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AliTVTeam / AliTV

Visualize whole genome alignments as linear maps
https://alitvteam.github.io/AliTV/d3/AliTV.html
MIT License
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MAF input file and buggy BioPerl detected #163

Open AllisonStander opened 3 years ago

AllisonStander commented 3 years ago

Good day,

I am getting output after running alitv.pl on two fasta files, and I can view the .json file online, I did, however, get the following warning:

You are using version v1.0.6.
INFO - Wrote temporary YAML file 'GetOrganelle_Repeat_Pattern_1.yml'
INFO - Sequence names contain non-word-characters and will be replaced by unique sequence names. Failing sequence names are: '514776+,514184+,514064-,514704+,514064-,514782+,514788-,514782-,514064+,514704-,514064+,514184-(circular)', '514776+,514184+,514064-,514704+,514064-,514782+,514788+,514782-,514064+,514704-,514064+,514184-(circular)'

INFO - Created temporary folder at '/tmp/g1TJpBCFG1'
INFO - Starting alignment generation... (3 alignments required)
INFO - Finished 1. alignment (2 to go; 33.33 % done)
INFO - Finished 2. alignment (1 to go; 66.67 % done)
INFO - Finished 3. alignment (0 to go; 100.00 % done)
INFO - Finished alignment generation
INFO - MAF input file and buggy BioPerl detected... Therefore, workaround for revcom issue activated
INFO - MAF input file and buggy BioPerl detected... Therefore, workaround for revcom issue activated
INFO - MAF input file and buggy BioPerl detected... Therefore, workaround for revcom issue activated
INFO - Deleting temporary folder
INFO - Ticks will be drawn every 1000 basepair

Is this having an effect on the output? I noticed the inverted repeats are not showing.

image

Kind regards, Allison

greatfireball commented 3 years ago

Morning Allison,

this is no warning, also indicated by the "INFO" message level. Nevertheless, we discovered an issue with some bioperl versions producing correct revcomp results. Therefore, we detect the buggy bioperl and use our workaround the bug. To give you the information, that your bioperl has that issue, we print the message. Maybe your bioperl is a little outdated?

And last but not least, it has no influence on your result.

Best, Frank

AllisonStander commented 3 years ago

Hi Frank,

Thank you very much! Any idea why the inverted repeats are not shown?

Regards, Allison

iimog commented 3 years ago

Hi Allison,

short note on the inverted repeat: You can infer the inverted repeat regions from the alignment. But there is no feature drawn for the inverted repeat (pink arrow). This is not an error. The inverted repeat is not automatically annotated by AliTV. If you want it to be drawn you have to provide the IR location as feature_files to AliTV. See: https://github.com/AliTVTeam/AliTV-perl-interface/blob/master/doc/alitv.md#section-genomes

Best regards, Markus

AllisonStander commented 3 years ago

Thank you for the reply Markus!