Posso usar variável em um arquivo .csv no loop for?

Question

Estou tentando substituir esses números "A00002 X53307 BB145968 CAA42669 V00181 AH002406 HQ844023" no loop a seguir, com uma nova lista de números. Mas minha nova lista é um arquivo .CSV e existem centenas de números. Minha pergunta é, posso ler o arquivo .CSV diretamente e fazê-lo funcionar como a lista no loop for?

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

O arquivo .csv tem esta aparência:

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

    

Answer 1

Se o @Mark solicitar que o arquivo CSV contenha um valor por linha, você poderá fazer isso trivialmente substituindo sua lista inicial por uma substituição de comando:

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

    

Answer 2

Se você sabe a quais valores substituirá "A00002 X53307 BB145968 CAA42669 V00181 AH002406 HQ844023" para fazer isso:

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

Explicação do comando Sed:

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

O que este comando está fazendo é: Substitua X53307 por NewValue diretamente no arquivo $ CSV.

    

Answer 3

Você está esquecendo duas coisas aqui:

1. A expansão de sequência na sua instrução Curl produz saída.
2. Você pode usar o arquivo CSV para o controle de entrada, como sugerido por @John.

Assim, você não precisa substituir os valores da string, basta sobrescrevê-los.

Antigo:

<?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>

Novo:

<?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>