除非回荡，否则尴尬仅在循环时才在内部印刷第一行，理论解释

Question

我有一个尴尬命令，该命令在循环中输出线模式的结果：

clinvar_db=$1
output_file=$2
if [ -f "$output_file" ]; then
  rm "$output_file"
fi
zcat < "$clinvar_db" | grep -v '^#' | while read line; do
  chr=`echo $line | awk '{print $1}' | tr -d '[:space:]'`
  pos=`echo $line | awk '{print $2}' | tr -d '[:space:]'`

  clnrevstat=`echo $line | sed -e 's/.*CLNREVSTAT=(.*);CLNSIG.*/1/' | cut -d';' -f1`
  ref_all=`echo $line | awk '{print $4}' | tr -d '[:space:]'`
  alt_all=`echo $line | awk '{print $5}' | tr -d '[:space:]'`
  effect=`echo $line | sed -e 's/.*MC=(.*);.*/1/' | cut -d';' -f1 | cut -d'|' -f2`
  ref_length=`printf $ref_all | wc -c | tr -d '[:space:]'`
  alt_length=`printf $alt_all | wc -c | tr -d '[:space:]'`
  if [ "$ref_length" -ne "$alt_length " ] || [ "$effect" == 'frameshift_variant' ] || [ "$effect" == 'nonsense' ] || [ "$effect" == 'splice_acceptor_variant' ] || [ "$effect" == 'splice_donor_variant' ]; then
    var_effect='lof'
  elif [ "$effect" == 'missense_variant' ]; then
    var_effect='miss'
  elif [ "$effect" == 'synonymous_variant' ]; then
    var_effect='syn'
  elif [ "$effect" == 'intron_variant' ] || [ "$effect" == '3_prime_UTR_variant' ]; then
    var_effect='intron'
  else
    var_effect='NA'
  fi
  if [ "$clnrevstat" == 'criteria_provided,_conflicting_interpretations' ] || [ "$clnrevstat" == 'criteria_provided,_single_submitter' ]; then
    clnstar=1
  elif [ "$clnrevstat" == 'no_assertion_criteria_provided' ] || [ "$clnrevstat" == 'no_assertion_provided' ] || [ "$clnrevstat" == 'no_interpretation_for_the_single_variant' ]; then
    clnstar=0
  elif [ "$clnrevstat" == 'criteria_provided,_multiple_submitters,_no_conflicts' ]; then
    clnstar=2
  elif [ "$clnrevstat" == 'reviewed_by_expert_panel' ]; then
    clnstar=3
  elif [ "$clnrevstat" == 'practice_guideline' ]; then
    clnstar=2
  else
    clnstar=NA
  fi
  awk -v OFS='t' -v chr="$chr" -v pos="$pos" -v ref="$ref_all" -v alt="$alt_all" -v var_effect="$var_effect" -v clnstar="$clnstar" '{print chr,pos,".",ref,alt,".",".",".",var_effect,clnstar}'
done

此一遍又一遍地输出相同的(第一(行：

1   949422  .   G   A   .   .   .   miss    1
1   949422  .   G   A   .   .   .   miss    1
1   949422  .   G   A   .   .   .   miss    1
1   949422  .   G   A   .   .   .   miss    1
1   949422  .   G   A   .   .   .   miss    1
1   949422  .   G   A   .   .   .   miss    1
1   949422  .   G   A   .   .   .   miss    1
# ...

如果我在上次awk

之前添加了echo

# ... rest of my script ...
  echo  | awk -v OFS='t' -v chr="$chr" -v pos="$pos" -v ref="$ref_all" -v alt="$alt_all" -v var_effect="$var_effect" -v clnstar="$clnstar" '{print chr,pos,".",ref,alt,".",".",".",var_effect,clnstar}'
# ... rest of my script ...

输出：

1   949422  .   G   A   .   .   .   miss    1
1   949502  .   C   T   .   .   .   miss    1
1   949523  .   C   T   .   .   .   lof 0
1   949559  .   C   T   .   .   .   miss    1
1   949597  .   C   T   .   .   .   syn 1
1   949608  .   G   A   .   .   .   miss    1
1   949635  .   G   A   .   .   .   miss    1
1   949656  .   G   A   .   .   .   miss    1
1   949696  .   C   CG  .   .   .   lof 0
# ...

它解决了问题，但我想从您那里知道专家，为什么！每个迭代都不应该这样做一次吗？我已经在这里和网络搜索过，但我自己无法弄清楚...

预先感谢您的任何帮助！

Answer 1

当您不回声调用awk时，它是从与while read循环相同的管道中读取的。while循环读取第一行，awk读取其余的所有内容。