Questions about the sed command to remove the characters and create a new file-CodePudding

I have a file called "Jimbleprot.pep" and It looks like this:

  119 >TRINITY_DN10025_c0_g1::TRINITY_DN10025_c0_g1_i1::g.7937::m.7937 TRINITY_DN10025_c0_g1::TRINITY_DN10025_c0_g1_i1::g.7937  ORF type:5prime_partial len:201 (-),score=29.41 TRINITY_DN10025_c0_g1_i1:192-794(-)
  120DEDDEPQELQVHVDVSLPGTPLGSENSVHSGCSHKSNVSSSLVAA
  123 TPTCVRLEEELHGPIRDGLS*
  124 >TRINITY_DN10026_c0_g1::TRINITY_DN10026_c0_g1_i1::g.7944::m.7944 TRINITY_DN10026_c0_g1::TRINITY_DN10026_c0_g1_i1::g.7944  ORF type:internal len:115 ( ),score=15.25,NACHT|PF05729.12|0.068,Tti2|PF10521.9|0.1      4 TRINITY_DN10026_c0_g1_i1:2-343( )
  125 SVEDLAIKILTTCGIPAPSVGEKEKLQELLKIVTRKCLLILDNLDHAFHADDKRRDSMDK
  126 SIRTTYKPSFSGNSTASSNISESSAAAFASSSANLPGIPTSISFAPYRSGIVHS
  127 >TRINITY_DN10028_c0_g1::TRINITY_DN10028_c0_g1_i1::g.7938::m.7938 TRINITY_DN10028_c0_g1::TRINITY_DN10028_c0_g1_i1::g.7938  ORF type:5prime_partial len:223 (-),score=32.40,gi|114149223|sp|Q9NUQ8.2|ABCF3_HUMA      N|66.97|6e-103,gi|114149223|sp|Q9NUQ8.2|ABCF3_HUMAN|23.39|7e-11,ABC_tran|PF00005.27|3.4e-23,AAA_21|PF13304.6|0.00057,AAA_21|PF13304.6|3.2e-05,SMC_N|PF02463.19|0.082,SMC_N|PF02463.19|6.7e-05,AAA_22|PF13401.      6|0.00019,AAA_30|PF13604.6|0.00038,AAA_16|PF13191.6|0.0019,AAA_29|PF13555.6|0.0081,NACHT|PF05729.12|0.0075,AAA_15|PF13175.6|0.015,AAA_15|PF13175.6|1.1e 03,Pox_A32|PF04665.12|0.01,Dynamin_N|PF00350.23|0.016      ,MobB|PF03205.14|0.026,DUF87|PF01935.17|0.039,DUF87|PF01935.17|3.3e 03,AAA_23|PF13476.6|0.033,AAA_24|PF13479.6|0.2,AAA_24|PF13479.6|1.1e 03,FtsK_SpoIIIE|PF01580.18|0.069,AAA_18|PF13238.6|0.079,AAA_18|PF132      38.6|3e 03,DLIC|PF05783.11|0.046,T2SSE|PF00437.20|0.063,SbcCD_C|PF13558.6|0.33,MMR_HSR1|PF01926.23|0.059,TniB|PF05621.11|36,TniB|PF05621.11|3.7,Arf|PF00025.21|0.27,Arf|PF00025.21|2.2e 03,AAA_19|PF13245.6|0      .18,TsaE|PF02367.17|0.23,Roc|PF08477.13|0.22 TRINITY_DN10028_c0_g1_i1:59-727(-)
  128IAVVGDNGSGKTTLLKILLGELEPVKLATKFPGKNVEHYRHQLG
RYGVSGDLATRFQGGVILVSHDERLVRSMCDEVWVCGNRQVKSIEGGFDQYKRMVQEELQAVLQ*
  132 >TRINITY_DN1002_c0_g1::TRINITY_DN1002_c0_g1_i1::g.2343::m.2343 TRINITY_DN1002_c0_g1::TRINITY_DN1002_c0_g1_i1::g.2343  ORF type:5prime_partial len:174 ( ),score=44.19,EF-hand_7|PF13499.6|0.15,EF-hand_6|PF13      405.6|1.2,EF-hand_6|PF13405.6|8.8e 02,EF-hand_6|PF13405.6|6e 03,EF-hand_6|PF13405.6|1.3e 03,EF-hand_1|PF00036.32|0.16,EF-hand_1|PF00036.32|5.8e 03,EF-hand_1|PF00036.32|6.3e 03,EF-hand_1|PF00036.32|8.6e 03       TRINITY_DN1002_c0_g1_i1:2-523( )
  133 EQHPKIRMQIAQKVFNVLDPDKKGYANKDDIMALTVDKLKAIADIVDPDYANTEEYEHVL
  134 FGEAEVRDAFQDALEEGNGELHLQKLIQKYKDLGGSEKVARELFAMLKPKSKDKATADEV
  135 EENLSNVLELYKKIRDEDKSGIFYDRHLQEDKEIMAKTLHEKTDTDGTKHDEL*
  136 >TRINITY_DN1002_c0_g1::TRINITY_DN1002_c0_g1_i2::g.2344::m.2344 TRINITY_DN1002_c0_g1::TRINITY_DN1002_c0_g1_i2::g.2344  ORF type:5prime_partial len:174 ( ),score=54.09,EF-hand_7|PF13499.6|0.13,EF-hand_8|PF13      833.6|1.6,EF-hand_8|PF13405.6|1.2,EF-hand_6|PF13405.6|1.5e 03,EF-hand_6|PF13405.6|6e 03,EF-hand_6|PF13405.6|8.8e 02,EF-hand_1|PF00036.32|0.16,EF-hand _1|PF00036.32|PF00036.32|6.7e 03 TRINITY_DN1002_c0_g1_i2:2-523( )
  137 EQHPKIRMQIAQKVFNVLDPDKKGYANKDDIMALTVDKLKAIADIVDPDYANTEEYEHVL
  138 FGEEEVRDAFQDALEEGNGELHLQKLILKYKDLGGSEKVARELFAMLKPKSKDKATADEV
  139 EENLSNVLELYKKIRDDDKSGVFYDRHLQEDKEIMAKTLDEGTNTDGAKHEEL*

