Sorting of fasta file according to gene name in alphabetical order

[garethboy]

Hi all,

I am kinda new in bioinformatics. I have a question regarding sort of data, hope you all can guide me.

I have a single fasta file as follow:

>final_100_00001 hypothetical protein
GTGTATAAGAGACAGGGCGTTGTCCAGCGCGATCTTCTGGCCGTCGCGATCGAGGGCCTGCCCGAGCGCCGACAGCTTGAGCGACACCTCGAGCGGTCGCACCCCGTCGCATGCGATATCGCCGCGGCGGC
.
.
.
.
.
>final_106_02271 hypothetical protein
ATGCGCACTACGATCGACCTCGATGACGACATACTGCGGGCGTTGAAACGACGCCAGCGCGAGGAGCGCAAAACGTTAGGGCAGCTCGCCTCCGAATTGCTTGCGCAAGCTCTGG
>final_106_02272 putative ribonuclease VapC43
GTGAGCGAAACCTTTGACGTCGATGTTCTGGTCCATGCGACGCACCGAGCCAGCCCGTTTCACGATAAGGCGAAGACGCTCGTTGAGCGATTCCTGGCTGGGCCAGGGCTGGTATATCTA
>final_106_00001 Glycerol kinase
GTGTCCGACGCCATCCTAGGAGAGCAATTGGCCGAGTCCTCGGATTTCATAGCCGCCATCGACCAGGGCACCACCAGCACCCGCTGCATGATCTTCGATCACCACGGTGCCGAGG
>final_107_00002 RDD family protein
ATGTCGGAGGTGGTGACCGGCGACGCCGTGGTGCTCGACGTACAGATCGCCCAGTTGCCGGTGCGCGCGGTCAGCGCGGTCATCGATATCACCATAATATTCATCGG
>final_107_00003 hypothetical protein
ATGCTGCCGCCTGGCTACCCGGTTGAACCACCGCCCGTGGCGCCGGGATATGCGCCGGCCGGATATCCGCCCTACCCCGCTACACCACCCGGGTACGGCCCGCCGGGTTA
.
.
.
.
.
>final_120_02354 hypothetical protein
ATGACGATGGCTCGGGTGCGTCGCGGCACGGAACTGTTGTTGTCACCTCAGTCGCCGCCGGCCACCGGCGGGCTGATCGTGTTGACCGGTCTGCGGCTGTTGGCTGGGTTGATCTG
>final_120_02355 Soluble secreted antigen MPT53 precursor
GTGACTCATTCCCGTCTGATTGGCGCACTTACCGTAGTCGCAATTATCGTCACTGCATGTGGTTCGCAGCCGAAATCCCAGCCCGCAGTGGCACCTACCGGGGACGCGGCCGCT
>final_120_02356 AhpC/TSA family protein
GTGCCGACTCGCCGTCTGCAGGACATCAACGATCAACCGGTGGACGTCCCGGCTGCGACCGGAAGGACACACCTGCAGTTTCGGCGGTTCGCGGCCTGTCCGATCTGCCA
>final_120_02357 transcriptional activator FtrB
ATGGCAGATCGGTCGGTGCGCCCGCTGCGGCATCTCGTTCATGCGGTGACTGGGGGCCAACCGCCTTCCGAGGCCCAGGTCCGACAGGCAGCCTGGATTGCGCGGTGCGTCGG

What should I do in order to sort them according to gene name such as the following?

