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lmrodriguezr / enveomics

Scripts and libraries for Environmental Genomics
http://enve-omics.ce.gatech.edu/enveomics
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Aln.convert.pl: XMFA -> FastA incomplete output #34

Closed yseif closed 4 years ago

yseif commented 6 years ago

I'm using Aln.convert.pl to convert an XMFA file to a fasta format. In the process, a few sequences are removed and I end up with a smaller number of sequences than I started with. Is that normal?

lmrodriguezr commented 6 years ago

Hello @yseif Aln.convert.pl is simply a wrapper for Bio::Perl, so I'm inclined to think it's probably an issue with the parent function rather than this script. However, if you post an example of an input file causing the issue I can take a look and try to resolve it.

AlisaGU commented 4 years ago

I wrote a short test file. However, it ran a long time and no output. Do you know the reason?

here is the code: perl Aln.convert.pl XMFA fasta test.xmfa test.fasta

AlisaGU commented 4 years ago

@lmrodriguezr I can't post the test .xmfa for unknown reasons. If you noticed this message, please tell me you email. I can deliver it to you

lmrodriguezr commented 4 years ago

Hello @AlisaGU The reason is that the script is waiting for input. Please check the correct syntax in the help message:

Aln.convert.pl in-format out-format < in_file > output_file

The < and the > are to redirect input from in_file and output to output_file, respectively. In your case, the command should be:

Aln.convert.pl XMFA fasta < test.xmfa > test.fasta
AlisaGU commented 4 years ago

I thought mistakenly “<>” just stands for there is a input file.

Thank you very much

Shanshan Gu

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On 07/07/2020 21:08, Luis M Rodriguez-R wrote:

Closed #34.

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