do this on a few of our docstrings (Python</div><div>documentation strings) due to wanting to use those special</div><div>strings in the examples in the text.</div><div><br></div><div><a href="https://github.com/biopython/biopython/blob/master/Bio/SeqIO/__init__.py" target="_blank">https://github.com/biopython/biopython/blob/master/Bio/SeqIO/__init__.py</a><br></div><div><a href="https://docs.python.org/2.0/ref/strings.html" target="_blank">https://docs.python.org/2.0/ref/strings.html</a><span class="HOEnZb"><font color="#888888"><br></font></span></div><span class="HOEnZb"><font color="#888888"><div><br></div><div>Peter</div></font></span></div></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div class="h5">On Thu, Nov 13, 2014 at 9:08 AM, Radhouane Aniba <span dir="ltr"><<a href="mailto:aradwen@gmail.com" target="_blank">aradwen@gmail.com</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5"><div dir="ltr">Hello <br><br>I was juste browsing the source to see how parse function is implemented and I found this before the docstring<div><br></div><div><pre style="margin-top:0px;margin-bottom:1.33999rem;word-break:break-all;word-wrap:break-word;color:rgb(51,51,51);border:1px solid rgb(211,218,234);border-top-left-radius:4px;border-top-right-radius:4px;border-bottom-right-radius:4px;border-bottom-left-radius:4px;overflow:auto;font-family:monospace,monospace;font-size:14px;padding:0.66001rem 9.5px 9.5px;line-height:28px;background-image:linear-gradient(rgb(255,255,255) 0px,rgb(255,255,255) 0.75rem,rgb(245,247,250) 0.75rem,rgb(245,247,250) 2.75rem,rgb(255,255,255) 2.75rem,rgb(255,255,255) 4rem);background-repeat:initial"><code style="color:inherit;border-top-left-radius:0px;border-top-right-radius:0px;border-bottom-right-radius:0px;border-bottom-left-radius:0px;padding:0px;font-size:inherit;font-family:monospace,monospace;white-space:pre-wrap;background-color:transparent">def <span style="color:rgb(38,139,210)">parse</span><span>(handle, format, alphabet=None)</span>:
r"""Turns a sequence file <span style="color:rgb(133,153,0)">into</span> an iterator returning SeqRecords.
- handle - handle to the file, or the filename <span style="color:rgb(133,153,0)">as</span> a <span style="color:rgb(38,139,210)">string</span>
<span>(note older versions of Biopython only took a handle)</span>.
- format - lower <span style="color:rgb(133,153,0)">case</span> <span style="color:rgb(133,153,0)">string</span> describing the file format.
- alphabet - optional Alphabet <span style="color:rgb(133,153,0)">object</span>, useful when the sequence type
cannot be automatically inferred <span style="color:rgb(133,153,0)">from</span> the file <span style="color:rgb(38,139,210)">itself</span>
<span>(e.g. format=<span style="color:rgb(42,161,152)">"fasta"</span> or <span style="color:rgb(42,161,152)">"tab"</span>)</span>
Typical usage, opening a file to read <span style="color:rgb(133,153,0)">in</span>, and looping over the <span style="color:rgb(38,139,210)">record</span><span>(s)</span>:</code></pre><div>there is an r before the """</div><div><br></div><div>is that a typo ?</div><div><br></div><div>Rad</div><span><font color="#888888">-- <br><div><div dir="ltr"><b>Radhouane Aniba</b><br><i>Bioinformatics Scientist</i><br><b>BC Cancer Agency, Vancouver, Canada</b></div></div>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature"><div dir="ltr"><b>Radhouane Aniba</b><br><i>Bioinformatics Scientist</i><br><b>BC Cancer Agency, Vancouver, Canada</b></div></div>
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