>final_120_R1_02356 AhpC/TSA family protein
GTGCCGACTCGCCGTCTGCAGGACATCAACGATCAACCGGTGGACGTCCCGGCTGCGACCGGAAGGACACACCTGCAGTTTCGGCGGTTCGCGGCCTGTCCGATCTGCCA
>final_106_00001 Glycerol kinase
GTGTCCGACGCCATCCTAGGAGAGCAATTGGCCGAGTCCTCGGATTTCATAGCCGCCATCGACCAGGGCACCACCAGCACCCGCTGCATGATCTTCGATCACCACGGTGCCGAGG
>final_100_00001 hypothetical protein
GTGTATAAGAGACAGGGCGTTGTCCAGCGCGATCTTCTGGCCGTCGCGATCGAGGGCCTGCCCGAGCGCCGACAGCTTGAGCGACACCTCGAGCGGTCGCACCCCGTCGCATGCGATATCGCCGCGGCGGC
>final_106_02271 hypothetical protein
ATGCGCACTACGATCGACCTCGATGACGACATACTGCGGGCGTTGAAACGACGCCAGCGCGAGGAGCGCAAAACGTTAGGGCAGCTCGCCTCCGAATTGCTTGCGCAAGCTCTGG
>final_107_00003 hypothetical protein
ATGCTGCCGCCTGGCTACCCGGTTGAACCACCGCCCGTGGCGCCGGGATATGCGCCGGCCGGATATCCGCCCTACCCCGCTACACCACCCGGGTACGGCCCGCCGGGTTA
>final_120_R1_02354 hypothetical protein
ATGACGATGGCTCGGGTGCGTCGCGGCACGGAACTGTTGTTGTCACCTCAGTCGCCGCCGGCCACCGGCGGGCTGATCGTGTTGACCGGTCTGCGGCTGTTGGCTGGGTTGATCTG
>final_106_02272 putative ribonuclease VapC43
GTGAGCGAAACCTTTGACGTCGATGTTCTGGTCCATGCGACGCACCGAGCCAGCCCGTTTCACGATAAGGCGAAGACGCTCGTTGAGCGATTCCTGGCTGGGCCAGGGCTGGTATATCTA
>final_107_00002 RDD family protein
ATGTCGGAGGTGGTGACCGGCGACGCCGTGGTGCTCGACGTACAGATCGCCCAGTTGCCGGTGCGCGCGGTCAGCGCGGTCATCGATATCACCATAATATTCATCGG
>final_120_02355 Soluble secreted antigen MPT53 precursor
GTGACTCATTCCCGTCTGATTGGCGCACTTACCGTAGTCGCAATTATCGTCACTGCATGTGGTTCGCAGCCGAAATCCCAGCCCGCAGTGGCACCTACCGGGGACGCGGCCGCT
>final_120_02357 transcriptional activator FtrB
ATGGCAGATCGGTCGGTGCGCCCGCTGCGGCATCTCGTTCATGCGGTGACTGGGGGCCAACCGCCTTCCGAGGCCCAGGTCCGACAGGCAGCCTGGATTGCGCGGTGCGTCGG

[dpryan]

For a file named "foo.fa":

awk '{idx=index($0, " "); ID=$1; NAME=substr($0, idx+1); getline SEQ; printf("%s\t%s\t%s\n", NAME, ID, SEQ);}' foo.fa | sort -k1d,1 | awk -F"\t" '{printf("%s %s\n%s\n", $2,$1,$3)}' > foo.sorted.fa

The general idea is to linearize each entry, sort by the appropriate column, and then put back in the right format. This won't work if any of the sequences span multiple lines (while you could do that in awk, I'd do that in python for convenience).

[garethboy]

Hi, thank you for the help. The sequences in the original file (foo.fa in your reply) already in a linearized format.

After trying out the given command, the output is as following :-(

AGAGTTTGATCCTGGCTCAGATTGAACGCTGGCGGCATGCCTTACACATGCAAGTCGAACGGCAGCATGATCTAGCTTGCTAG...
AGAGTTTGATCCTGGCTCAGATTGAACGCTGGCGGCATGCCTTACACATGCAAGTCGAACGGCAGCATGATCTAGCTTGCTAG...
>final_107_R1_04115 Transposase
AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGCCCTTCGGGGTACTCG...
AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGCCCTTCGGGGTACTCG...
>final_226_R1_00419 Sugar diacid utilization regulator
AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGCCCTTCGGGGTACTCG...
AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGCCCTTCGGGGTACTCG...
>final_230_R1_00884 Beta-ketoadipyl-CoA thiolase
AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGTCTCTTCGGAGATACT...
AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGTCTCTTCGGAGATACT...
>final_103_R1_03549 UDP-N-acetylglucosamine 1-carboxyvinyltransferase
AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGTCTCTTCGGAGATACT...
AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGTCTCTTCGGAGATACT...
>final_105_R1_03559 23S ribosomal RNA
AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGTCTCTTCGGAGATACT...
AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGTCTCTTCGGAGATACT...
>final_106_R1_03486 UDP-N-acetylglucosamine 1-carboxyvinyltransferase
AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGTCTCTTCGGAGATACT...
AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGTCTCTTCGGAGATACT...
>final_107_R1_03459 UDP-N-acetylglucosamine 1-carboxyvinyltransferase
AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGTCTCTTCGGAGATACT...
AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGTCTCTTCGGAGATACT...
>final_108_R1_03464 UDP-N-acetylglucosamine 1-carboxyvinyltransferase
AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGTCTCTTCGGAGATACT...
AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGTCTCTTCGGAGATACT...
>final_109_R1_03413 UDP-N-acetylglucosamine 1-carboxyvinyltransferase
AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGTCTCTTCGGAGATACT...
AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGTCTCTTCGGAGATACT...
>final_110_R1_03462 UDP-N-acetylglucosamine 1-carboxyvinyltransferase
AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGTCTCTTCGGAGATACT...
AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGTCTCTTCGGAGATACT...

