MiscGenomicsTools

broccoli_ortho_files

Bash scripts to make single-copy orthologue fasta files ready for phylogenomics from Broccoli output.

GenePull

A bash tool which extracts a certain gene from an assembly using BLAST and bedtools.

One(ish)-liners

Convert leading or trailing gaps (-) in a fasta file to ?.

awk '/^>/ {
  printf("\n%s\n",$0);next; 
  } {
  printf("%s",$0);
  } END {
  printf("\n");
  }' file.fasta | \
awk -F '[^-](.*[^-]|$)' '{
  s=$0;
  h=gsub(/./,"?",$1);
  t=gsub(/./,"?",$2);
  print $1 substr(s,h+1, length(s)-h-t) $2
  }' > file_edited.fasta

Result:

cat file.fasta
>test
-------------agtc-cgcatgaggatagctcgtagataaaa---------
>test2
-----atta--------------atttgacc--------tga-----------
>test3
ataaagctcggctaa-----------------------tggac----------

cat file_edited.fasta
>test
?????????????agtc-cgcatgaggatagctcgtagataaaa?????????
>test2
?????atta--------------atttgacc--------tga???????????
>test3
ataaagctcggctaa-----------------------tggac??????????

Print length of all sequences in a fasta file.

awk '/^>/ {
  if (seqlen){print seqlen}; print ;seqlen=0;next; 
  } { 
  seqlen += length($0)
  }END{
  print seqlen
  }' file.fasta

Result:

>ptg000001
4551850
>ptg000002
10701577
>ptg000003
6461149
>ptg000004
6151846
>ptg000005
8702012

Sort multifasta file by alphanumeric headers.

sed 's/^>/\x00&/' file.fasta  | sort -z | tr -d '\0'