Sequence retrieval from miRBase using miRBase sequence ids
1
0
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7.0 years ago

Hi everyone,

I have got a set of miRBase ids , I want to get its sequence from mirbase . I have downloaded mature microRNA sequences from miRBase my mirBase ids : 

miR1171
miR1436
miR1439
miR1446
miR1446a
miR156
miR156a
miR-34-5p
miR156a-3p
miR156a-5p
miR156ad
miR156b
miR156b-3p
miR156c
miR156c-3p
miR156d-3p
miR156e
miR156e-5p
miR156f
miR-1-5p
miR156f-3p
miR156f-5p
miR156g
miR156g-5p
miR156h
miR-35-3p
miR156i
miR156i-3p
miR156j

mature microRNA sequence from miRBase :

>cel-let-7-5p MIMAT0000001 Caenorhabditis elegans let-7-5p
UGAGGUAGUAGGUUGUAUAGUU
>cel-let-7-3p MIMAT0015091 Caenorhabditis elegans let-7-3p
CUAUGCAAUUUUCUACCUUACC
>cel-lin-4-5p MIMAT0000002 Caenorhabditis elegans lin-4-5p
UCCCUGAGACCUCAAGUGUGA
>cel-lin-4-3p MIMAT0015092 Caenorhabditis elegans lin-4-3p
ACACCUGGGCUCUCCGGGUACC
>cel-miR-1-5p MIMAT0020301 Caenorhabditis elegans miR-1-5p
CAUACUUCCUUACAUGCCCAUA
>cel-miR-1-3p MIMAT0000003 Caenorhabditis elegans miR-1-3p
UGGAAUGUAAAGAAGUAUGUA
>cel-miR-2-5p MIMAT0020302 Caenorhabditis elegans miR-2-5p
CAUCAAAGCGGUGGUUGAUGUG
>cel-miR-2-3p MIMAT0000004 Caenorhabditis elegans miR-2-3p
UAUCACAGCCAGCUUUGAUGUGC
>cel-miR-34-5p MIMAT0000005 Caenorhabditis elegans miR-34-5p
AGGCAGUGUGGUUAGCUGGUUG
>cel-miR-34-3p MIMAT0015093 Caenorhabditis elegans miR-34-3p
ACGGCUACCUUCACUGCCACCC
>cel-miR-35-5p MIMAT0020303 Caenorhabditis elegans miR-35-5p
UGCUGGUUUCUUCCACAGUGGUA
>cel-miR-35-3p MIMAT0000006 Caenorhabditis elegans miR-35-3p
UCACCGGGUGGAAACUAGCAGU

I want to get the result like:

>miR-34-5p
ACGGCUACCUUCACUGCCACCC
>miR-1-5p
CAUACUUCCUUACAUGCCCAUA
 miR-35-3p
UCACCGGGUGGAAACUAGCAGU

Please do help me on this regard

Thank you
miRNA RNA-Seq awk grep perl • 3.3k views
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download the data from mirbase ftp and then write a fast python script such as:

my_list = [miR1171, miR1436, miR1439, miR1446, miR1446a...] 
seq = ''

with open(sys.argv[1], 'r') as fasta:
    for line in fasta:
        line = line.rstrip('\n')
        if line.startswith('>'):
            if seq:
                if name in my_list:
                    print name + seq + '\n' 
                seq = ''
            name = line
        else:
            seq = seq + line
    if name in my_list:
        print name + seq + '\n'

It is almost done, complete it :).

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Or with shell's grep 

grep -A 1 -f IDs.txt miRBase.fa
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with this one liner .. I am able to fetch only one sequence as result I got this as output :

jinu@server:~$ grep -A 1 -f id.txt mature.fa

tae-miR9774 MIMAT0036985 Triticum aestivum miR9774 CAAGAUAUUGGGUAUUUCUGUC jinu@server:~$

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I am not really good with programming .. even though i tried but it ended with an errorr.. also I have 272 entries in my id list.. This is the result obtained :

