vi regex: Find specific chromosomes and their fragments containing KSP protein fragments

Question

There is a fasta file of a protein sequence, and I want to find chromosome 2 or 5 containing three amino acids of KSP. How do I write a pattern string.

Here is a brief overview of the fasta file:

>AT1G05230.1
MFEPNMLLAAMNNADSNNHNYNHEDNNNEGFLRDDEFDSPNTKSGSENQEGGSGNDQDPLHPNKKKRYHRHTQLQIQEME
. . . .
DFLRDENSRNEWDILSNGGVVQEMAHIANGRDTGNCVSLLRVNSANSSQSNMLILQESCTDPTASFVIYAPVDIVAMNIV
LNGGDPDYVALLPSGFAILPDGNANSGAPGGDGGSLLTVAFQILVDSVPTAKLSLGSVATVNNLIACTVERIKASMSCET
A*

>AT1G05230.2
MFEPNMLLAAMNNADSNNHNYNHEDNNNEGFLRDDEFDSPNTKSGSENQEGGSGNDQDPLHPNKKKRYHRHTQLQIQEME
. . . . . .
DFLRDENSRNEWDILSNGGVVQEMAHIANGRDTGNCVSLLRVNSANSSQSNMLILQESCTDPTASFVIYAPVDIVAMNIV
LNGGDPDYVALLPSGFAILPDGNANSGAPGGDGGSLLTVAFQILVDSVPTAKLSLGSVATVNNLIACTVERIKASMSCET
A*

>AT2G35940.1
MAAYFHGNPPEISAGSDGGLQTLILMNPTTYVQYTQQDNDSNNNNNSNNSNNNNTNTNTNNNNSSFVFLDSHAPQPNASQ
..........
....KSP......TNYHMNPNHNGDLEGVTGMQGSPKRLRTSDETMMQPINADFSSNEKLTMKILEERQGIRSDGGYPFM
..........
NGGSSTTTAHSSAAAAAAYNGMNIQNQKRYVAQLLPDFVA*

>AT2G35940.2
MAAYFHGNPPEISAGSDGGLQTLILMNPTTYVQYTQQDNDSNNNNNSNNSNNNNTNTNTNNNNSSFVFLDSHAPQPNASQ
................................................................................
RAWLFEHFLHPYPKDSDKHMLAKQTGLTRSQVSNWFINARVRLWKPMVEEMYMEEMKEQAKNMGSMEKTPLDQSNEDSAS
.....KSP..................EGVTGMQGSPKRLRTSDETMMQPINADFSSNEKLTMKILEERQGIRSDGGYPFM
................................................................................
NGGSSTTTAHSSAAAAAAYNGMNIQNQKRYVAQLLPDFVA*

>AT3G03660.1
MDQEQTPHSPTRHSRSPPSSASGSTSAEPVRSRWSPKPEQILILESIFHSGMVNPPKEETVRIRKMLEKFGAVGDANVFY
................................................................................
VPLPTDEFGFLMHSLQHGEAYFLVPRQT*

>AT3G11260.1
MSFSVKGRSLRGNNNGGTGTKCGRWNPTVEQLKILTDLFRAGLRTPTTDQIQKISTELSFYGKIESKNVFYWFQNHKARE
................................................................................
PYSSCGAEMEHPPPLDLRLSFL*

>AT3G61890.1
MEEGDFFNCCFSEISSGMTMNKKKMKKSNNQKRFSEEQIKSLELIFESETRLEPRKKVQVARELGLQPRQVAIWFQNKRA
...KSP..........................................................................
RLDQGSVLCNDGDYNNNIKTEYFGFEEETDHELMNIVEKADDSCLTSSENWGGFNSDSLLDQSSSNYPNWWEFWS*

................................................................................
(lots of sequences)
................................................................................

