<div dir="ltr"><div class="markdown-here-wrapper" style=""><p style="margin:0px 0px 1.2em!important">If I understand, your files are lists of names, one name per line. Python has a builtin <code style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;margin:0px 0.15em;padding:0px 0.3em;white-space:pre-wrap;border:1px solid rgb(234,234,234);border-radius:3px;display:inline;background-color:rgb(248,248,248)">set</code> type, which lets you apply set operations (intersection, union, difference) on collections. Here’s an example of how to use them to solve your problem:</p>
<pre style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;font-size:1em;line-height:1.2em;margin:1.2em 0px"><code class="hljs language-python" style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;margin:0px 0.15em;padding:0px 0.3em;white-space:pre-wrap;border:1px solid rgb(234,234,234);border-radius:3px;display:inline;background-color:rgb(248,248,248);white-space:pre;overflow:auto;border-radius:3px;border:1px solid rgb(204,204,204);padding:0.5em 0.7em;display:block!important;display:block;overflow-x:auto;color:rgb(104,97,94);padding:0.5em;background:rgb(241,239,238)">database_proteins_file = <span class="hljs-string" style="color:rgb(90,183,56)">"sorted.a"</span>
organism_proteins_file = <span class="hljs-string" style="color:rgb(90,183,56)">"sorted.b"</span>
<span class="hljs-comment" style="color:rgb(118,110,107)"># set() iterates over the input, storing unique entries</span>
database_proteins = set(open(database_proteins_file))
organism_proteins = set(open(organism_proteins_file))
<span class="hljs-keyword" style="color:rgb(102,102,234)">with</span> open(<span class="hljs-string" style="color:rgb(90,183,56)">"common_proteins"</span>, <span class="hljs-string" style="color:rgb(90,183,56)">"w"</span>) <span class="hljs-keyword" style="color:rgb(102,102,234)">as</span> common_file: <span class="hljs-comment" style="color:rgb(118,110,107)"># use with statement to ensure the file closes after the block ends</span>
<span class="hljs-comment" style="color:rgb(118,110,107)"># the & operator of set objects will compute intersections. Alternatively</span>
<span class="hljs-comment" style="color:rgb(118,110,107)"># you could write database_proteins.intersect(organism_proteins)</span>
<span class="hljs-keyword" style="color:rgb(102,102,234)">for</span> prot <span class="hljs-keyword" style="color:rgb(102,102,234)">in</span> sorted(database_proteins & organism_proteins):
common_file.write(prot)
</code></pre>
<p style="margin:0px 0px 1.2em!important">However, this just produces a common protein list. To build that matrix, you can adjust the above code:</p>
<pre style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;font-size:1em;line-height:1.2em;margin:1.2em 0px"><code class="hljs language-python" style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;margin:0px 0.15em;padding:0px 0.3em;white-space:pre-wrap;border:1px solid rgb(234,234,234);border-radius:3px;display:inline;background-color:rgb(248,248,248);white-space:pre;overflow:auto;border-radius:3px;border:1px solid rgb(204,204,204);padding:0.5em 0.7em;display:block!important;display:block;overflow-x:auto;color:rgb(104,97,94);padding:0.5em;background:rgb(241,239,238)">database_proteins_file = <span class="hljs-string" style="color:rgb(90,183,56)">"sorted.a"</span>
organism_proteins_file = <span class="hljs-string" style="color:rgb(90,183,56)">"sorted.b"</span>
<span class="hljs-comment" style="color:rgb(118,110,107)"># set() iterates over the input, storing unique entries</span>
database_proteins = set(open(database_proteins_file))
organism_proteins = set(open(organism_proteins_file))
<span class="hljs-keyword" style="color:rgb(102,102,234)">with</span> open(<span class="hljs-string" style="color:rgb(90,183,56)">"output_matrix"</span>, <span class="hljs-string" style="color:rgb(90,183,56)">"w"</span>) <span class="hljs-keyword" style="color:rgb(102,102,234)">as</span> matrix_file:
<span class="hljs-keyword" style="color:rgb(102,102,234)">for</span> prot <span class="hljs-keyword" style="color:rgb(102,102,234)">in</span> sorted(database_proteins):
line = prot.replace(<span class="hljs-string" style="color:rgb(90,183,56)">"\n"</span>, <span class="hljs-string" style="color:rgb(90,183,56)">""</span>) <span class="hljs-comment" style="color:rgb(118,110,107)"># Trim newline from each entry in the set, since we need to append to the line</span>
present = prot <span class="hljs-keyword" style="color:rgb(102,102,234)">in</span> organism_proteins <span class="hljs-comment" style="color:rgb(118,110,107)"># like for dict objects the in operator checks for set membership of the first term in the second term</span>
line += <span class="hljs-string" style="color:rgb(90,183,56)">" 1\n"</span> <span class="hljs-keyword" style="color:rgb(102,102,234)">if</span> present <span class="hljs-keyword" style="color:rgb(102,102,234)">else</span> <span class="hljs-string" style="color:rgb(90,183,56)">" 0\n"</span> <span class="hljs-comment" style="color:rgb(118,110,107)"># add the textual flag using inline if expression. Also called the ternary operator</span>
matrix_file.write(line)
</code></pre>
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<p>I'm new with python so i'm reaaally struggling in making a script.</p>
<p>So, what I need is to make a comparison between two files. One file
contains all proteins of some data base, the other contain only some of
the proteins presents in the other file, because it belongs to a
organism. So I need to know wich proteins of this data base is present
in my organism. For that I want to build a output like a matrix, with 0
and 1 referring to every protein present in the data base that may or
may not be in my organism.</p>
<p>Does anybody have any idea of how could I do that?
I'm trying to use something like this
$ cat sorted.a
A
B
C
D
$ cat sorted.b
A
D
$ join sorted.a sorted.b | sed 's/^/1 /' && join -v 1 sorted.a sorted.b | sed 's/^/0 /'
1 A
1 D
0 B
0 C</p>
<p>But I'm not being able to use it because sometimes a protein is present but its not in the same line.
Here is a example:</p><p>
1-cysPrx_C<br>14-3-3<br>2-Hacid_dh<br>2-Hacid_dh_C<br>2-oxoacid_dh<br>2H-phosphodiest<br>2OG-FeII_Oxy<br>2OG-FeII_Oxy_3<br>2OG-FeII_Oxy_4<br>2OG-FeII_Oxy_5<br>2OG-Fe_Oxy_2<br>2TM<br>2_5_RNA_ligase2</p>
<p>comparing with</p>
<p>1-cysPrx_C<br>120_Rick_ant<br>14-03-2003<br>2-Hacid_dh<br>2-Hacid_dh_C<br>2-oxoacid_dh<br>2-ph_phosp<br>2CSK_N<br>2C_adapt<br>2Fe-2S_Ferredox<br>2H-phosphodiest<br>2HCT<br>2OG-FeII_Oxy<br></p>
<p>Does anyone have an idea of how could I do that?
Thanks so far.</p>
</div></div>
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