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Asked: 2019-02-19 09:38:45 +0800 CST

如何使用键从另一个数据中选择一个数据

  • 772

我有两个数据，1.txt 和 2.txt，我试图从 2.txt 中获取 1.txt 中的数据

1.txt 是

P13674
Q7Z4N8
O14683
Q9UHX1

和 2.txt 如下

>sp|Q96A73|P33MX_HUMAN Putative monooxygenase p33MONOX OS=Homo sapiens OX=9606 GN=KIAA1191 PE=1 SV=1
RNDDDDTSVCLGTRQCSWFAGCTNRTWNSSAVPLIGLPNTQDYKWVDRNSGLTWSGNDTCLYSCQNQTKGLLYQLFRNLFCSYGLTEAHGKWRCADASITNDKGHDGHRTPTWWLTGSNLTLSVNNSGLFFLCGNGVYKGFPPKWSGRCGLGYLVPSLTRYLTLNASQITNLRSFIHKVTPHR
>sp|P13674|P4HA1_HUMAN Prolyl 4-hydroxylase subunit alpha-1 OS=Homo sapiens OX=9606 GN=P4HA1 PE=1 SV=2
VECCPNCRGTGMQIRIHQIGPGMVQQIQSVCMECQGHGERISPKDRCKSCNGRKIVREKKILEVHIDKGMKDGQKITFHGEGDQEPGLEPGDIIIVLDQKDHAVFTRRGEDLFMCMDIQLVEALCGFQKPISTLDNRTIVITSHPGQIVKHGDIKCVLNEGMPIYRRPYEKGRLIIEFKVNFPENGFLSPDKLSLLEKLLPERKEVEE
>sp|Q7Z4N8|P4HA3_HUMAN Prolyl 4-hydroxylase subunit alpha-3 OS=Homo sapiens OX=9606 GN=P4HA3 PE=1 SV=1
MTEQMTLRGTLKGHNGWVTQIATTPQFPDMILSASRDKTIIMWKLTRDETNYGIPQRALRGHSHFVSDVVISSDGQFALSGSWDGTLRLWDLTTGTTTRRFVGHTKDVLSVAFSSDNRQIVSGSRDKTIKLWNTLGVCKYTVQDESHSEWVSCVRFSPNSSNPIIVSCGWDKLVKVWNLANCKLK
>sp|P04637|P53_HUMAN Cellular tumor antigen p53 OS=Homo sapiens OX=9606 GN=TP53 PE=1 SV=4
IQVVSRCRLRHTEVLPAEEENDSLGADGTHGAGAMESAAGVLIKLFCVHTKALQDVQIRFQPQL
>sp|P10144|GRAB_HUMAN Granzyme B OS=Homo sapiens OX=9606 GN=GZMB PE=1 SV=2
MQPILLLLAFLLLPRADAGEIIGGHEAKPHSRPYMAYLMIWDQKSLKRCGGFLIRDDFVLTAAHCWGSSINVTLGAHNIKEQEPTQQFIPVKRPIPHPAYNPKNFSNDIMLLQLERKAKRTRAVQPLRLPSNKAQVKPGQTCSVAGWGQTAPLGKHSHTLQEVKMTVQEDRKCES
>sp|Q9UHX1|PUF60_HUMAN Poly(U)-binding-splicing factor PUF60 OS=Homo sapiens OX=9606 GN=PUF60 PE=1 SV=1
MGKDYYQTLGLARGASDEEIKRAYRRQALRYHPDKNKEPGAEEKFKEIAEAYDVLSDPRKREIFDRYGEEGLKGSGPSGGSGGGANGTSFSYTFHGDPHAMFAEFFGGRNPFDTFFGQRNGEEGMDIDDPFSGFPMGMGGFTNVNFGRSRSAQEPARKKQDPPVTHDLRVSLEEIYSGCTKKMKISHK
>sp|Q06416|P5F1B_HUMAN Putative POU domain, class 5, transcription factor 1B OS=Homo sapiens OX=9606 GN=POU5F1B PE=5 SV=2
IVVKGHSTCLSEGALSPDGTVLATASHDGYVKFWQIYIEGQDEPRCLHEWKPHDGRPLSCLLFCDNHKKQDPDVPFWRFLITGADQNRELKMWCTVSWTCLQTIRFSPDIFSSVSVPPSLKVCLDLSAEYLILSDVQRKVLYVMELLQNQEEGHACFSSISEFLLTHPVLSFGIQVVSRCRLRHTEVLPAEEENDSLGADGTHGAGAMESAAGVLIKLFCVHTKALQDVQIRFQPQLNPDVVAPLPTHTAHEDFTFGESRPELGSEGLGSAAHGSQPDLRRIVELPAPADFLSLSSETKPKLMTPDAFMTPSASLQQITASPSSSSSGSSSSSSSSSSSLTAVSAMSSTSAVDPSLTRPPEELTLSPKLQLDGSLTMSSSGSLQASPRGLLPGLLPAPADKLTPKGPGQVPTATSALSLELQEVEP
>sp|O14683|P5I11_HUMAN Tumor protein p53-inducible protein 11 OS=Homo sapiens OX=9606 GN=TP53I11 PE=1 SV=2
MIHNYMEHLERTKLHQLSGSDQLESTAHSRIRKERPISLGIFPLPAGDGLLTPDAQKGGETPGSEQWKFQELSQPRSHTSLKVSNSPEPQKAVEQEDELSDVSQGGSKATTPASTANSDVATIPTDTPLKEENEGFVKVTDAPNKSEISKHIEVQVAQETRNVSTGSAENEEKSEVQAIIESTPELDMDKDLSGYKGSSTPTKGIENKAFDRNTESLFEELSSAGSGLIGDVDEGADLLGMGREVENLILENTQLLETKNALNIVKNDLIAKVDELTCEKDVLQGELEAVKQAKLKLEEKNRELEEELRKARAEAEDARQKAKDDDDSDIPTAQRKRFTRVEMARVLMERNQYKERLMELQEAVRWTEMIRASRENPAMQEKKRSSIWQFFSRLFSSSSNTTKKPEPPVNLKYNAPTSHVTPSVK

