GAWK does not terminate after ENDFILE block with single file - awk

Question

I have a gawk script below that reads a protein FASTA file and only prints out the records that don't have an X in their sequence and are within a certain range length. I wanted to modify the file in place so I had the script write to a temporary file and then rename it to the original file. The BEGINFILE and ENDFILE constructs in gawk seemed convenient for this. However, for some reason, gawk does not exit after executing the code in the ENDFILE even if it is given a single file argument. It seems to jump back to another line of code and then just hang. Does anyone know what could cause this to happen? The weird part is that this doesn't happen for every FASTA file, only a few and I can't tell what is different between the ones that trigger the bug and the ones that don't
#! /bin/gawk -f
function trim(s) {
gsub(/^[ \t]+|[ \t]+$/, "", s)
return s
}
function printFasta(header, seq, outfile, seq_line_max_chars) {
print ">" header > outfile
seq_line_max_chars = 80
start = 1
end = length(seq)
while (start <= end) {
print substr(seq, start, seq_line_max_chars) > outfile
start += seq_line_max_chars
}
}
BEGIN {
min_prot_len = 400
}
BEGINFILE {
tmp_out = FILENAME ".tmp"
}
/^>.+/ {
headerStartIdx = index($0, ">") + 1
header = trim(substr($0, headerStartIdx))
getline
sequence = ""
while ($0 !~ /(^>.+)|(^[[:space:]]*$)/) {
x_matched = match($0, "X")
if (x_matched != 0) {
next
}
gsub("*", "")
sequence = sequence $0
getline
}
if (length(sequence) >= min_prot_len) {
printFasta(header, sequence, tmp_out)
}
}
ENDFILE {
print "move called"
# system(("mv " tmp_out " " FILENAME))
}
I called the script with
$ ./filter_proteins.awk test.faa
When I run this, move called is printed and then it hangs. I tried stepping through with the debugger and I see that it reaches the ENDFILE block having processed all the lines in the input file, but when I type the next command, it jumps to the getline statement on line 44. After several iterations of next and print $0 it seems that the program is stuck reading the last line of the input file till the end of time. Perhaps this is a bug?
I am using GAWK 5.1.0
Edit
A minimal input file.
https://github.com/CuriousTim/pastebin/blob/main/mb.34.faa
When I run the script with only a few sequences, it works, but when I use the whole file, it hangs. I wasn't sure how to make a minimal example without providing the whole file.

Answer 1

We'll know for sure after you provide sample input to test with but my money's on the call to getline within the loop reaching the end of the file and so triggering the ENDFILE condition to be true but you're still in the loop.
Look:
$ cat file
foo
bar
$ cat tst.awk
{
while (1) {
print "about to execute getline"
getline
print "just executed getline:", $0
if (++c == 5) {
exit
}
}
}
ENDFILE {
print "*** in ENDFILE ***"
}
$ awk -f tst.awk file
about to execute getline
just executed getline: bar
about to execute getline
*** in ENDFILE ***
just executed getline: bar
about to execute getline
just executed getline: bar
about to execute getline
just executed getline: bar
about to execute getline
just executed getline: bar
Calling getline in a loop is not how you want to write an awk script and what you have in your code is the wrong syntax to use when calling getline at any time - see http://awk.freeshell.org/AllAboutGetline.

Answer 2

I modified my script to remove the getline in case anyone finds it useful.
#! /bin/gawk -f
function printFasta(header, seq, seq_line_max_chars) {
print ">" header
seq_line_max_chars = 80
start = 1
end = length(seq)
while (start <= end) {
print substr(seq, start, seq_line_max_chars)
start += seq_line_max_chars
}
}
BEGIN {
FS = ">"
min_prot_len = 400
max_prot_len = 700
}
NF > 1 {
if (sequence &&
length(sequence) >= min_prot_len &&
length(sequence) <= max_prot_len) {
printFasta(header, sequence)
}
}
{
if (!header) {
next
} else {
x_in_seq = match($0, "X")
if (!x_in_seq) {
gsub("*", "")
sequence = sequence $0
} else {
header = ""
}
}
}
END {
if (header) {
printFasta(header, sequence)
}
}