jinu@server:~$ python 1.py mature.fa > 1_res File "1.py", line 1 my_list = [miR1171, miR1436, miR1439, miR1446, miR1446a, miR156 , miR156a, miR156a-3p, miR156a-5p, miR156ad, miR156b, miR156b-3p, miR156c, miR156c-3p, miR156d-3p, miR156e, miR156e-5p, miR156f, miR156f-3p, miR156f-5p, miR156g, miR156g-5p, miR156h, miR156i, miR156i-3p, miR156j, miR156j-3p, miR156k, miR156k-3p, miR156k-5p, miR156l, miR156l-5p, miR156q, miR156r, miR157a-5p, miR157b-3p, miR157d, miR157d-3p, miR159 , miR159a, miR159a-3p, miR159a-5p, miR159a.1 , miR159b, miR159b-3p, miR159c, miR159d, miR159e, miR159e-5p, miR159f, miR159h-3p, miR160 , miR160a-3p, miR160a-5p, miR160b, miR160c, miR160d, miR160e-5p, miR160g, miR160h, miR162 , miR162-3p , miR162a-3p, miR164 , miR164a, miR164b, miR164c, miR164c-5p, miR164d, miR164e, miR164e-5p, miR164g-3p, miR164h-5p, miR165a-3p, miR166 , miR166a, miR166a-3p, miR166b, miR166b-5p, miR166c-5p, miR166d-5p, miR166e, miR166e-3p, miR166e-5p, miR166g-3p, miR166g-5p, miR166h-3p, miR166h-5p, miR166i, miR166i-3p, miR166j, miR166j-3p, miR166k, miR166m, miR166n, miR166p, miR166u, miR167 , miR167a, miR167a-5p, miR167b, miR167b-3p, miR167b-5p, miR167c, miR167c-3p, miR167c-5p, miR167d, miR167d-3p, miR167d-5p, miR167f-3p, miR167f-5p, miR167h, miR167h-5p, miR167k, miR168 , miR168a, miR168a-3p, miR168a-5p, miR168b, miR169 , miR169a, miR169a-5p, miR169b-5p, miR169c, miR169d, miR169d-5p, miR169e, miR169e-5p, miR169f, miR169f.1 , miR169g, miR169h, miR169k, miR169l, miR169m, miR169o, miR169s, miR169u, miR169v, miR170-3p , miR171a, miR171a-3p, miR171b, miR171b-3p, miR171c, miR171c-3p, miR171d, miR171e, miR171f, miR171f-3p, miR171g, miR171h, miR171i, miR171k, miR172a, miR172a-3p, miR172a-5p, miR172b, miR172b-5p, miR172c, miR172c-3p, miR172c-5p, miR172d, miR172d-5p, miR172e-3p, miR172f, miR172g-3p, miR172j, miR172k, miR2118, miR319 , miR319a, miR319a-3p, miR319b, miR319c, miR319c-5p, miR319e, miR319g, miR319i, miR319p, miR319q, miR3630-3p, miR3711, miR390 , miR390.1, miR390a-3p, miR390a-5p, miR390b-3p, miR390c-5p, miR390d-3p, miR390e, miR393 , miR393-5p , miR393a, miR393a-3p, miR393a-5p, miR393b-5p, miR393h, miR394a, miR395a, miR395a-3p, miR395b, miR395c-3p, miR395d, miR395g, miR395h, miR395k, miR395t, miR396 , miR396-3p , miR396a, miR396a-3p, miR396a-5p, miR396b, miR396b-3p, miR396b-5p, miR396c, miR396c-3p, miR396d, miR396e, miR396f, miR396g-3p, miR396g-5p, miR396h, miR397 , miR397-5p , miR397a, miR397b, miR398 , miR398a-3p, miR398a-5p, miR398b, miR398b-3p, miR398f, miR399 , miR399a, miR399b, miR399c, miR399d, miR399e, miR399f, miR399g, miR399g-3p, miR399g-5p, miR399i, miR399j, miR403-3p , miR403-5p , miR403a, miR408 , miR408-3p , miR408-5p , miR408a, miR408a-3p, miR408b, miR408d, miR408e, miR473 , miR477a, miR477a-5p, miR477b, miR477d, miR477e, miR477h, miR477i, miR479 , miR482b-3p, miR482c, miR5072, miR5141, miR5174d-3p, miR530 , miR530-5p , miR530a, miR5368, miR5532, miR5538, miR6167, miR6173, miR6478, miR8175, miR827, miR827-3p, miR827a, miR838-3p, miR845, miR858, miR858a, miR858b, miR894, miR9773, miR9774] ^ SyntaxError: invalid syntax jinu@server:~$

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7.0 years ago

command: 

$ grep --no-group-separator -A 1 -f ids.txt sequences.txt | sed '/^>/ s/\(>\).*\(miR.*\)$/\1\2/'

output:

>miR-1-5p
CAUACUUCCUUACAUGCCCAUA
>miR-34-5p
AGGCAGUGUGGUUAGCUGGUUG
>miR-35-3p
UCACCGGGUGGAAACUAGCAGU

Input (copy/pasted from OP):