输出将如下所示

 >sp|P13674|P4HA1_HUMAN Prolyl 4-hydroxylase subunit alpha-1 OS=Homo sapiens OX=9606 GN=P4HA1 PE=1 SV=2
VECCPNCRGTGMQIRIHQIGPGMVQQIQSVCMECQGHGERISPKDRCKSCNGRKIVREKKILEVHIDKGMKDGQKITFHGEGDQEPGLEPGDIIIVLDQKDHAVFTRRGEDLFMCMDIQLVEALCGFQKPISTLDNRTIVITSHPGQIVKHGDIKCVLNEGMPIYRRPYEKGRLIIEFKVNFPENGFLSPDKLSLLEKLLPERKEVEE
>sp|Q7Z4N8|P4HA3_HUMAN Prolyl 4-hydroxylase subunit alpha-3 OS=Homo sapiens OX=9606 GN=P4HA3 PE=1 SV=1
MTEQMTLRGTLKGHNGWVTQIATTPQFPDMILSASRDKTIIMWKLTRDETNYGIPQRALRGHSHFVSDVVISSDGQFALSGSWDGTLRLWDLTTGTTTRRFVGHTKDVLSVAFSSDNRQIVSGSRDKTIKLWNTLGVCKYTVQDESHSEWVSCVRFSPNSSNPIIVSCGWDKLVKVWNLANCKLK
>sp|Q9UHX1|PUF60_HUMAN Poly(U)-binding-splicing factor PUF60 OS=Homo sapiens OX=9606 GN=PUF60 PE=1 SV=1
MGKDYYQTLGLARGASDEEIKRAYRRQALRYHPDKNKEPGAEEKFKEIAEAYDVLSDPRKREIFDRYGEEGLKGSGPSGGSGGGANGTSFSYTFHGDPHAMFAEFFGGRNPFDTFFGQRNGEEGMDIDDPFSGFPMGMGGFTNVNFGRSRSAQEPARKKQDPPVTHDLRVSLEEIYSGCTKKMKISHK
>sp|O14683|P5I11_HUMAN Tumor protein p53-inducible protein 11 OS=Homo sapiens OX=9606 GN=TP53I11 PE=1 SV=2
MIHNYMEHLERTKLHQLSGSDQLESTAHSRIRKERPISLGIFPLPAGDGLLTPDAQKGGETPGSEQWKFQELSQPRSHTSLKVSNSPEPQKAVEQEDELSDVSQGGSKATTPASTANSDVATIPTDTPLKEENEGFVKVTDAPNKSEISKHIEVQVAQETRNVSTGSAENEEKSEVQAIIESTPELDMDKDLSGYKGSSTPTKGIENKAFDRNTESLFEELSSAGSGLIGDVDEGADLLGMGREVENLILENTQLLETKNALNIVKNDLIAKVDELTCEKDVLQGELEAVKQAKLKLEEKNRELEEELRKARAEAEDARQKAKDDDDSDIPTAQRKRFTRVEMARVLMERNQYKERLMELQEAVRWTEMIRASRENPAMQEKKRSSIWQFFSRLFSSSSNTTKKPEPPVNLKYNAPTSHVTPSVK

