Sorting fasta file according to header

[zillur]

Hi there,
I have a fasta file like this:

[zillur@genomics filter]$ head new_12.fasta 
>000000M00365:7:000000000-A48JK:1:1110:10044:9619
TACGGAGGGTGCAAGCGTTATCCGGAATCACTGGGTTTAAAGGGTGCGTAGGCGGATATATAAGTCAGAGGTGAAAGCTCGCAGCTTAACTGCGGAATTGCCTTTGATACTGTTTATCTTGAATTATGTTGAGGTTAGCGGAATGAGTCAT
>000000M00365:7:000000000-A48JK:1:2105:14983:8496
TACGGAGGGGGTTAGCGTTGTTCGGAATTACTGGGCGTAAAGCGTACGTAGGCGGATTGGAAAGTATGGGGTGAAATCCCAGGGCTCAACCCTGGAACTGCCCTGTAAACTATCAGTCTAGAGTTCTGGAGAGGTGAGTGGAATTGCTAGG
>000000M00365:7:000000000-A48JK:1:2113:12381:28279
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGCGGTTTGATAAGTCAGATGTGAAATCCCCGGGCTTAACCTGGGAACTGCATTTGATACTGTCAGACTAGAGTATGTTAGAGGAATGCGGAATTCCGGGT
>000001M00365:7:000000000-A48JK:1:1110:15899:9619
TACGAACTGTGCAAACGTTATTCGGAATCACTGGGCTTAAAGGGTGCGTAGGCGGGTTTGTAAGTCAGAGGTGAAAGTTTGCAGCTTAACTGTAAAATTGCCTTTGAAACTGTAGAACTTGAGTAGCGTTGAGGTCAGCGGAATGTGACAT
>000001M00365:7:000000000-A48JK:1:2105:15157:8497
TACGAAGGTCCCAAGCGTTATTCGGAATCACTGGGCGTAAAGGGAGCGTAGGCGGCGTGGAAAGTCAGATGTGAAATCTCAAGGCTCAACCTTGAAACTGCATCCGATACTTCCATGCTAGAGGACTGGAGAGGTGTTTGGAATTATCGGT

I want to sort this file according to header informations. How can I do this?

Best Regards
Zillur

[wdecoster]

Can you be more specific about which header information? Alphabetical sorting?

[zillur]

Thank you very much. alphabetically/numerically whichever convenient.

Best Regards
Zillur

[GenoMax]

And the reason you want to do this, if I may ask?

[zillur]

Thanks.

And the reason you want to do this, if I may ask?

Yeah sure. I wanted to create fastq file using my .qual ahd fasta file using qiime. But it gaves me:

KeyError: 'QUAL header (M00365:7:000000000-A48JK:1:1101:14885:1320) does not match FASTA header (M00365:7:000000000-A48JK:1:1101:16466:1388)

In my qual file I have many other sequences including my fasta. So, I think sorting may resolve the issue. I appreciate your suggestions.

Best Regards
Zillur

[Persistent LABS]

I guess sort on linux will work.
cat file.fasta|paste - -|sort|sed 's/\t/\n/g'
Try this.

[GenoMax]

Following is untested but you could give it a try and see if it works. It may avoid the sort etc. You will find reformat.sh in BBMap suite.

reformat.sh in=your_fasta_file.fa qfin=your_qual_file.qual out=fastq_format_file.fq

[zillur]

Thank your very much. I have tried this:

cat file.fasta|paste - -|sort|sed 's/\t/\n/g'

But it doesn't resolve all:

(qiime191) [zillur@genomics final]$ head new_sorted_1.fasta 
>M00365:7:000000000-A48JK:1:1101:10000:14343
TACGGAGGGGGCTAGCGTTGTTCGGAATTACTGGGCGTAAAGCGTGCGTAGGCGGATTATTAAGTTAGGGGTGAAATCCCGAGGCTCAACCTCGGAACTGCCCTTAAAACTGTTGGTCTTGAGTTCTGGAGAGGTGAGTGGAATTGCTAGT
>M00365:7:000000000-A48JK:1:1101:10000:18084
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGCGGCTAGGTCAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTTGATACTGCCTAGCTAGAGTATGTTAGAGGAATGCGGAATTCCAGGT
>M00365:7:000000000-A48JK:1:1101:10000:25105
TACGAAGGGGGCTAGCGTTGTTCGGAATTACTGGGCGTAAAGAGTTCGTAGGCGGGTTATTAAGTCAGATGTGAAATCCCAGGGCTCAACCTTGGAACTGCATTTGAAACTGGTAACCTAGAGACTAGGAGAGGTCAGTGGAATACCGAGT
>M00365:7:000000000-A48JK:1:1101:10000:5055
CACGTAGGGGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGGGCTCGTAGGCTGTTCAGTAAGTCAGGTGTGAAAATCCAAGGCTCAACCTTGGGACGCCACCTGATACCGCTGTGACTAGAGTCCGGTAGAGGAGATTGGAATTCCTGG
>M00365:7:000000000-A48JK:1:1101:10001:16084
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGCGGCTAGGTCAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTTGATACTGCCTAGCTAGAGTATGTTAGAGGATTGCGGAATTCCAGGT

refomart.sh gives me:

