How to remove these a subset fasta file

Question

[CHINMAYA]

so i use and run my fasta file in my terminal using orfipy like:-

orfipy normal.fasta --dna orfs.fa --min 300 --max 10000 --table 1 --outdir orfs_out

$cat orfs.fa 

>MSTRG.942.2_j_ORF.1 [85-439](+) type:complete length:354 frame:2 start:CTG stop:TAA
CTGTTGAGTATAGATTCCTTTTTCACTCAgtaagcaaaaaaaaaagtagatctGAAACCCAT
CTTTCTATCAAGAACCCCCAGCTCCATTTCCACGCCCCATCTCCGGCCTCCGCGACACATAT
ATCCATTTTCGTGCTCTTCATCTCCTAAGCTTTCATTTGAACCGAATAAATCAACTTTTGAA
GCAACTTCGTGGTCAACCCATTTTCTTCCCTTCCCGGTAATACTCTTTTTCCGGTCACCTTT
CCTCTTTTCTTCCTTCTCTCTTACCtatttattccttttttttgtctttcaaaACTGTAGTT
TTTgtcctttttattttcttcttctagaTGCATTTTTTATTCCT

orf.fa is the subset of original fasta file, so after analysis i want remove these subset fasta file from my original file

any suggestion how to do it?

[CHINMAYA]

i physically check it is not working because may be header is differenet in orfs.fa and normal.fasta

$cat normal.fasta

>MSTRG.942.2_j
GAGATTAAGTgcttcttaaatataaaatgagttaATACATTGAATTGTGTCGGGGTGATTCTTTATATAGAGTAGTACTGTCCTACTGTTGAGTATAGATTCCTTTTTCACTCAgtaagcaaaaaaaaaagtagatctGAAACCCATCTTTCTATCAAGAACCCCCAGCTCCATTTCCACGCCCCATCTCCGGCCTCCGCGACACATATATCCATTTTCGTGCTCTTCATCTCCTAAGCTTTCATTTGAACCGAATAAATCAACTTTTGAAGCAACTTCGTGGTCAACCCATTTTCTTCCCTTCCCGGTAATACTCTTTTTCCGGTCACCTTTCCTCTTTTCTTCCTTCTCTCTTACCtatttattccttttttttgtctttcaaaACTGTAGTTTTTgtcctttttattttcttcttctagaTGCATTTTTTATTCCTTAAGGAAAAAGCTACCGTTTAATAAGtagtataattaataatgaattaaatgcATCTAGTTGTGATCTTGGTATGTTTACATGAATAAAATTCTAATTATATAGGTgaagatttacatttttggtgctCATGCTATGACTATAATTATGATTTTGACTAATATGCATAAGATTGAAAAAACATGAGGTCAAATTCTACAACACCGCCTTTGCAAGTTGCAACCTCACACTTTACCTCCCACATGAATTGTAAATTGCGATGTTTCATATTTTCTTCTTAAGATTTGTCtgttttatcttttttagtTTACAATGTTAATTATTCATCCTGTAGGCAATGATTGCTTTGTACATGAGTGTTTAATAACTTCAATTTGATCGTAATGGAAAGCTCAATTTGATTTATTCTGTTAATAACTTTTATATCTATATTGCAggtttaatgcaaaaacaaaacaaaagccATATTATCAACAACTTTCAGTCTGATCTTATTACCATAATATCTCAGATCTAGTCATGTGCTTTGAAATTGATTTCAGCAATGATATTTTTTCCCGCAACACAAATCATTGTAGGaataaattttctttcaaaagcTAATGAGATAATCAGCTTACCTAACAACCAAAAGTAAAATCTCAACAATATGCTCCATATATATTAGAGTTGATGAATGTTATTGAAGTATAACCAGGAGTTTTGTTTTACTACTTTGTTAAAGCATAAATTAAGTCAACTTCCAAACTACCAGTTCTTTGGTTTGAATGTTGATCCAACTTCTACTTCAATAAAGTACTAAAATAGAGCTCTTTGCTGCACATCATCAACAATAATGTATCCGACATATTGGTGGAATTTCACTTTTGGTTGTTTAGGTAAGTTAATTATCTTATCAGCTCTTGAAAGAAAACGTATTCATACAATGATTTGCGTTTCGAGAACAAATATCATTGTTGCAACTAGCACATGATTGAGTCTGAGATATAATGGCAATAAGAGCACCTCCAACAAAGGTTCACGATGAGTTGTTAGAATGGAAAGGCAAGTTCTTTGAGAGGTTAACTGCAGGGTATGAAAGTGACGTGGCACAGACTAGTTCACCATGCTTCAGGTTTGAGATCATGTTTTTAGTGTAGTTTCTTTATTTAAGTCCTGGTATTTTTTGATCCTTCACTTTGTATTATGTATGATCAGAATATTCTCAATAATTCATCAGAATGTTGTTTAAATTAACTATTGTTTATGCGTTGATCAAAAGTTCTTCTTTCATTTGCCTATTTGCTAACTACCACTATTGTAAAATCTCTATAGCTTACATTTTGTTACAGGATGAAGATCATTTTGAATGATGATgagttttttgtgttttttcatGTGGATGATGAAatgatgagttttttttttttttttgcgaaGGTTGAGTCTCTTATTGTCATGTATTTAACCATTCACATGTTGACAATTAATTTTTGGATTGGTCATGTATTATCAGTTCCTATCAAAGTGAGATGCAATGACTCGTAGGCTGCTTTCAAATGAAAAGAACTGAAAAAATAGGTACATTTGATATCAAGTACTTAGATAGTTAGATTATGACTCACAAATTGCGATTGTTTGTGTTAGAATTTTGAGAATCTCAGTTTTGTCCGTGATGCAGAGTTGCAGCTGCAGGAGtgcaataatatttcaaaatcatcaaGAAACAACATAAATGATAATGGGTGCATGACATGATGTCCAATTTTTGTAGCTCATGAGGGAGTTGCAAATTGTTGTACtgtttttgatttattatttaggTTTATGGTCTTTAGGAAGATACTACAAGTGTTATGAATCAATATCATATGTATGATTCAAAAGCAAAACAAGTTGATAccataatatcatttttaaggattaaacacaaataaaacaaaCTTTAATTGAATCTTCCACTAAGCTTGATCTAAATGAACCTTTATAAAAGAAGGGTATAATTTTATAGAACATGACAGTAATACTTTGTGGACACATGATTTACTTTTTTATCATCAGAAATTGAACTTACTTCCACCCCACCACCTAGGAGGTTACAACACTCACTTTATACTCCAACGTGATCATATtgtttaatgataataatagtTAGTAAGTACATTTTGACTATCTTACAATTA

