Change fasta file header to include number of times a read apears

Question

[Gabe Anderson]

Hello,

I have a data set that looks like this:

>JAMESBROWN_1_FC20423AAXX_7_1_82_883
GTTAGAGGTTCGAAG
>JAMESBROWN_1_FC20423AAXX_7_1_198_886
GGCTCAGTGGTCTAGTGGTATGATTCTCGCTT
>JAMESBROWN_1_FC20423AAXX_7_1_115_888
GGGGGTGTAGGGTGGGGTTGG
>JAMESBROWN_1_FC20423AAXX_7_1_99_894
GTTCGTATCCCACTTCTGACACCA
>JAMESBROWN_1_FC20423AAXX_7_1_226_900
GCAAACTGTGCGTCATCGTGT

And I'd like to edit it to look like this:

>cel1_count=3
TGCCTTGTCTGTCCTAAAAATC
>cel2_count=9
GTTAAGTGGGAAACGATGT
>cel3_count=7
CCGACCTTGAAATACCAC
>cel4_count=7
TAGAAATCCACTATGCTTTGG
>cel5_count=5
CGCGGGTGAGCAGCCTGGTAGCTCGTC

Count in the header line specifies the number of times a sequence occurs in the data set. Kindly assist. Thanks!

Answer 1

[Pierre Lindenbaum]

cat in.fa | paste - - | cut -f 2 | LC_ALL=C sort |\
 uniq -c | sed 's/^[ ]*//' |\
 awk '{printf(">cel%d_count=%s\n%s\n",NR,$1,$2);}'

[Gabe Anderson]

Thanks for your input. For some reason, the reads are also altered instead of the header line only. A lot of bases are replaced by A. Here is what my result looked like:

>dme1_count=329515

>dme2_count=534
A
>dme3_count=15
AA
>dme4_count=4
AAA
>dme5_count=1719
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
>dme6_count=1
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAC
>dme7_count=1
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAN
>dme8_count=2
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAT
>dme9_count=3
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACA

[GouthamAtla]

The command is not doing anything to your sequences other than counting.I guess, as they sorted, the sequences with "A" appeared first in your output. The order is not maintained.

[Gabe Anderson]

Thank you, Pierre and Goutham! It's clear now.

Answer 2

[Charles Plessy]

The command fastx_collapser from the FASTX-Toolkit will produce what you want, except for the sequence name, which will look like x-y, where x is the position of the sequence in the output file, and y is the number of times it occurred in the input file.

For example:

$ cat in.fa
>JAMESBROWN_1_FC20423AAXX_7_1_82_883
GTTAGAGGTTCGAAG
>JAMESBROWN_1_FC20423AAXX_7_1_198_886
GGCTCAGTGGTCTAGTGGTATGATTCTCGCTT
>JAMESBROWN_1_FC20423AAXX_7_1_82_883
GTTAGAGGTTCGAAG
>JAMESBROWN_1_FC20423AAXX_7_1_198_886
GGCTCAGTGGTCTAGTGGTATGATTCTCGCTT
>JAMESBROWN_1_FC20423AAXX_7_1_115_888
GGGGGTGTAGGGTGGGGTTGG
>JAMESBROWN_1_FC20423AAXX_7_1_99_894
GTTCGTATCCCACTTCTGACACCA
>JAMESBROWN_1_FC20423AAXX_7_1_226_900
GCAAACTGTGCGTCATCGTGT

$ fastx_collapser < in.fa
>1-2
GTTAGAGGTTCGAAG
>2-2
GGCTCAGTGGTCTAGTGGTATGATTCTCGCTT
>3-1
GGGGGTGTAGGGTGGGGTTGG
>4-1
GTTCGTATCCCACTTCTGACACCA
>5-1
GCAAACTGTGCGTCATCGTGT