$ cat ids.txt 
miR1171
miR1436
miR1439
miR1446
miR1446a
miR156
miR156a
miR-34-5p
miR156a-3p
miR156a-5p
miR156ad
miR156b
miR156b-3p
miR156c
miR156c-3p
miR156d-3p
miR156e
miR156e-5p
miR156f
miR-1-5p
miR156f-3p
miR156f-5p
miR156g
miR156g-5p
miR156h
miR-35-3p
miR156i
miR156i-3p
miR156

and

$ cat sequences.txt 
>cel-let-7-5p MIMAT0000001 Caenorhabditis elegans let-7-5p
UGAGGUAGUAGGUUGUAUAGUU
>cel-let-7-3p MIMAT0015091 Caenorhabditis elegans let-7-3p
CUAUGCAAUUUUCUACCUUACC
>cel-lin-4-5p MIMAT0000002 Caenorhabditis elegans lin-4-5p
UCCCUGAGACCUCAAGUGUGA
>cel-lin-4-3p MIMAT0015092 Caenorhabditis elegans lin-4-3p
ACACCUGGGCUCUCCGGGUACC
>cel-miR-1-5p MIMAT0020301 Caenorhabditis elegans miR-1-5p
CAUACUUCCUUACAUGCCCAUA
>cel-miR-1-3p MIMAT0000003 Caenorhabditis elegans miR-1-3p
UGGAAUGUAAAGAAGUAUGUA
>cel-miR-2-5p MIMAT0020302 Caenorhabditis elegans miR-2-5p
CAUCAAAGCGGUGGUUGAUGUG
>cel-miR-2-3p MIMAT0000004 Caenorhabditis elegans miR-2-3p
UAUCACAGCCAGCUUUGAUGUGC
>cel-miR-34-5p MIMAT0000005 Caenorhabditis elegans miR-34-5p
AGGCAGUGUGGUUAGCUGGUUG
>cel-miR-34-3p MIMAT0015093 Caenorhabditis elegans miR-34-3p
ACGGCUACCUUCACUGCCACCC
>cel-miR-35-5p MIMAT0020303 Caenorhabditis elegans miR-35-5p
UGCUGGUUUCUUCCACAGUGGUA
>cel-miR-35-3p MIMAT0000006 Caenorhabditis elegans miR-35-3p
UCACCGGGUGGAAACUAGCAGU
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Thank you so much for your prompt response .. But still i am able to fetch only one sequence sequence as result.. I don't know whats wrong :(

Result obtained :

jinu@server:~$ grep --no-group-separator -A 1 -f id.txt mature.txt | sed '/^>/ s/(>).(miR.)$/\1\2/'

miR9774 CAAGAUAUUGGGUAUUUCUGUC

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could you please host part of your data (i.e to know original format of your file- 10 lines should suffice for this) elsewhere and share a link with the forum?

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jinu@server:~$ cat id.txt miR1171 miR1436 miR1439 miR1446 miR1446a miR156 miR156a miR156a-3p miR156a-5p miR156ad miR156b miR156b-3p miR156c miR156c-3p miR156d-3p miR156e miR156e-5p miR156f miR156f-3p miR156f-5p miR156g miR156g-5p miR156h miR156i miR156i-3p miR156j miR156j-3p miR156k miR156k-3p miR156k-5p miR156l miR156l-5p miR156q miR156r miR157a-5p miR157b-3p miR157d miR157d-3p miR159 miR159a miR159a-3p miR159a-5p miR159a.1 miR159b

cat mature.txt

ame-miR-9882 MIMAT0037286 Apis mellifera miR-9882 AGCGAUGAGACUAGAUCUUGGC ame-miR-9883 MIMAT0037287 Apis mellifera miR-9883 UUCGGGCGGGCUCGGGCGAGA ame-miR-9884 MIMAT0037288 Apis mellifera miR-9884 UCGGUCGGUGACGAAGCUCCC ame-miR-9885 MIMAT0037289 Apis mellifera miR-9885 UCGGCAAUGAUCGGACGUGGUC ame-miR-9886 MIMAT0037290 Apis mellifera miR-9886 UAGGCGUCACGUUGUGGAACG ame-miR-9887 MIMAT0037291 Apis mellifera miR-9887 AAGGGCUGGGAAGGGCGGAG ame-miR-2b MIMAT0037292 Apis mellifera miR-2b UCAUCAAAGCUGGCUGUGAUAUGA ame-miR-9888 MIMAT0037293 Apis mellifera miR-9888 UGGUGGUCAAGCAAGUAGAACGUU ame-miR-9889 MIMAT0037294 Apis mellifera miR-9889 AGUGUCGAGCCGAAGAAACGCGC ame-miR-9890 MIMAT0037295 Apis mellifera miR-9890 UUCGGAAGAAUGUAGAGAAAAAG ame-miR-9891 MIMAT0037296 Apis mellifera miR-9891 UCGGCUUCGUCCUCGUCGUCG ame-miR-9892 MIMAT0037297 Apis mellifera miR-9892 UGACGCGAUUGUGGAAAUCG ame-miR-9893 MIMAT0037298 Apis mellifera miR-9893 UUAUGAUCUGGAAUACUAGG ame-miR-9894 MIMAT0037299 Apis mellifera miR-9894 GAGGGCGAGGAGAGGAGGAA ame-miR-9895 MIMAT0037300 Apis mellifera miR-9895 UCGUGUCCGUUUCUCGUUUCGA ame-miR-9896 MIMAT0037301 Apis mellifera miR-9896 ACAAUAAUCGGACACAAUCGGC ame-miR-3478 MIMAT0037302 Apis mellifera miR-3478 CACACCGGACGAGAUUUCAU cre-miR9897-5p MIMAT0037303 Chlamydomonas reinhardtii miR9897-5p UACCGGGCGUGGGGAGGGCAGG cre-miR9897-3p MIMAT0037304 Chlamydomonas reinhardtii miR9897-3p UUACGGCUCCUUCUUAUCGGC

