# Importing lowercase alignment file
**URL:** https://forum.qiime2.org/t/importing-lowercase-alignment-file/5294
**Category:** User Support
**Tags:** align, import
**Created:** [July 27, 2018, 6:40pm UTC](https://forum.qiime2.org/t/importing-lowercase-alignment-file/5294 "2018-07-27T18:40:49Z")
**Posts on this page:** 5
**Page:** 1
### Author:  [@Maxy](https://forum.qiime2.org/u/Maxy)
#### Post date: [July 27, 2018, 6:40pm UTC](https://forum.qiime2.org/t/importing-lowercase-alignment-file/5294/1 "2018-07-27T18:40:49Z")
I had to use an online mafft program program because of memory issues. I am now trying to import the alignment file, but for some reason all the nucleotides were converted to lowercase. How do I import lowercase nucleotides? I could write a janky script to do it, but I am trying as much as possible to do this using qiime tools. My command was as follows:
qiime tools import
--input-path EXP\_type1\_rep-seqs-or-99/\_out.18072802055553becwu7zMjlmSU9hBaKFHdlsflarge.pir
--output-path type1\_rep-seqs-or-99\_aligned-sequences.qza
--type 'FeatureData[AlignedSequence]'
---
### Author:  [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [July 27, 2018, 6:44pm UTC](https://forum.qiime2.org/t/importing-lowercase-alignment-file/5294/2 "2018-07-27T18:44:06Z")
> [@Maxy](#):
>
> How do I import lowercase nucleotides?
lowercase nucleotides can cause issues with some tools downstream, so I'd recommend just converting to uppercase. [I don't think a bash one-liner would be too janky](https://forum.qiime2.org/t/troubles-importing-fasta-file/2546/10), provided it does not cause issues with your seq IDs.
Good luck!
---
### Author:  [@Maxy](https://forum.qiime2.org/u/Maxy)
#### Post date: [July 27, 2018, 6:55pm UTC](https://forum.qiime2.org/t/importing-lowercase-alignment-file/5294/3 "2018-07-27T18:55:32Z")
Unfortunately it does interfere with naming, but if there isn't an easy solution I'll write some kind of masticated perl script.
---
### Author:  [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)
#### Post date: [July 27, 2018, 7:04pm UTC](https://forum.qiime2.org/t/importing-lowercase-alignment-file/5294/4 "2018-07-27T19:04:48Z")
Try this command in bash:
```bash
awk '/^>/ {print($0)}; /^[^>]/ {print(toupper($0))}' file.fasta > file_upper.fasta
```
:qiime2: : 🙌
Colin
---
### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [August 28, 2018, 1:04am UTC](https://forum.qiime2.org/t/importing-lowercase-alignment-file/5294/5 "2018-08-28T01:04:51Z")
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