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Rescued by code: Unix & programming skills for life-scientists

1–30 of 117

We think that more life-scientists should learn how to code, and so we created a course to help them do just that. This started out as a Graduate student course at UC Davis, but the positive feedback we received convinced us to make all of our course material freely available to anyone who wants to learn Unix & Perl. We then turned the material from this 'Primer' into a much more extensive book (4.5 star rating on Amazon). We have also made available a free command-line Linux bootcamp, and currently we are writing a new book titled 'Unix & Python to the Rescue!'.

For more information about all of these resources, please see our rescuedbycode.com website.

The discussion group is very much aimed at people with no prior experience in either programming or Unix. Therefore, this group should primarily be used by people who have questions about:

1. the course material in our free Unix and Perl for Biologists Primer

2. any exercises or problems in our Unix & Perl to the Rescue! book

3. information in our free command-line Linux bootcamp

3. any other relevant issue involving Unix or coding in a biological context

0 selected

M. Olalla Lorenzo-Carballa, … Pedro jose Martinez5

6/21/16

sed find an replace help

better: cat test-sed | sed -e 's/\_/-/' | cut -d_ -f 1-2 Cheers, PJ On Mon, Jun 20, 2016 at 3

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sed find an replace help

better: cat test-sed | sed -e 's/\_/-/' | cut -d_ -f 1-2 Cheers, PJ On Mon, Jun 20, 2016 at 3

6/21/16

sanks, … Anthony Doran7

4/28/15

greping a fastq file

Probably a bit late, but you could also do this with a perl one-liner, though unless you're very

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greping a fastq file

Probably a bit late, but you could also do this with a perl one-liner, though unless you're very

4/28/15

gtuohy...@gtempaccount.com, Keith Bradnam5

4/21/15

setting up profile in unix

Perfect! All working now. Many thanks for your prompt replies! Best wishes, Gearoid On Tuesday, 21

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setting up profile in unix

Perfect! All working now. Many thanks for your prompt replies! Best wishes, Gearoid On Tuesday, 21

4/21/15

Yeorgia Argirou, Keith Bradnam4

3/25/15

How do I find the number of animals within a certain distance of a certain point

Other comments on your code: There are no comments!!! This doesn't make it easy for you (or for

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How do I find the number of animals within a certain distance of a certain point

Other comments on your code: There are no comments!!! This doesn't make it easy for you (or for

3/25/15

Leandro de Mattos, … Alex Van Dam4

3/11/15

Help - how to execute multiple lot of file to blast

ls -1 *my_file_handle | awk '{ print "blastp -options -db etc. -query "$1" -o

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Help - how to execute multiple lot of file to blast

ls -1 *my_file_handle | awk '{ print "blastp -options -db etc. -query "$1" -o

3/11/15

phs...@asu.edu, Keith Bradnam2

12/15/14

study material 28 - 30

On Monday, December 15, 2014 11:40:24 AM UTC-8, phs...@asu.edu wrote: I have downloaded the material

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study material 28 - 30

On Monday, December 15, 2014 11:40:24 AM UTC-8, phs...@asu.edu wrote: I have downloaded the material

12/15/14

jabir m, raghvendra singh4

10/15/14

Aggregate Boolean values using AND operation in Shell

I hope you haven't understood the question. Uniq will work only for the condition two rows are

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Aggregate Boolean values using AND operation in Shell

I hope you haven't understood the question. Uniq will work only for the condition two rows are

10/15/14

Anand Rao, … Claudius Kerth7

9/26/14

creating an array of n-dimensional array references, and sorting by each of the n column

Hi Anand, here $$a[0] is a equivalent to ${$a}[0] and is equivalent to $a->[0] . It's

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creating an array of n-dimensional array references, and sorting by each of the n column

Hi Anand, here $$a[0] is a equivalent to ${$a}[0] and is equivalent to $a->[0] . It's

9/26/14

9/22/14

Re: to convert a csv file to fixed width File

In Perl you could read the file one line at a time, split each line on commas (using the split

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Re: to convert a csv file to fixed width File

In Perl you could read the file one line at a time, split each line on commas (using the split

9/22/14

R A J Rajkishore, … Keith Bradnam4

9/22/14

Foo bar in reverse for 10 times _ Perl program

On Wednesday, September 10, 2014 12:37:47 AM UTC-7, RAJ Rajkishore wrote: Cant we do this using split

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Foo bar in reverse for 10 times _ Perl program

On Wednesday, September 10, 2014 12:37:47 AM UTC-7, RAJ Rajkishore wrote: Cant we do this using split

9/22/14

jabir m, Marek Borowiec4

9/4/14

search and replace string occurance in a specific column

Awk certainly is more elegant, but depending on how stable the patterns in your file are, you could

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search and replace string occurance in a specific column

Awk certainly is more elegant, but depending on how stable the patterns in your file are, you could

9/4/14

R A J Rajkishore, … Anthony Doran4

9/1/14

Finding Palindromes(perfect palindromes) in more than one protein sequences using perl

More information would be useful... we shouldnt have to google to find out what exactly you are

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Finding Palindromes(perfect palindromes) in more than one protein sequences using perl

More information would be useful... we shouldnt have to google to find out what exactly you are

9/1/14

jabir m, … Claudius Kerth4

8/28/14

converting fixed width file to a delimited file

Hi Jabir, try this on a Mac: sed -E 's/ +/|/g' filename or this on Linux: sed -r 's/ +/|/

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converting fixed width file to a delimited file