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Please post the original format or format OP proper

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cat mature.fa

enter link description here

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enter link description here

result of cat mature.txt

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result of cat id.txt enter link description here

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not sure, why it is not working on your machine. With the output you posted, i reconstructed the ids and sequences:

$ cat ids.txt 
miR-9887
miR9897-5p

$ cat test.txt 
>ame-miR-9882 MIMAT0037286 Apis mellifera miR-9882 
AGCGAUGAGACUAGAUCUUGGC 
>ame-miR-9883 MIMAT0037287 Apis mellifera miR-9883 
UUCGGGCGGGCUCGGGCGAGA 
>ame-miR-9884 MIMAT0037288 Apis mellifera miR-9884 
UCGGUCGGUGACGAAGCUCCC 
>ame-miR-9885 MIMAT0037289 Apis mellifera miR-9885 
UCGGCAAUGAUCGGACGUGGUC 
>ame-miR-9886 MIMAT0037290 Apis mellifera miR-9886 
UAGGCGUCACGUUGUGGAACG 
>ame-miR-9887 MIMAT0037291 Apis mellifera miR-9887 
AAGGGCUGGGAAGGGCGGAG 
>ame-miR-2b MIMAT0037292 Apis mellifera miR-2b 
UCAUCAAAGCUGGCUGUGAUAUGA 
>ame-miR-9888 MIMAT0037293 Apis mellifera miR-9888 
UGGUGGUCAAGCAAGUAGAACGUU 
>ame-miR-9889 MIMAT0037294 Apis mellifera miR-9889 
AGUGUCGAGCCGAAGAAACGCGC 
>ame-miR-9890 MIMAT0037295 Apis mellifera miR-9890 
UUCGGAAGAAUGUAGAGAAAAAG 
>ame-miR-9891 MIMAT0037296 Apis mellifera miR-9891 
UCGGCUUCGUCCUCGUCGUCG 
>ame-miR-9892 MIMAT0037297 Apis mellifera miR-9892 
UGACGCGAUUGUGGAAAUCG 
>ame-miR-9893 MIMAT0037298 Apis mellifera miR-9893 
UUAUGAUCUGGAAUACUAGG 
>ame-miR-9894 MIMAT0037299 Apis mellifera miR-9894 
GAGGGCGAGGAGAGGAGGAA 
>ame-miR-9895 MIMAT0037300 Apis mellifera miR-9895 
UCGUGUCCGUUUCUCGUUUCGA 
>ame-miR-9896 MIMAT0037301 Apis mellifera miR-9896 
ACAAUAAUCGGACACAAUCGGC 
>ame-miR-3478 MIMAT0037302 Apis mellifera miR-3478 
CACACCGGACGAGAUUUCAU 
>cre-miR9897-5p MIMAT0037303 Chlamydomonas reinhardtii miR9897-5p 
UACCGGGCGUGGGGAGGGCAGG 
>cre-miR9897-3p MIMAT0037304 Chlamydomonas reinhardtii miR9897-3p 
UUACGGCUCCUUCUUAUCGGC

output:

$ grep --no-group-separator -A 1 -f ids.txt test.txt | sed '/^>/ s/\(>\).*\(miR.*\)$/\1\2/'
>miR-9887 
AAGGGCUGGGAAGGGCGGAG 
>miR9897-5p 
UACCGGGCGUGGGGAGGGCAGG
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In addition, in your code, there is sed '/^>/ s/(>).(miR.)$/\1\2/'. It should be sed '/^>/ s/\(>\).*\(miR.*\)$/\1\2/'. Is it copy/paste mistake or is the code problem?

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I am sorry...Its just a copy paste mistake :(

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