>final_111_R1_03536 UDP-N-acetylglucosamine 1-carboxyvinyltransferase
AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGTCTCTTCGGAGATACT...
AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGTCTCTTCGGAGATACT...
>final_112_R1_01396 UDP-N-acetylglucosamine 1-carboxyvinyltransferase
AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGTCTCTTCGGAGATACT...
AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGTCTCTTCGGAGATACT...

[dpryan]

Ah, I had assumed that the sequences were on their own line. Are there tabs separating the ID (e.g., ">final_112_R1_01396") from the gene name or spaces? If the actual fields are tab separated, then just directly use "sort -k2d,2". Otherwise, you just have to replace the appropriate spaces with tabs and pass that to sort (though, you might need to change the field separator for sort, which I think defaults to blank to non-blank transitions).

[dariober]

What should I do in order to sort them according to gene name such as the following?

Hello,

Try this one to see if it does what you need. Input is a fasta file, sequences can span multiple lines. Guessing from your example, "gene name" is considered to be the string after the first blank in the sequence name.

awk 'BEGIN{RS=">"} NR>1 {gsub("\n", "\t"); print ">"$0}' test.fa  \
| sort -t ' ' -k2,2 \
| awk '{sub("\t", "\n"); gsub("\t", ""); print $0}' > test.sorted.out

Input (test.fa):

>final_106_02271 hypothetical protein
ATGCGCACTACGATCGACCTCGATGACGACATACTGCGGGCGTTG
AAACGACGCCAGCGCGAGGAGCGCAAAACGTTAGGGCAGCTCGCCTCCGAATTGCTTGCGCAAGCTCTGG
>final_106_02272 putative ribonuclease VapC43
GTGAGCGAAACCTTTGACGTCGATGTTCTGGTCCATGCGACGCA
CCGAGCCAGCCCGTTTCACGATAAGGCGAAGACGCTCGTTGAGCGATTCCTGGCTGGGCCAGGGCTGGTATATCTA
>final_106_00001 Glycerol kinase
GTGTCCGACGCCATCCTAGGAGAGCAATTGGCCGAGTCCTCGGATTTCATAGCCGCCATCGACCAGGGCACCACCAGCACCCGCTGCATGATCTTCGATCACCACGGTGCCGAGG
>final_107_00002 RDD family protein
ATGTCGGAGGTGGTGACCGGCGACGCCGTGGTGCTCGACGTACAGATCGCCCAGTTGCCGGTGCGCGCGGTCAGCGCGGTCATCGATATCACCATAATATTCATCGG
>final_107_00003 hypothetical protein
ATGCTGCCGCCTGGCTACCCGGTTGAACCACCGCCCGTGGCGCCGGGATATGCGCCGGCCGGATATCCGCCCTACCCCGCTACACCACCCGGGTACGGCCCGCCGGGTTA
>final_120_02354 hypothetical protein
ATGACGATGGCTCGGGTGCGTCGCGGCACGGAACTGTTGTTGTCACCTCAGTCGCCGCCGGCCACCGGCGGGCTGATCGTGTTGACCGGTCTGCGGCTGTTGGCTGGGTTGATCTG
>final_120_02355 Soluble secreted antigen MPT53 precursor
GTGACTCATTCCCGTCTGATTGGCGCACTTACCGTAGTCGCAATTATCGTCACTGCATGTGGTTCGCAGCCGAAATCCCAGCCCGCAGTGGCACCTACCGGGGACGCGGCCGCT
>final_120_02356 AhpC/TSA family protein
GTGCCGACTCGCCGTCTGCAGGACATCAACGATCAACCGGTGGACGTCCCGGCTGCGACCGGAAGGACACACCTGCAGTTTCGGCGGTTCGCGGCCTGTCCGATCTGCCA
>final_120_02357 transcriptional activator FtrB
ATGGCAGATCGGTCGGTGCGCCCGCTGCGGCATCTCGTTCATGCGGTGACTGGGGGCCAACCGCCTTCCGAGGCCCAGGTCCGACAGGCAGCCTGGATTGCGCGGTGCGTCGG

