Question: grep chromosome on blast result
0
gravatar for ettetuani.boutaina
2.9 years ago by
ettetuani.boutaina0 wrote:

It is a blastx file , I want to select all the chromosomes number 4 for example and I tested this command but it does not work

grep  "^>" .chromosome:TAIR10:4 file >reslt_grep


> AT4G23310.2 pep chromosome:TAIR10:4:12185369:12188961:1 gene:AT4G23310
transcript:AT4G23310.2 gene_biotype:protein_coding
transcript_biotype:protein_coding gene_symbol:CRK23 description:Putative
cysteine-rich receptor-like protein kinase 23
[Source:UniProtKB/Swiss-Prot;Acc:O65482]
Length=790

 Score = 27.3 bits (59),  Expect = 1.7, Method: Composition-based stats.
 Identities = 12/38 (32%), Positives = 21/38 (55%), Gaps = 0/38 (0%)
 Frame = +3

Query  42   SLIAAASKMIPISILHCCHSYLLHPRTNTKHYSLISVL  155
            S +   S + P  + H C S+   PR++T   +LI++L
Sbjct  129  SNLVVTSALDPTYVYHVCPSWATFPRSSTYMTNLITLL  166

> AT1G31420.2 pep chromosome:TAIR10:1:11249600:11253915:1 gene:AT1G31420
transcript:AT1G31420.2 gene_biotype:protein_coding
transcript_biotype:protein_coding gene_symbol:FEI1 description:Leucine-rich
repeat receptor kinase [Source:UniProtKB/TrEMBL;Acc:F4I9D5]
Length=591

 Score =   124 bits (312),  Expect = 3e-34, Method: Compositional matrix adjust.
 Identities = 63/88 (72%), Positives = 68/88 (77%), Gaps = 3/88 (3%)
 Frame = -1

Query  265  GFGTVYKLIMDDNSAFAVKKILNNGVRSDRLFERELEILGSIKHRNLVNLRGYCNSPSAK  86
            GFGTVYKL MDD   FA+K+IL      DR FERELEILGSIKHR LVNLRGYCNSP++K
Sbjct  316  GFGTVYKLAMDDGKVFALKRILKLNEGFDRFFERELEILGSIKHRYLVNLRGYCNSPTSK  375

Query  85   LLIYDYLPLGSLDELLHEHRETDSTLDW  2
            LL+YDYLP GSLDE LHE  E    LDW
Sbjct  376  LLLYDYLPGGSLDEALHERGE---QLDW  400
grep chromosome • 718 views
ADD COMMENTlink modified 2.9 years ago by Pierre Lindenbaum128k • written 2.9 years ago by ettetuani.boutaina0

How about:

man grep
ADD REPLYlink written 2.9 years ago by 5heikki8.7k

If you don't need to see the alignment, using flag -outfmt 6 (text tab-delimited) will be much easier to parse. Then you can get all the lines in the file that match your query sequence: grep -e 'chromosome:TAIR10:4' blastout.txt

ADD REPLYlink written 2.9 years ago by st.ph.n2.5k
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