>AT5G11060.1
MAFHNNHFNHFTDQQQHQPPPPPQQQQQQHFQESAPPNWLLRSDNNFLNLHTAASAAATSSDSPSSAAANQWLSRSSSFL
................................................................................
SVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNPSSSTVSKNKRRSNAGENSGRDR*

>AT5G15150.1
MYMYEEERNNINNNQEGLRLEMAFPQHGFMFQQLHEDNAHHLPSPTSLPSCPPHLFYGGGGNYMMNRSMSFTGVSDHHHL
..KSP...........TTTNNMNDQDQVGEEDNLSDDGSHMMLGEKKKRLNLEQVRALEKSFELGNKLEPERKMQLAKAL
QNRRARWKTKQLERDYDSLKKQFDVLKSDNDSLLAHNKKLHAELVALKKHDRKESAKIKREFAEASWSNNGSTENNHNNN
SSDANHVSMIKDLFPSSIRSATATTTSTHIDHQIVQDQDQGFCNMFNGIDETTSASYWAWPDQQQQHHNHHQFN*

First I can write pattern string that match number 2 or 5 chromosome, such as >AT[25]G。 I failed when I wrote the pattern string like this（>AT[25]G.*KSP.*) to match the sequence that met the condition.

By the way, all sequences start with a greater than sign> and end with an asterisk*, and all the amino acids are capitalized.

For example, the expected result would be a sequence of all three amino acids of KSP on chromosomes 2 and 5

>AT2G35940.1
MAAYFHGNPPEISAGSDGGLQTLILMNPTTYVQYTQQDNDSNNNNNSNNSNNNNTNTNTNNNNSSFVFLDSHAPQPNASQ
..........
....KSP......TNYHMNPNHNGDLEGVTGMQGSPKRLRTSDETMMQPINADFSSNEKLTMKILEERQGIRSDGGYPFM
..........
NGGSSTTTAHSSAAAAAAYNGMNIQNQKRYVAQLLPDFVA*

>AT2G35940.2
MAAYFHGNPPEISAGSDGGLQTLILMNPTTYVQYTQQDNDSNNNNNSNNSNNNNTNTNTNNNNSSFVFLDSHAPQPNASQ
................................................................................
RAWLFEHFLHPYPKDSDKHMLAKQTGLTRSQVSNWFINARVRLWKPMVEEMYMEEMKEQAKNMGSMEKTPLDQSNEDSAS
.....KSP..................EGVTGMQGSPKRLRTSDETMMQPINADFSSNEKLTMKILEERQGIRSDGGYPFM
................................................................................
NGGSSTTTAHSSAAAAAAYNGMNIQNQKRYVAQLLPDFVA*

>AT5G15150.1
MYMYEEERNNINNNQEGLRLEMAFPQHGFMFQQLHEDNAHHLPSPTSLPSCPPHLFYGGGGNYMMNRSMSFTGVSDHHHL
..KSP...........TTTNNMNDQDQVGEEDNLSDDGSHMMLGEKKKRLNLEQVRALEKSFELGNKLEPERKMQLAKAL
QNRRARWKTKQLERDYDSLKKQFDVLKSDNDSLLAHNKKLHAELVALKKHDRKESAKIKREFAEASWSNNGSTENNHNNN
SSDANHVSMIKDLFPSSIRSATATTTSTHIDHQIVQDQDQGFCNMFNGIDETTSASYWAWPDQQQQHHNHHQFN*

How do I write regular expressions in vim to match them, I hope you can help me, thank you very much for reading my question.

Try `/\_^>AT[25]G$\(\_^>AT[25]G$\@!\_.\)\{-}KSP\_.\{-}\*/` — Wiktor Stribiżew, Mar 16 '20 at 10:36

score 1 · Accepted Answer · answered Mar 16 '20 at 10:14

1

That is a multiline search. Try something like the following and modify as required. I have included newline, tab, and alphanumerics in the matched character classes.

^>AT[25]G[\t\n[:alnum:].]*KSP[\t\n[:alnum:].]*\*$

answered Mar 16 '20 at 10:14

Sukanta K. Hazra

89
1
2

1

Thank you for your patience, but this seems to have failed – I love python Mar 16 '20 at 10:45

vi regex: Find specific chromosomes and their fragments containing KSP protein fragments

1 Answers1