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    <p>Create a <a href="http://docs.python.org/2/tutorial/classes.html#generators" rel="nofollow noreferrer">generator function</a> that yields smaller and smaller <a href="https://stackoverflow.com/questions/509211/pythons-slice-notation">slices</a> of the given string.</p> <pre><code>def shrink(s): for i in range(len(s)): yield s[i:] </code></pre> <p>Create a function that splits a string into a list of five character segments.</p> <pre><code>def split_into_five_character_segments(s): ret = [] while len(s) &gt; 5: ret.append(s[:5]) s = s[5:] ret.append(s) return ret </code></pre> <p>Combine the two in a <a href="http://docs.python.org/2/tutorial/datastructures.html#list-comprehensions" rel="nofollow noreferrer">list comprehension</a> to generate your fragment library.</p> <pre><code>sequence = "MSSPPPARSGFYRQEVTKTAWEVRAVYRDLQ" fragments = [split_into_five_character_segments(s) for s in shrink(sequence)] </code></pre> <p><a href="http://docs.python.org/2/library/functions.html#enumerate" rel="nofollow noreferrer">Enumerate</a> through each fragment. Use <a href="http://docs.python.org/2/library/stdtypes.html?highlight=join#str.join" rel="nofollow noreferrer"><code>join</code></a> to combine the pieces of the fragment into a single space-separated string.</p> <pre><code>for idx, fragment in enumerate(fragments): fragment_number = idx + 1 indent = " " * idx print indent + str(fragment_number) print indent + " ".join(fragment) </code></pre> <p>Result:</p> <pre><code>1 MSSPP PARSG FYRQE VTKTA WEVRA VYRDL Q 2 SSPPP ARSGF YRQEV TKTAW EVRAV YRDLQ 3 SPPPA RSGFY RQEVT KTAWE VRAVY RDLQ 4 PPPAR SGFYR QEVTK TAWEV RAVYR DLQ 5 PPARS GFYRQ EVTKT AWEVR AVYRD LQ 6 PARSG FYRQE VTKTA WEVRA VYRDL Q 7 ARSGF YRQEV TKTAW EVRAV YRDLQ 8 RSGFY RQEVT KTAWE VRAVY RDLQ 9 SGFYR QEVTK TAWEV RAVYR DLQ 10 GFYRQ EVTKT AWEVR AVYRD LQ 11 FYRQE VTKTA WEVRA VYRDL Q 12 YRQEV TKTAW EVRAV YRDLQ 13 RQEVT KTAWE VRAVY RDLQ 14 QEVTK TAWEV RAVYR DLQ 15 EVTKT AWEVR AVYRD LQ 16 VTKTA WEVRA VYRDL Q 17 TKTAW EVRAV YRDLQ 18 KTAWE VRAVY RDLQ 19 TAWEV RAVYR DLQ 20 AWEVR AVYRD LQ 21 WEVRA VYRDL Q 22 EVRAV YRDLQ 23 VRAVY RDLQ 24 RAVYR DLQ 25 AVYRD LQ 26 VYRDL Q 27 YRDLQ 28 RDLQ 29 DLQ 30 LQ 31 Q </code></pre>
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    1. POhow can I generate a fragment library from a protein sequence file?
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    1. COThanks for your quick reply Kevin its really working great for me.
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