UNIX for Beginners Questions & Answers

!/usr/bin/env bash

# @(#) s1       Demonstrate awk template for reading FASTA files.

LC_ALL=C ; LANG=C ; export LC_ALL LANG
pe() { for _i;do printf "%s" "$_i";done; printf "\n"; }
pl() { pe;pe "-----" ;pe "$*"; }
em() { pe "$*" >&2 ; }
db() { ( printf " db, ";for _i;do printf "%s" "$_i";done;printf "\n" ) >&2 ; }
db() { : ; }
C=$HOME/bin/context && [ -f $C ] && $C awk

FILE=${1-data1}

pl " Input file $FILE:"
head -25 $FILE

pl " Results, $FG extracted lines from $FILE:"
fastagrep 'seq1|seq2' $FILE

pl " Results, awk print from $FILE, awk FASTA template:"
awk '
function fformat(id, sequence)
{
  printf ">%s\n", id
  while (length(sequence) >= 60) {
    print substr(sequence, 1, 60)
    gsub(/^.{60}/, "", sequence)
  }
  if (length(sequence) > 0) { print sequence }
}
function operate(id, sequence)
{
  print id, length(sequence)
}
BEGIN {
  getline
  id = substr($1, 2)
  sequence = ""
}
$0 ~ /^>/ {
  fformat(id, sequence)
  # operate(id, sequence)
  id = substr($1, 2)
  sequence = ""
  next
}
{
  sequence = sequence $0
}
END { fformat(id, sequence) }
# END { operate(id, sequence) }

' $FILE

pl " Results, fastagrep and print length with \"operate\" function:"
fastagrep 'seq1|seq2' $FILE |
./s0

exit 0

$ ./s1 data3

Environment: LC_ALL = C, LANG = C
(Versions displayed with local utility "version")
OS, ker|rel, machine: Linux, 3.16.0-7-amd64, x86_64
Distribution        : Debian 8.11 (jessie) 
bash GNU bash 4.3.30
awk GNU Awk 4.1.1, API: 1.1 (GNU MPFR 3.1.2-p3, GNU MP 6.0.0)

-----
 Input file data3:
>seq1
ATGCTA
>seq2
CGAAACGCAAACAGCCCACGACAGTTAGCCTAGATTGGAACCTCCGGGAAATATGAGACT
GGGTTTAAGGGATGGCAGCCATAGCCACGACATCACGTAG
>seq3
TAGC


-----
 Results,  extracted lines from data3:
>seq1
ATGCTA
>seq2
CGAAACGCAAACAGCCCACGACAGTTAGCCTAGATTGGAACCTCCGGGAAATATGAGACT
GGGTTTAAGGGATGGCAGCCATAGCCACGACATCACGTAG

-----
 Results, awk print from data3, awk FASTA template:
>seq1
ATGCTA
>seq2
CGAAACGCAAACAGCCCACGACAGTTAGCCTAGATTGGAACCTCCGGGAAATATGAGACT
GGGTTTAAGGGATGGCAGCCATAGCCACGACATCACGTAG
>seq3
TAGC

-----
 Results, fastagrep and print length with "operate" function:
seq1 6
seq2 100

fastagrep       extract sequences from a multi-FASTA file by regex. (what)
Path    : ~/bin/fastagrep
Version : fastagrep version 0.3
Length  : 392 lines
Type    : Perl script, ASCII text executable
Shebang : #!/usr/bin/env perl
Home    : GitHub - rec3141/rec-genome-tools (doc)
Modules : (for perl codes)
 strict 1.08
 warnings       1.23
 Getopt::Std    1.10
 IO::File       1.16
 Data::Dumper   2.151_01