Some gene alignments in aligned_gene_sequences/ have fragmented entries

[mudymudy]

Hello there,

thank you for developing this software. I was looking at the results in the folder aligned_gene_sequences/ , and I realised that some of those MSA contain fragmented genes (I changed the names from aln.fas to fasta):

$ cat nfrA2.fasta

>GCF_028335125.1_ASM2833512v1
atgaaacagattcctcaagattttcgtttgatagaagatttcttccgcacgcgcagatccgtacgcaagtttatcgatcgtcctgtggaggaagagaagttgatggccatcctcgaagccggacgcatagctccttcggcacataattaccagccgtggcatttcctcgtggtcagagaagaagagggccgcaaacgcttggctccctgttcccaacaaccttggttcccgggtgcccccatctatatcatcacgcttggcgatcatcaaagagcatggaagcgaggagcaggcgattccgtagacatcgatacctctatcgccatgacttatatgatgctggaagcacatagtctgggacttggatgtacgtgggtctgtgctttcgatcaagctctttgttcggagatcttcgacatcccttcgcacatgacacctgtttccatattggctctcggctatggcgatccgaccgtacctccgcgtgaggctttcaatcgcaaatccatcgaagaggtagtcagcttcgagaaattatga
>GCF_030144345.1_ASM3014434v1
atgaaacagattcctcaagattttcgtttgatagaagatttcttccgcacgcgcagatccgtacgcaagtttatcgatcgtcctgtggaggaagagaagttgatggccatcctcgaagccggacgcatagctccttcggcacataattaccagccgtggcatttcctcgtggtcagagaagaagagggccgcaaacgcttggctccctgttcccaacaaccttggttcccgggtgcccccatctatatcatcacgcttggcgatcatcaaagagcatggaagcgaggagcaggcgattccgtagacatcgatacctctatcgccatgacttatatgatgctggaagcacatagtctgggacttggatgtacgtgggtctgtgctttcgatcaagctctttgttcggagatcttcgacatcccttcgcacatgacacctgtttccatattggctctcggctatggcgatccgaccgtacctccgcgtgaggctttcaatcgcaaatccatcgaagaggtagtcagcttcgagaaattatga
>GCF_030252365.1_ASM3025236v1
atgaaacagattcctcaagattttcgtttgatagaagatttcttccgcacgcgcagatccgtacgcaagtttatcgatcgtcctgtggaggaagagaagttgatggccatcctcgaagccggacgcatagctccttcggcacataattaccagccgtggcatttcctcgtggtcagagaagaagagggccgcaaacgcttggctccctgttcccaacaaccttggttcccgggtgcccccatctatatcatcacgcttggcgatcatcaaagagcatggaagcgaggagcaggcgattccgtagacatcgatacctctatcgccatgacttatatgatgctggaagcacatagtctgggacttggatgtacgtgggtctgtgctttcgatcaagctctttgttcggagatcttcgacatcccttcgcacatgacacctgtttccatattggctctcggctatggcgatccgaccgtacctccgcgtgaggctttcaatcgcaaatccatcgaagaggtagtcagcttcgagaaattatga
>GCF_030440475.1_ASM3044047v1
atgaaacagattcctcaagattttcgtttgatagaagatttcttccgcacgcgcagatccgtacgcaagtttatcgatcgtcctgtggaggaagagaagttgatggccatcctcgaagccggacgcatagctccttcggcacataattaccagccgtga---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>GCF_030440475.1_ASM3044047v1
------------------------------------------------------------------------------------------------------------------------------------------------------------------------gtggtcagagaagaagagggccgcaaacgcttggctccctgttcccaacaaccttggttcccgggtgcccccatctatatcatcacgcttggcgatcatcaaagagcatggaagcgaggagcgggcgattcggtagacatcgatacctctatcgccatgacttatatgatgctggaagcacatagtctgggacttggatgtacgtgggtctgtgctttcgatcaagctctttgttcggagatcttcgacatcccttcgcacatgacacctgtttccatattggctctcggctatggcgatccgaccgtacctccgcgtgaggctttcaatcgcaaatccatcgaagaggtagtcagcttcgagaaattatga
>GCF_030440495.1_ASM3044049v1
atgaaacagattcctcaagattttcgtttgatagaagatttcttccgcacgcgcagatccgtacgcaagtttatcgatcgtcctgtggaggaagagaagttgatggccatcctcgaagccggacgcatagctccttcggcacataattaccagccgtga---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>GCF_030440495.1_ASM3044049v1
------------------------------------------------------------------------------------------------------------------------------------------------------------------------gtggtcagagaagaagagggccgcaaacgcttggctccctgttcccaacaaccttggttcccgggtgcccccatctatatcatcacgcttggcgatcatcaaagagcatggaagcgaggagcgggcgattcggtagacatcgatacctctatcgccatgacttatatgatgctggaagcacatagtctgggacttggatgtacgtgggtctgtgctttcgatcaagctctttgttcggagatcttcgacatcccttcgcacatgacacctgtttccatattggctctcggctatggcgatccgaccgtacctccgcgtgaggctttcaatcgcaaatccatcgaagaggtagtcagcttcgagaaattatga

In this example you can see that both GCF_030440475.1_ASM3044047v1 and GCF_030440495.1_ASM3044049v1 have two sequences for the same gene, probably because there is a gap between those two sequences. I'm wondering, does Panaroo offer some script to merge these two fragmented sequences into just one? I want to build specific MSAs from set of genes but before trying to make a homemade script to handle this I was thinking that maybe there is already a script that can do this?

Thanks!

[gtonkinhill]

Hi, I am afraid Panaroo doesn't currently have a script to do this. We are hoping to address this in the future.