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for 루프에서 .csv 파일의 변수를 사용할 수 있나요?

tag-icon • tag-icon scripting variable csv
for 루프에서 .csv 파일의 변수를 사용할 수 있나요?

다음 for 루프의 "A00002 X53307 BB145968 CAA42669 V00181 AH002406 HQ844023" 숫자를 새로운 숫자 목록으로 바꾸려고 합니다. 하지만 내 새 목록은 수백 개의 숫자가 포함된 .CSV 파일입니다. 제 질문은 .CSV 파일을 직접 읽고 for 루프에서 목록으로 작동하게 할 수 있습니까?입니다.

for ACC in A00002 X53307 BB145968 CAA42669 V00181  AH002406  HQ844023
do
   echo -n -e "$ACC\t"
   curl -s "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=${ACC}&rettype=fasta&retmode=xml" |\
   grep TSeq_taxid |\
   cut -d '>' -f 2 |\
   cut -d '<' -f 1 |\
   tr -d "\n"
   echo
 done

.csv 파일은 다음과 같습니다.

WP_004064712.1
WP_023555236.1
WP_051593235.1
KAJ52037.1
WP_012103448.1
WP_049740904.1
WP_003346264.1
WP_026134014.1
WP_051870539.1
AKF93952.1
XP_008397367.1
XP_014896959.1
XP_007567109.1
XP_014847432.1
EHG27035.1
EGX75147.1
WP_033630878.1

답변1

@Mark가 CSV 파일에 한 줄에 하나의 값을 포함해야 하는 경우 초기 목록을 명령 대체로 바꾸면 쉽게 이를 수행할 수 있습니다.

for ACC in `cat csvfile`
do 
  ...
done

답변2

"A00002 X53307 BB145968 CAA42669 V00181 AH002406 HQ844023"을 어떤 값으로 바꾸려는지 알고 있는 경우 다음을 수행할 수 있습니다.

CSV=`cat csvfile`
for LINE in $CSV
do 
  sed -i "s/A00002/NewValue/g" $CSV
  sed -i "s/X53307/NewValue/g" $CSV
  ...
done

sed 명령 설명:

sed -i "s/X53307/NewValue/g"$CSV

이 명령의 목적은 $CSV 파일에서 X53307을 NewValue로 직접 바꾸는 것입니다.

답변3

여기서 두 가지를 잊고 계십니다.

  1. Curl 문의 문자열 확장은 출력을 생성합니다.
  2. @John의 제안에 따라 CSV 파일을 입력 컨트롤로 사용할 수 있습니다.

따라서 문자열 값을 바꿀 필요 없이 덮어쓰기만 하면 됩니다.

오래된:

<?xml version="1.0"?>
 <!DOCTYPE TSeqSet PUBLIC "-//NCBI//NCBI TSeq/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_TSeq.dtd">
 <TSeqSet>
<TSeq>
  <TSeq_seqtype value="nucleotide"/>
  <TSeq_gi>39899</TSeq_gi>
  <TSeq_accver>X53307.1</TSeq_accver>
  <TSeq_taxid>1423</TSeq_taxid>
  <TSeq_orgname>Bacillus subtilis</TSeq_orgname>
  <TSeq_defline>Bacillus subtilis epr gene for a novel serine protease</TSeq_defline>
  <TSeq_length>2521</TSeq_length>
  <TSeq_sequence>GTTAACAGGATATCCGAGCTTATCGGCCCACTCGTTCCCAAACACACTCGCCATGAAATCAGCATACCCCGGAATCGGCAAGCTCGTTAAAATCAAGAAGACAGACCCGATAATAATCAGCGGCATGGACTGGATAATTCCGTCACGCAAAGCGCTGAGATGCCGCTGCCCGGCAATTTTCCCGGCGACAGGCATTATTTTTTCCTCCATCACCCGAGTGAATGTGCTCATCTTAAAAACCCCCTTTTCTCATTGCTTTGTGAACAACAACCTCCGCAATGTTTTCTTTATCTTATTTTGAAAACGCTTAGAAATTCATTTGGAAAATTTCCTCTTCATGCGGAAAAAATCTGCATTTTGCTAAACAACCCTGCCCATGAAAATTTTTTCCTTCTTACTATTAATCTCTCTTTTTTTCTCCGATATATATATCAAACATCATAGAAAAAGGAGATGAATCATGAAAAACATGTCTTGCAAACTTGTTGTATCAGTCACTCTGTTTTTCAGTTTTCTCACCATAGGCCCTCTCGCTCATGCGCAAAACAGCAGCGAGAAAGAGGTTATTGTGGTTTATAAAAACAAGGCCGGAAAGGAAACCATCCTGGACAGTGATGCTGATGTTGAACAGCAGTATAAGCATCTTCCCGCGGTAGCGGTCACAGCAGACCAGGAGACAGTAAAAGAATTAAAGCAGGATCCTGATATTTTGTATGTAGAAAACAACGTATCATTTACCGCAGCAGACAGCACGGATTTCAAAGTGCTGTCAGACGGCACTGACACCTCTGACAACTTTGAGCAATGGAACCTTGAGCCCATTCAGGTGAAACAGGCTTGGAAGGCAGGACTGACAGGAAAAAATATCAAAATTGCCGTCATTGACAGCGGGATCTCCCCCCACGATGACCTGTCGATTGCCGGCGGGTATTCAGCTGTCAGTTATACCTCTTCTTACAAAGATGATAACGGCCACGGAACACATGTCGCAGGGATTATCGGAGCCA
AGCATAACGGCTACGGAATTGACGGCATCGCACCGGAAGCACAAATATACGCGGTTAAAGCGCTTGATCAGAACGGCTCGGGGGATCTTCAAAGTCTTCTCCAAGGAATTGACTGGTCGATCGCAAACAGGATGGACATCGTCAATATGAGCCTTGGCACGACGTCAGACAGCAAAATCCTTCATGACGCCGTGAACAAAGCATATGAACAAGGTGTTCTGCTTGTTGCCGCAAGCGGTAACGACGGAAACGGCAAGCCAGTGAATTATCCGGCGGCATACAGCAGTGTCGTTGCGGTTTCAGCAACAAACGAAAAGAATCAGCTTGCCTCCTTTTCAACAACTGGAGATGAAGTTGAATTTTCAGCACCGGGGACAAACATCACAAGCACTTACTTAAACCAGTATTATGCAACGGGAAGCGGAACATCCCAAGCGACACCGCACGCCGCTGCCATGTTTGCCTTGTTAAAACAGCGTGATCCTGCCGAGACAAACGTCCAGCTTCGCGAGGAAATGCGGAAAAACATCGTTGATCTTGGTACCGCAGGCCGCGATCAGCAATTTGGCTACGGCTTAATCCAGTATAAAGCACAGGCAACAGATTCAGCGTACGCGGCAGCAGAGCAAGCGGTGAAAAAAGCGGAACAAACAAAAGCACAAATCGATATCAACAAAGCGCGAGAACTCATCAGCCAGCTGCCGAACTCCGACGCCAAAACTGCCCTGCACAAAAGACTGGATAAAGTACAGTCATACAGAAATGTAAAAGATGCGAAAGACAAAGTCGCAAAGGCAGAAAAATATAAAACACAGCAAACCGTTGACACAGCACAAACTGCCATCAACAAGCTGCCAAACGGAACAGACAAAAAGAACCTTCAAAAACGCTTAGACCAAGTAAAACGATACATCGCGTCAAAGCAAGCGAAAGACAAAGTTGCGAAAGCGGAAAAAAGCAAAAAGAAAACAGATGTGGACAGCGCACAATCAGCAATTGGCAAGCTGCCTGCAAGTTCAGAAAA
AACGTCCCTGCAGAAACGCCTTAACAAAGTGAAGAGCACCAATTTGAAGACGGCACAGCAATCCGTATCTGCGGCTGAAAAGAAATCAACTGATGCAAATGCGGCAAAAGCACAATCAGCCGTCAATCAGCTTCAAGCAGGCAAGGACAAAACGGCATTGCAAAAACGGTTAGACAAAGTGAAGAAAAAGGTGGCGGCGGCTGAAGCAAAAAAAGTGGAAACTGCAAAGGCAAAAGTGAAGAAAGCGGAAAAAGACAAAACAAAGAAATCAAAGACATCCGCTCAGTCTGCAGTGAATCAATTAAAAGCATCCAATGAAAAAACAAAGCTGCAAAAACGGCTGAACGCCGTCAAACCGAAAAAGTAACCAAAAACCTTTAAGATTTGCATTCCAAGTCTTAAAGGTTTTTTTCATTCTAAGAACACCACACACAACCTTTTTCCCATCCATTGTACAGGCTTTTCATACTATTGCTATACAGCCATGAAC</TSeq_sequence>
</TSeq>
</TSeqSet>

새로운:

<?xml version="1.0"?>
 <!DOCTYPE TSeqSet PUBLIC "-//NCBI//NCBI TSeq/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_TSeq.dtd">
 <TSeqSet>
<TSeq>
  <TSeq_seqtype value="protein"/>
  <TSeq_gi>490166065</TSeq_gi>
  <TSeq_accver>WP_004064712.1</TSeq_accver>
  <TSeq_taxid>97253</TSeq_taxid>
  <TSeq_orgname>Eubacterium plexicaudatum</TSeq_orgname>
  <TSeq_defline>hypothetical protein [Eubacterium plexicaudatum]</TSeq_defline>
  <TSeq_length>1508</TSeq_length>
  <TSeq_sequence>MKKSFMTRVLAVSLSAAMAFSMSSASNLVTASAASTVNLKTTFKTLKVGQTYKLTLKKNTLNWKITKVQTTNKKICTVYGKTASSVMLKGKGVGRAKISVKVKTTKRKYPKNIKIMKCTANVKAADGSGTTDEFKVTSATASSNTEVRVMFSKAIDAAEMTNFTVSDSVTVSKAELSEDKKSVLLTIAGAEYGKNYELTVNGIKVAGKEQAAQKVTFTTPSASEKYPTTLEAKDPVLASDGHSQTLVTFTIKDANGNPITDKGVEVAFATSLGKFAEQRVSIQNGVATVMYTSEALMETQTSAITATVVESTDNQELMGLSATSSITLTPNPDEFNIVPIITSITAPTADRVIAYFNEKVSASDFKTASGKLDHSKFTANVAWGFDNGFDELGNRLVGRSNVVGILDVPGSDNALQLLVDRPMTDNTNISVTFENKTKASSLVSASNTVYTKLTDAHQPSVLTAKGDGLRTVVVNFSEAVLPTAYCDNVETDKKNANQTLFAADNIENYLIDGKPLSYWGVTEVKTPDSETPDDTSSNLKKESSKNDATKTGSEKPGEIQVGSYKDGEDNRHVVTIKLSRERFLEPGTHSMTISNVGDWAAKTDRERNIVNTQTFDFVVENNDVIPTFEVEEQSPEQWLLKFNSDIEPVSETLTTPNSQYSDQASILKLQELVGSTWVDISDSDAAGKNPIRVSQVDDTRNYVVEVRKDWTEVYNTSSTKQNYFNKQLRLHIDAGKIVNIANNKQNGTIDIPLDGTIMRTPDVVSPEIGEVTPAEDTSGNVLDSYNVKLSEPVKLSDGTGGAGGANGEGLTPSQIQSANGSNSNNQGVPMPSAQFIRVDNGQTVEGIITSNVFVDAYDTTINIAPESALSAGKWRLVISSISDDYGNTASTVAHEIDVTQESVTTDFKIVWAAVSDQQTYAEDHIGVERGRYIFVKFSKPVTMTGNSVNAGVTGNYTVNGATLPTGTQIRANIVGYDDHDAVTDSVTIMLPTGNVNAGWGATGDYTV
SGKNAMLNVSRAITATTGENLSNGGLIRIPFQYGSATEDTGYNDYNDSLTALTDAVWGNYRSETRAGYDNLRDYYKALKSALENDKYRRVVLTAPLDLSNPDDNPNEDQKDAVAVFGRSHTLTIKRAVDFDLNGNNITGNVVISTTDAVNRIKLHSSKERAHIYGYANNKDNVATLTVNAGSAKEFLLDNVEVHETDKGNALNINDTWKASFVNNGVIDGKIRITDTNGCGFKNENTTDGFTNRTRFIIDSTGDVNLKGDLSALRNLTDEFGITVNQAAKLSFGVDSKDETTPCDISGVKIVVRGPGARVIFTPVATTTADTALTAEADNVRVQLSQANSGSGKIQFFTDRGGKIVAVDKDNKEVTSDSKDAVKISSDDIKVTGIQKALENLDVQTGVITDGKVDSTVTISCGAISGGSYNIEELAKNIKKAEFEYKGKPDTTGIVANYSLLSTNLLKKDSTHIWPKDNWTDQKDDVSDTIRVTLAYDGYTMVKYIKVTRV</TSeq_sequence>
</TSeq>
</TSeqSet>

답변4

다음은 전체 CSV 파일을 메모리로 읽는 것을 방지하고 사후 처리를 약간 단순화하는 리팩토링입니다.

# Use lower case for private variables
# and https://mywiki.wooledge.org/DontReadLinesWithFor
while read -r acc; do 
   curl -s "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=${acc}&rettype=fasta&retmode=xml" |
   # Run a single awk script for extraction and formatting
   awk -v acc="$acc" '/TSeq_taxid/ {
      sub(/>.*/, ""); sub(/.*</, ""); print acc "\t" $0 }'
done <csvfile

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