我试图用这样的bash来做到这一点

cat 1.txt | grep -A 2.txt | sed -n -e '1,/>/ {/>/ !' > myout.txt
awk text-processing

6 个回答

  1. 如果你的序列真的只有一行，你可以简单地使用

    $ grep -f 1.txt 2.txt

    您正在使用 fasta 文件。所以我强烈建议使用专门为此而设计的现有程序，例如seqkit

    $ seqkit grep -r -f 1.txt 2.txt

    seqkit 的标准输出会将 60 个字符后的序列拆分为新行。如果您想让它们仍然在一行中，请将结果传递给seqkit seqlike this

    $ seqkit grep -r -f 1.txt 2.txt|seqkit seq -w0
    • 4
  2. Best Answer
    awk -F '|' 'FNR == NR { id[$1]; next } /^>/ && ($2 in id) { print; getline; print }' 1.txt 2.txt

    该awk程序作为一个独立的awk脚本，带有注释：

    BEGIN {
    # Set input field separator to a pipe character.
    FS = "|"
}

FNR == NR {
    # This line comes from the first file.
    # Add the protein ID to the id array as a key,
    # then immediately continue with the next cycle.

    id[$1]
    next
}

# The rest will only ever be executed while reading the second file.

/^>/ && ($2 in id) {
    # This line is a Fasta header line (starts with >),
    # and the ID found in the second field is an index in the id array.

    print;   # output the current line (Fasta header)
    getline; # get the next line
    print;   # output that line too (Fasta sequence)
}

    这假设所有的蛋白质序列总是只使用一行（即，您的 Fasta 文件中从来没有多行序列）。

    脚本首先读取包含蛋白质 ID 的文件，并记住这些文件。然后它从 Fasta 文件中读取并输出与从第一个文件中读取的蛋白质 ID 相关的标题和序列。

    • 3

  3. 尝试这个，

    # grep -A1 -F -f  1.txt 2.txt | grep -v '\-\-'


>sp|P13674|P4HA1_HUMAN Prolyl 4-hydroxylase subunit alpha-1 OS=Homo sapiens OX=9606 GN=P4HA1 PE=1 SV=2
VECCPNCRGTGMQIRIHQIGPGMVQQIQSVCMECQGHGERISPKDRCKSCNGRKIVREKKILEVHIDKGMKDGQKITFHGEGDQEPGLEPGDIIIVLDQKDHAVFTRRGEDLFMCMDIQLVEALCGFQKPISTLDNRTIVITSHPGQIVKHGDIKCVLNEGMPIYRRPYEKGRLIIEFKVNFPENGFLSPDKLSLLEKLLPERKEVEE
>sp|Q7Z4N8|P4HA3_HUMAN Prolyl 4-hydroxylase subunit alpha-3 OS=Homo sapiens OX=9606 GN=P4HA3 PE=1 SV=1
MTEQMTLRGTLKGHNGWVTQIATTPQFPDMILSASRDKTIIMWKLTRDETNYGIPQRALRGHSHFVSDVVISSDGQFALSGSWDGTLRLWDLTTGTTTRRFVGHTKDVLSVAFSSDNRQIVSGSRDKTIKLWNTLGVCKYTVQDESHSEWVSCVRFSPNSSNPIIVSCGWDKLVKVWNLANCKLK
>sp|Q9UHX1|PUF60_HUMAN Poly(U)-binding-splicing factor PUF60 OS=Homo sapiens OX=9606 GN=PUF60 PE=1 SV=1
MGKDYYQTLGLARGASDEEIKRAYRRQALRYHPDKNKEPGAEEKFKEIAEAYDVLSDPRKREIFDRYGEEGLKGSGPSGGSGGGANGTSFSYTFHGDPHAMFAEFFGGRNPFDTFFGQRNGEEGMDIDDPFSGFPMGMGGFTNVNFGRSRSAQEPARKKQDPPVTHDLRVSLEEIYSGCTKKMKISHK
>sp|O14683|P5I11_HUMAN Tumor protein p53-inducible protein 11 OS=Homo sapiens OX=9606 GN=TP53I11 PE=1 SV=2
MIHNYMEHLERTKLHQLSGSDQLESTAHSRIRKERPISLGIFPLPAGDGLLTPDAQKGGETPGSEQWKFQELSQPRSHTSLKVSNSPEPQKAVEQEDELSDVSQGGSKATTPASTANSDVATIPTDTPLKEENEGFVKVTDAPNKSEISKHIEVQVAQETRNVSTGSAENEEKSEVQAIIESTPELDMDKDLSGYKGSSTPTKGIENKAFDRNTESLFEELSSAGSGLIGDVDEGADLLGMGREVENLILENTQLLETKNALNIVKNDLIAKVDELTCEKDVLQGELEAVKQAKLKLEEKNRELEEELRKARAEAEDARQKAKDDDDSDIPTAQRKRFTRVEMARVLMERNQYKERLMELQEAVRWTEMIRASRENPAMQEKKRSSIWQFFSRLFSSSSNTTKKPEPPVNLKYNAPTSHVTPSVK