[zillur@genomics final]$ ./bbmap/reformat.sh in=new_15.fasta qfin=qual_.1.qual out=f_nw_15_ql_.1.fq
java -ea -Xmx111g -cp /home/zillur/Desktop/zillur/yadira/study_1799_split_library_seqs_and_mapping/filter/final/bbmap/current/ jgi.ReformatReads in=new_15.fasta qfin=qual_.1.qual out=f_nw_15_ql_.1.fq
Executing jgi.ReformatReads [in=new_15.fasta, qfin=qual_.1.qual, out=f_nw_15_ql_.1.fq]

Input is being processed as unpaired
Exception in thread "Thread-1" java.lang.AssertionError: Quality and Base headers differ for read 0
	at stream.FastaQualReadInputStream.toReadList(FastaQualReadInputStream.java:128)
	at stream.FastaQualReadInputStream.toReads(FastaQualReadInputStream.java:110)
	at stream.FastaQualReadInputStream.fillBuffer(FastaQualReadInputStream.java:94)
	at stream.FastaQualReadInputStream.hasMore(FastaQualReadInputStream.java:54)
	at stream.ConcurrentGenericReadInputStream$ReadThread.readLists(ConcurrentGenericReadInputStream.java:643)
	at stream.ConcurrentGenericReadInputStream$ReadThread.run(ConcurrentGenericReadInputStream.java:635)

What should I do now?

Best Regards
Zillur

[khericlim]

When you sort the fasta file, did you also sort the qual file?

In my qual file I have many other sequences including my fasta.

What do you mean by having other sequences in your qual file?

[dgscofield]

If you have BioPerl ≥ 1.6.922 and Sort::Naturally, then

https://github.com/douglasgscofield/bioinfo/blob/master/scripts/fastaSort

shows how to sort on sequence name, using natural sort as it seems you require.

[Persistent LABS]

Thank your very much. I have tried this: But it doesn't resolve all:

(qiime191) [zillur@genomics final]$ head new_sorted_1.fasta 
>M00365:7:000000000-A48JK:1:1101:10000:14343
TACGGAGGGGGCTAGCGTTGTTCGGAATTACTGGGCGTAAAGCGTGCGTAGGCGGATTATTAAGTTAGGGGTGAAATCCCGAGGCTCAACCTCGGAACTGCCCTTAAAACTGTTGGTCTTGAGTTCTGGAGAGGTGAGTGGAATTGCTAGT
>M00365:7:000000000-A48JK:1:1101:10000:18084
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGCGGCTAGGTCAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTTGATACTGCCTAGCTAGAGTATGTTAGAGGAATGCGGAATTCCAGGT
>M00365:7:000000000-A48JK:1:1101:10000:25105
TACGAAGGGGGCTAGCGTTGTTCGGAATTACTGGGCGTAAAGAGTTCGTAGGCGGGTTATTAAGTCAGATGTGAAATCCCAGGGCTCAACCTTGGAACTGCATTTGAAACTGGTAACCTAGAGACTAGGAGAGGTCAGTGGAATACCGAGT
>M00365:7:000000000-A48JK:1:1101:10000:5055
CACGTAGGGGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGGGCTCGTAGGCTGTTCAGTAAGTCAGGTGTGAAAATCCAAGGCTCAACCTTGGGACGCCACCTGATACCGCTGTGACTAGAGTCCGGTAGAGGAGATTGGAATTCCTGG
>M00365:7:000000000-A48JK:1:1101:10001:16084
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGCGGCTAGGTCAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTTGATACTGCCTAGCTAGAGTATGTTAGAGGATTGCGGAATTCCAGGT

refomart.sh gives me:

[zillur@genomics final]$ ./bbmap/reformat.sh in=new_15.fasta qfin=qual_.1.qual out=f_nw_15_ql_.1.fq
java -ea -Xmx111g -cp /home/zillur/Desktop/zillur/yadira/study_1799_split_library_seqs_and_mapping/filter/final/bbmap/current/ jgi.ReformatReads in=new_15.fasta qfin=qual_.1.qual out=f_nw_15_ql_.1.fq
Executing jgi.ReformatReads [in=new_15.fasta, qfin=qual_.1.qual, out=f_nw_15_ql_.1.fq]

Input is being processed as unpaired
Exception in thread "Thread-1" java.lang.AssertionError: Quality and Base headers differ for read 0
	at stream.FastaQualReadInputStream.toReadList(FastaQualReadInputStream.java:128)
	at stream.FastaQualReadInputStream.toReads(FastaQualReadInputStream.java:110)
	at stream.FastaQualReadInputStream.fillBuffer(FastaQualReadInputStream.java:94)
	at stream.FastaQualReadInputStream.hasMore(FastaQualReadInputStream.java:54)
	at stream.ConcurrentGenericReadInputStream$ReadThread.readLists(ConcurrentGenericReadInputStream.java:643)
	at stream.ConcurrentGenericReadInputStream$ReadThread.run(ConcurrentGenericReadInputStream.java:635)

What should I do now?

Best Regards
Zillur

The sort example has sorted your data alphabetically. If you try to sort your qual file, I think you will get the same order of headers.