Full Discussion: Help with a bash loop script
Top Forums UNIX for Beginners Questions & Answers Help with a bash loop script Post 303037370 by dre on Tuesday 30th of July 2019 03:54:21 PM
Sorry didn't mean to offend anyone and thanks for the advice.&amp;lt;br /&amp;gt;&lt;br /&gt;<br />
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Quote:
Originally Posted by bakunin
Here we go again analysing FASTA-files. I wonder if we are going to be mentioned in the dozens of biological research papers we have helped to create over time.&amp;lt;br /&amp;gt;&lt;br /&gt;<br />
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Sorry, but this is not the way that works.&amp;lt;br /&amp;gt;&lt;br /&gt;<br />
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First: you come across like a teacher posing the homework for us. Actually we are all professionals here and have done our homework meticulously which is why we don't have to do more homework any more. In case it was homework given to &amp;lt;i&amp;gt;you&amp;lt;/i&amp;gt; by &amp;lt;i&amp;gt;your&amp;lt;/i&amp;gt; teacher: there is a special forum for this with special rules in place. Please re-create the thread there and provide the necessary information.&amp;lt;br /&amp;gt;&lt;br /&gt;<br />
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Second, in case this is not homework but actually your work: we do not insist on a lot of social conventions here (after all, we are sysadmins - being somewhat autistic is part of the requirement for this job), but still a well-placed &amp;amp;quot;please&amp;amp;quot; here and there, along with some of the common niceties called &amp;amp;quot;good manners&amp;amp;quot; oils the social machinery. If you ever wonder who writes the answers to your questions: it is not some clever machine and a fat server - it is actually living, breathing persons.&amp;lt;br /&amp;gt;&lt;br /&gt;<br />
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Third and foremost: we are here to help you help yourself. If you want a shell-script - WRITE IT! Attempts, however failing, will count. If you tried and it didn't work, post what you did and the error you got trying to run it. We will, regardless of how long it will take, explain to you what was wrong and how to do it better (actually quite like the way i explain to you right now why you need to change your problem statement) until you understand. We will also point out ways to better solve the problem, different tools, suggest sources to find valuable information and so on and so on. But we will NOT write your code for you. We are a help forum, not your unpaid programming staff.&amp;lt;br /&amp;gt;&lt;br /&gt;<br />
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I hope this helps.&amp;lt;br /&amp;gt;&lt;br /&gt;<br />
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bakunin
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&amp;lt;span style=&amp;quot;color:#738fbf;&amp;quot;&amp;gt;&amp;lt;span style=&amp;quot;font-size:1;&amp;quot;&amp;gt;--- Post updated at 08:32 PM ---&amp;lt;/span&amp;gt;&amp;lt;/span&amp;gt;&amp;lt;br /&amp;gt;&lt;br /&gt;<br />
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[ QUOTE=dre;303037350]Create a single bash script that does the following:&amp;lt;br /&amp;gt;&lt;br /&gt;<br />
a. Print out the number of occurrences for each motif that is found in the bacterial genome and output to a file called motif_count.txt&amp;lt;br /&amp;gt;&lt;br /&gt;<br />
b. Create a fasta file for each motif (so 3 in total) which contains all of the genes and their corresponding sequences that have that motif. Each file should be named after the motif (ie ATG.txt) and outputted to a new directory called motifs&amp;lt;br /&amp;gt;&lt;br /&gt;<br />
&amp;lt;br /&amp;gt;&lt;br /&gt;<br />
motif file is a txt file with these motifs : ATG, GGGGG, ATTTT&amp;lt;br /&amp;gt;&lt;br /&gt;<br />
the bacterial genome file is fasta file with the following lines&amp;lt;br /&amp;gt;&lt;br /&gt;<br />
Code:
 &amp;amp;gt;gene1&amp;lt;br /&amp;gt;&lt;br /&gt;<br />
GAAACTCGGTGTTGGCTTACCGGTCATTCCGAGCGTCATTTGGTTTTCGCGTCGTGGCGAAATGTGGTTCTACTACTCGTGGTGTATGCACTATTTATCCGGAATGTTCAGAGCGAGTAGACAATGGGTGCTCCACAATTGTGGCGGTCCCTAAGGGACTCACATATAGTGAGACACGCGTGAAATTCTGCTCACCACGTCCGAATCCGACAAATCATCTACTTCGACGGTA&amp;lt;br /&amp;gt;&lt;br /&gt;<br />
&amp;amp;gt;gene2&amp;lt;br /&amp;gt;&lt;br /&gt;<br />
CGGAGATAAAGGACCCATACTGTACGACATTGTATTGCTCACCATGGTCAATCTTTGCGAGTTGTTGCAGCTCGCAGCTTCGTTCTGTCAATATAGCTTAGATACTGAGAAGAAGTTGCAGAGAAAGTCGCA

Moderator's Comments:
Mod Comment edit by bakunin: please use CODE-tags to let data, code and terminal output stand out. Thank you.
[/QUOTE]<br />
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<span style="color:#738fbf;"><span style="font-size:1;">--- Post updated at 08:54 PM ---</span></span><br />
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This is my attempt<br />
#!/bin/bash<br />
<br />
# create a new directory motifs if it doesn't exist<br />
mkdir -p motifs<br />
cd motifs<br />
touch motif_count.txt<br />
&gt; motif_count.txt<br />
for motif in ATG GGGGG ATTTT<br />
do<br />
echo $motif &gt;&gt; motif_count.txt<br />
grep $motif -c r_bifella.fasta &gt;&gt; motif_count.txt<br />
touch $motif.fasta<br />
grep $motif -B 1 r_bifella.fasta &gt; $motif.fasta<br />
done<br />
<br />
]<br />
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<br />
Quote:
Originally Posted by dre
Create a single bash script that does the following:<br />
a. Print out the number of occurrences for each motif that is found in the bacterial genome and output to a file called motif_count.txt<br />
b. Create a fasta file for each motif (so 3 in total) which contains all of the genes and their corresponding sequences that have that motif. Each file should be named after the motif (ie ATG.txt) and outputted to a new directory called motifs<br />
<br />
motif file is a txt file with these motifs : ATG, GGGGG, ATTTT<br />
the bacterial genome file is fasta file with the following lines<br />
Code:
 &gt;gene1<br />
GAAACTCGGTGTTGGCTTACCGGTCATTCCGAGCGTCATTTGGTTTTCGCGTCGTGGCGAAATGTGGTTCTACTACTCGTGGTGTATGCACTATTTATCCGGAATGTTCAGAGCGAGTAGACAATGGGTGCTCCACAATTGTGGCGGTCCCTAAGGGACTCACATATAGTGAGACACGCGTGAAATTCTGCTCACCACGTCCGAATCCGACAAATCATCTACTTCGACGGTA<br />
&gt;gene2<br />
CGGAGATAAAGGACCCATACTGTACGACATTGTATTGCTCACCATGGTCAATCTTTGCGAGTTGTTGCAGCTCGCAGCTTCGTTCTGTCAATATAGCTTAGATACTGAGAAGAAGTTGCAGAGAAAGTCGCA

Moderator's Comments:
Mod Comment edit by bakunin: please use CODE-tags to let data, code and terminal output stand out. Thank you.
 
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