    • -F将 PATTERN 解释为固定字符串的列表

    • -f从 FILE 中获取模式，每行一个。

    • 2

  4. 从您的示例中，我假设您的文件2.txt包含 3 列，由 分隔，|并且只有第二列可以包含来自1.txt.

    fgrep -f <(sed 's/.*/|&|/`' 1.txt) 2.txt

    该sed命令添加了前导和尾随|，替换的输出<(...)用作 fgrep 的模式文件。

    • 2

  5. 使用 Perl5

    这将处理多行序列。

    process.pl

    获取 STDIN 上的键和 args 中的数据文件。

    use v5.10;
my %keys;
while (<STDIN>) {
  chomp;
  $keys{$_} = undef;
}
while ( <<>> ) {                  # read from args
  state $s = 0;                   # State; $s==1 for print
  if (/^>/) {                     # In header
    my $id = [split '\|',3]->[1]; #   get id
    $s = exists $keys{$id};       #   check for id in keys, set $s
  }
  print if $s;                    # check $s and print
}

    调用

    cat keys.txt | perl process.pl data.txt
    • 2

  6. 这就是join(1)程序的用途：

    $ join -t\| -1 1 -2 2 -o '2.1,2.2,2.3,2.4' <(sort 1.txt) <(sort -t\| -k2 2.txt)
>sp|O14683|P5I11_HUMAN Tumor protein p53-inducible protein 11 OS=Homo sapiens OX=9606 GN=TP53I11 PE=1 SV=2
>sp|P13674|P4HA1_HUMAN Prolyl 4-hydroxylase subunit alpha-1 OS=Homo sapiens OX=9606 GN=P4HA1 PE=1 SV=2
>sp|Q7Z4N8|P4HA3_HUMAN Prolyl 4-hydroxylase subunit alpha-3 OS=Homo sapiens OX=9606 GN=P4HA3 PE=1 SV=1
>sp|Q9UHX1|PUF60_HUMAN Poly(U)-binding-splicing factor PUF60 OS=Homo sapiens OX=9606 GN=PUF60 PE=1 SV=1

    此命令期望输入按相同的顺序排序，这就是我首先使用子命令执行此操作的原因。如果你有多个这样的查询和/或你没有使用 bash 作为 shell，最好先对文件进行排序，然后加入它们：

    sort 1.txt >1.sorted
sort -t\| -k2 2.txt >2.sorted
join -t\| -1 1 -2 2 -o '2.1,2.2,2.3,2.4' 1.sorted 2.sorted

    或者，更通用：

    # delimiter
d=\|
# left column
lc=1
# right column
rc=2
# output format
fmt=2.1,2.2,2.3,2.4

sort -t$d -k$lc 1.txt >1.sorted
sort -t$d -k$rc 2.txt >2.sorted
join -t$d -1 $lc -2 $rc -o $fmt 1.sorted 2.sorted
    • 0

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