sort and merge fasta files by chromosome number

Question

[woojoy14]

I have been practicing gatk best practice and got this problem stuck!

I downloaded h19.chromFa at ucsc and now am trying to sort and merge it by chromosome number.

I used the code below from this blog https://digibio.blogspot.com/2014/07/sort-and-merge-fasta-files-by.html

cat chrM.fa `ls  *.fa | sort -V | grep -i -v chrM `  > hg19.fa


>grep chr hg19.fa

>chrM
>chr1
>chr1_gl000191_random
>chr1_gl000192_random
>chr2
>chr3
>chr4
>chr4_ctg9_hap1
>chr4_gl000193_random
>chr4_gl000194_random
>chr5
>chr6
>chr6_apd_hap1
>chr6_cox_hap2
>chr6_dbb_hap3
>chr6_mann_hap4
>chr6_mcf_hap5
>chr6_qbl_hap6
>chr6_ssto_hap7
>chr7
>chr7_gl000195_random
>chr8
>chr8_gl000196_random
>chr8_gl000197_random
>chr9
>chr9_gl000198_random
>chr9_gl000199_random
>chr9_gl000200_random
>chr9_gl000201_random
>chr10
>chr11
>chr11_gl000202_random
>chr12
>chr13
>chr14
>chr15
>chr16
>chr17
>chr17_ctg5_hap1
>chr17_gl000203_random
>chr17_gl000204_random
>chr17_gl000205_random
>chr17_gl000206_random
>chr18
>chr18_gl000207_random
>chr19
>chr19_gl000208_random
>chr19_gl000209_random
>chr20
>chr21
>chr21_gl000210_random
>chr22
>chrX
>chrY

However, as you can see above, it didn't work.

How can I get rid of every file with 'hap' and 'random' and 'chrM'?

Thank you for your help in advance!

Answer 1

[Pierre Lindenbaum]

How can I get rid of every file with 'hap' and 'random' and 'chrM'?

ls *.fa | grep -vE '_|chrM' | sort -V | xargs  cat > hg19.fasta

[woojoy14]

Thank you very much!