and this file is about more than 8000 lines , I want to use the sed command to remove the * in the first 5000 line and output the result to a new file called "newprot.fasta". I think I may need the | to headbut I'm not sure how to do it and use them in the sed command. Thank you!

CodePudding user response：

ed is, as is usually the case when you're working with a file instead of a stream that's part of a pipeline, a better choice than sed here:

printf '%s\n' '1,5000 g/\*/s/\*//g' '1,5000 w newprot.fasta' Q | ed -s Jimbleprot.pep

will remove every * character in the first 5000 lines of the file, and then save those first 5000 lines in the new file.

Can also be written with ed's input as a heredoc instead if you prefer it for readability:

ed -s Jimbleprot.pep <<EOF
1,5000 g/\*/s/\*//g
1,5000 w newprot.fasta
Q
EOF

CodePudding user response：

My way is to divide it to 3 parts (maybe there is better way):

take only the first 5000 lines in new file and delete the *.

sed '5001,$ d' Jimbleprot.pep | tr -d '*' > temp_file.txt

save only the last 3000 - raws in the Jimbleprot.pep file:

tail -n  5001 Jimbleprot.pep > test.tmp && mv test.tmp Jimbleprot.pep

Unify all files to the newprot.fasta:

cat temp_file.txt Jimbleprot.pep > newprot.fasta

It should work, again i don't know if it's the best way but it's my way.

Edit: if you want only the first 5000 lines without the * just do step 1.

CodePudding user response：

This might work for you (GNU sed):

sed '1,5000s/\*//g;w newprot.fasta' Jimbleprot.pep

This will alter the first 5000 lines removing any *'s and the write every line to newprot.fasta.

If only the first 5000 line are required in newprot.fasta, use:

sed -e '1,5000s/\*//g;w newprot.fasta' -e '5000q' Jimbleprot.pep