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Old 01-25-2017, 06:00 PM   #1
sadiexiaoyu
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Location: Switzerland

Join Date: Apr 2013
Posts: 55
Default would like to convert aln to axt for Ka Ks calculator

Hello, everyone,

I would like to ask how to convert fasta file or .aln to .axt for ka ks calculation.

I have the .aln file now and have to convert it to .axt, and I have a huge amount of data so that I cannot do it one by one. Is there any python or perl script can do this? Otherwise how could you deal with large sets of data for ka ks calculation?

To make it much more clearer,
the original .aln file is like this:
AM_Ensembl001_A1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
DT_Ensembl001_A1 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
UW_Ensembl001_A1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC


AM_Ensembl001_A1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
DT_Ensembl001_A1 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
UW_Ensembl001_A1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC


AM_Ensembl002_A2 DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD
DT_Ensembl002_A2 EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE
UW_Ensembl002_A2 FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF


AM_Ensembl002_A2 DDDDDDDD
DT_Ensembl002_A2 EE
UW_Ensembl002_A2 FFFFF


And I would like to convert it like this:

Ensembl001
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC

Ensembl002

DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD

EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE

FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF


Looking forward to your reply!

All the best,

Sadiexiaoyu

Last edited by sadiexiaoyu; 01-25-2017 at 06:07 PM. Reason: make the question much more clearer
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