Hi Jabir, try this on a Mac: sed -E 's/ +/|/g' filename or this on Linux: sed -r 's/ +/|/

8/28/14

Maimu PV, … Keith Bradnam6

8/20/14

group by data in a unix file based on multiple columns

See http://perldoc.perl.org/functions/split.html On Wednesday, August 20, 2014 6:08:34 PM UTC-7,

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group by data in a unix file based on multiple columns

See http://perldoc.perl.org/functions/split.html On Wednesday, August 20, 2014 6:08:34 PM UTC-7,

8/20/14

Keith Bradnam, … daisy yu6

8/7/14

Some general comments: 1. Assign everything out of @ARGV to named variables as soon as possible. $

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Some general comments: 1. Assign everything out of @ARGV to named variables as soon as possible. $

8/7/14

R A J Rajkishore, Keith Bradnam3

7/15/14

Append the alignment lines of Multiple Sequence Alignment using Perl

Sorry Sir , for late response. For example, I got the multiple sequence alignment files, let may be

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Append the alignment lines of Multiple Sequence Alignment using Perl

Sorry Sir , for late response. For example, I got the multiple sequence alignment files, let may be

7/15/14

Disa Bäckström, Keith Bradnam4

7/9/14

Help with loops for project 2

You only should declare 'my $median' once. This should happen before the if else statement.

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Help with loops for project 2

You only should declare 'my $median' once. This should happen before the if else statement.

7/9/14

Joyce Wang, … Keith Bradnam6

6/26/14

Help with U28 and 29 please!

Hi Jessie, The issue might be that you seem to be using zsh as your default shell rather than bash.

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Help with U28 and 29 please!

Hi Jessie, The issue might be that you seem to be using zsh as your default shell rather than bash.

6/26/14

Srinivas Janaswamy, … Mike Covington5

6/10/14

What is wrong with the following code?

Do you mean var=`wc -l $fname` instead of var=( cat $fname | we -l ) ? On Monday, June 9, 2014 1:21:

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What is wrong with the following code?

Do you mean var=`wc -l $fname` instead of var=( cat $fname | we -l ) ? On Monday, June 9, 2014 1:21:

6/10/14

Kirthi Pulakanti, Keith Bradnam2

5/13/14

parsing the data

Some more information might help. How many rows in your input file? Does every row contain a unique

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parsing the data

Some more information might help. How many rows in your input file? Does every row contain a unique

5/13/14

4/16/14

decode -- join "\n" => map {join " " => map {shift @$_} @_} @{$_ [0]}

I am new to Perl. Appreciate if someone can explain what the following function is doing. sub zup {

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decode -- join "\n" => map {join " " => map {shift @$_} @_} @{$_ [0]}

I am new to Perl. Appreciate if someone can explain what the following function is doing. sub zup {

4/16/14

Marie-Line Faucillion, Keith Bradnam4

2/19/14

Project 4 The name game. My script does not report all sequences containing the name.

Thank you so much for your quick reply. I fixed this kind of problems in my codes by splitting the

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Project 4 The name game. My script does not report all sequences containing the name.

Thank you so much for your quick reply. I fixed this kind of problems in my codes by splitting the

2/19/14

LFM, … Keith Bradnam8

1/30/14

Why didn't storing the value of $x in a temporary variable ($x1) work? If you were in a kitchen

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Why didn't storing the value of $x in a temporary variable ($x1) work? If you were in a kitchen

1/30/14

10/22/13

How to set up your .profile file if using your computer's home directory and not the USB drive

Our Unix & Perl Primer is written in a way that explicitly assumes that you are using a USB drive

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How to set up your .profile file if using your computer's home directory and not the USB drive

Our Unix & Perl Primer is written in a way that explicitly assumes that you are using a USB drive

10/22/13

Keith Bradnam, rana islam3

10/2/13

Re: Project 5 page 147

We don't have any solutions on file for the problems in the Primer. This is because there is

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Re: Project 5 page 147

We don't have any solutions on file for the problems in the Primer. This is because there is

10/2/13

jenna.e....@gmail.com, Keith Bradnam2

10/1/13

Double check the Primer. You are not running this command in the same way that we describe. On Sunday

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Double check the Primer. You are not running this command in the same way that we describe. On Sunday

10/1/13

vivien, … RENATO AUGUSTO CORREA DOS SANTOS9

9/15/13

perl regular expression

Sure, thanks. I would say "profile", not alignment. Best, Renato. On Sun, Sep 15, 2013 at

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perl regular expression

Sure, thanks. I would say "profile", not alignment. Best, Renato. On Sun, Sep 15, 2013 at

9/15/13

9/12/13

Can't locate object method error

Dear all, I am trying to run a perl program using a Math module named Math::Vector which has a

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Can't locate object method error

Dear all, I am trying to run a perl program using a Math module named Math::Vector which has a

9/12/13

Timothy Butterfield, Ian Korf4

9/5/13

Perl Project 2 Questions

print "@array" will put spaces between the array elements. You can use other things with

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Perl Project 2 Questions

print "@array" will put spaces between the array elements. You can use other things with

9/5/13

Timothy Butterfield

9/2/13

Perl Project 2 - solved but with alternate tools

Hi, I was able to solve Perl Project 2: Descriptive Statistics successfully. However, I'd like to

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Perl Project 2 - solved but with alternate tools

Hi, I was able to solve Perl Project 2: Descriptive Statistics successfully. However, I'd like to

9/2/13

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