Enhancement - specify trim sequences in file?

[marcelm]

From kga1...@gmail.com on November 12, 2011 20:20:02

Would it be possible to specify sequences to be trimmed in a file, rather than directly on the command line? Right now I do this:

$cutadapt -m 20 -a AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTG -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCTTG -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGCCGTCTTCTGCTTG -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCCGTCTTCTGCTTG -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCCGTCTTCTGCTTG -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCCGTCTTCTGCTTG -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGCCGTCTTCTGCTTG -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATGCCGTCTTCTGCTTG -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTATCTCGTATGCCGTCTTCTGCTTG -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCTACATCTCGTATGCCGTCTTCTGCTTG -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAATCTCGTATGCCGTCTTCTGCTTG -a CTTCACCGTGCCAGACTAGAGTCAAGCTCAACAGGGTCTTCTTTCCCCGCTG -a GGATGAACGAGATTCCCACTGTCCCTACCTACTATCCAGCGAAACCACAGCC -a CTCCCTTTCGATCGGCCGAGGGCAACGGAGGCCATCGCCCGTCCCTTCGGAA -a CGAGATTCCCACTGTCCCTACCTACTATCCAGCGAAACCACAGCCAAGGGAA -a CCACTCTCGACTGCCGGCGACGGCCGGGTATGGGCCCGACGCTCCAGCGCCA -a TGGAAGTCGGAATCCGCTAAGGAGTGTGTAACAACTCACCTGCCGAATCAAC -a CCTATACCCAGGTCGGACGACCGATTTGCACGTCAGGACCGCTACGGACCTC -a CACGAGCGCACGTGTTAGGACCCGAAAGATGGTGAACTATGCCTGGGCAGGG -a GTCGGAATCCGCTAAGGAGTGTGTAACAACTCACCTGCCGAATCAACTAGCC -a CTCCCGTCCACTCTCGACTGCCGGCGACGGCCGGGTATGGGCCCGACGCTCC -a CGCAGGTTCAGACATTTGGTGTATGTGCTTGGCTGAGGAGCCAATGGGGCGA -a GAACGAGATTCCCACTGTCCCTACCTACTATCCAGCGAAACCACAGCCAAGG -a CAGAAGGGCAAAAGCTCGCTTGATCTTGATTTTCAGTACGAATACAGACCGT -a TTTCGATCGGCCGAGGGCAACGGAGGCCATCGCCCGTCCCTTCGGAACGGCG input.fastq > output.fastq

I would be much easier if I could do:
$cutadapt -m 20 -a <trim_sequence_file> input.fastq > output.fastq

Original issue: http://code.google.com/p/cutadapt/issues/detail?id=33

[marcelm]

From marcel.m...@tu-dortmund.de on March 09, 2012 02:12:26

Sorry for the late reply. I have had little time to work on cutadapt. What you desire actually works by using a feature of the Bashs shell. Write a “configuration file” adapters.conf that contains the necessary command-line parameters, for example:

-a AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
-a GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG
and so on. The file can contain line breaks. They will be replaced by spaces.

Then run cutadapt as follows:
cutadapt -m 20 $(<adapters.conf) input.fastq > output.fastq

If you don’t use Bash, then writing $(cat adapters.conf) may work.

I know this is not quite what one wants as a proper configuration file would support comments and proper syntax checking. I hope it will do for now. Sorry again this has taken so long. I will leave this report open for now.

Status: Accepted
Labels: -Type-Defect -Priority-Medium Type-Enhancement Priority-Low

[marcelm]

From marcel.m...@tu-dortmund.de on August 05, 2014 04:36:24

This has now been implemented and is part of cutadapt 1.5.

Status: Fixed