Output (test.sorted.fa):

>final_120_02356 AhpC/TSA family protein
GTGCCGACTCGCCGTCTGCAGGACATCAACGATCAACCGGTGGACGTCCCGGCTGCGACCGGAAGGACACACCTGCAGTTTCGGCGGTTCGCGGCCTGTCCGATCTGCCA
>final_106_00001 Glycerol kinase
GTGTCCGACGCCATCCTAGGAGAGCAATTGGCCGAGTCCTCGGATTTCATAGCCGCCATCGACCAGGGCACCACCAGCACCCGCTGCATGATCTTCGATCACCACGGTGCCGAGG
>final_107_00002 RDD family protein
ATGTCGGAGGTGGTGACCGGCGACGCCGTGGTGCTCGACGTACAGATCGCCCAGTTGCCGGTGCGCGCGGTCAGCGCGGTCATCGATATCACCATAATATTCATCGG
>final_120_02355 Soluble secreted antigen MPT53 precursor
GTGACTCATTCCCGTCTGATTGGCGCACTTACCGTAGTCGCAATTATCGTCACTGCATGTGGTTCGCAGCCGAAATCCCAGCCCGCAGTGGCACCTACCGGGGACGCGGCCGCT
>final_106_02271 hypothetical protein
ATGCGCACTACGATCGACCTCGATGACGACATACTGCGGGCGTTGAAACGACGCCAGCGCGAGGAGCGCAAAACGTTAGGGCAGCTCGCCTCCGAATTGCTTGCGCAAGCTCTGG
>final_107_00003 hypothetical protein
ATGCTGCCGCCTGGCTACCCGGTTGAACCACCGCCCGTGGCGCCGGGATATGCGCCGGCCGGATATCCGCCCTACCCCGCTACACCACCCGGGTACGGCCCGCCGGGTTA
>final_120_02354 hypothetical protein
ATGACGATGGCTCGGGTGCGTCGCGGCACGGAACTGTTGTTGTCACCTCAGTCGCCGCCGGCCACCGGCGGGCTGATCGTGTTGACCGGTCTGCGGCTGTTGGCTGGGTTGATCTG
>final_106_02272 putative ribonuclease VapC43
GTGAGCGAAACCTTTGACGTCGATGTTCTGGTCCATGCGACGCACCGAGCCAGCCCGTTTCACGATAAGGCGAAGACGCTCGTTGAGCGATTCCTGGCTGGGCCAGGGCTGGTATATCTA
>final_120_02357 transcriptional activator FtrB
ATGGCAGATCGGTCGGTGCGCCCGCTGCGGCATCTCGTTCATGCGGTGACTGGGGGCCAACCGCCTTCCGAGGCCCAGGTCCGACAGGCAGCCTGGATTGCGCGGTGCGTCGG

[dpryan]

I should note that changing the sort command in my earlier reply to:

sort -t $'\t' -k1d,1

will be helpful, since then it'll sort by the whole gene name rather than just the first word. darioober's solution has similar issues. BTW, my solution works correctly under Ubuntu, so perhaps you have a different awk variant if you're getting weird output.

[garethboy]

thank you dariober and dpryan. it works. :-)

[htetre]

Thanks dpryan for the sort code. It works great for me except that in my sorted file it has the sequence name twice. ie >106x2447112 >106x2447112.

What part of the code removes the printing the name twice?

Thanks for your help

[zillur]

Hi there,
I was trying to sort my fasta file according to the script from this thread:

awk 'BEGIN{RS=">"} NR>1 {gsub("\n", "\t"); print ">"$0}' new_15.fasta | sort -t $'\t' -k1d,1| awk '{sub("\t", "\n"); gsub("\t", ""); print $0}' > new_sorted.fasta

It works. But not perfectly. Here is the output:

(qiime191) [zillur@genomics final]$ head new_sorted.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

>M00365:7:000000000-A48JK:1:1101:10000:5055 this should be my 1st sequence!!! What you think!!! Thanks in advance for your suggestions.

Best Regards
Zillur

[SNPsaurus]

Things can be sorted alphabetically or numerically. In this case it is alphabetical. In your case it looks like you want a much more complicated sort involving numerical sorting of the ends (1101:10000:14343) with each number sorted independently.