so any method to remove header part like( _ORF.1 85-439 type:complete length:354 frame:2 start:CTG stop:TAA ) in orfs.fa?

[GenoMax]

See if this works:

$ cat your.fa | sed -e 's/_ORF.*//'
>MSTRG.942.2_j
CTGTTGAGTATAGATTCCTTTTTCACTCAgtaagcaaaaaaaaaagtagatctGAAACCCAT
CTTTCTATCAAGAACCCCCAGCTCCATTTCCACGCCCCATCTCCGGCCTCCGCGACACATAT

[CHINMAYA]

wanted.fa gives same sequence in normal.fasta so any help

[GenoMax]

See the following. You need to keep in mind that MSTRG.944.3_j is no longer unique so it is going to remove multiple sequences which have that id. I took the example below from the other thread you had posted this morning.

$ more n.fa
>MSTRG.942.2_j_ORF.1 [85-439](+) type:complete length:354 frame:2 start:CTG stop:
TAACTGTTGAGTATAGATTCCTTTTTCACTCAgtaagcaaaaaaaaaagtagatctGAAACCCAT
CTTTCTATCAAGAACCCCCAGCTCCATTTCCACGCCCCATCTCCGGCCTCCGCGACACATAT
ATCCATTTTCGTGCTCTTCATCTCCTAAGCTTTCATTTGAACCGAATAAATCAACTTTTGAA
GCAACTTCGTGGTCAACCCATTTTCTTCCCTTCCCGGTAATACTCTTTTTCCGGTCACCTTT
CCTCTTTTCTTCCTTCTCTCTTACCtatttattccttttttttgtctttcaaaACTGTAGTT
TTTgtcctttttattttcttcttctagaTGCATTTTTTATTCCT

>MSTRG.944.3_j_ORF.1 [162-489](+) type:complete length:327 frame:1 start:ATG stop:
TGAATGCCGACGTACAAGATTAGGGGAATCGACGTAGATTTTCCCTACGAAGCCTATGATTCCCA
ACTCGTTTACATGGACAAAGTCATGCAATCGCTTCAGGAGGTAGCGATTGACTCACTCAATC
ATTGCACTTTTGATTATTTAAGctacttttgatgtatttttattttattttatggtagTTCC
GCTGTGGTTGTTGTAATAATcgactaataattaattataaacatgATTTTGGATCAATTGGA
AGTGATCacaaaatgttaatatttaCTTGTTGTCAGGCAATTTGAAATTGATGTTGTTAAGA
TCATGATTGATCAGCAG

>MSTRG.944.3_j_ORF.2 [3141-3549](+) type:complete length:408 frame:1 start:TTG stop:
TAGTTGAAAATTTGTGCTGTATATTTTCTGCTATCTCGGGTACAGGatgatattttctttattgc
agCACTTCTTCTAAAACTTGAAAAGCGCATTGCTGAGGTGCATATTGAATCTAAGGAGTTGG
GGTTTACTAAACCCGGGCCCTATATGTTTGAACTGCTTGCTGATCTTAATATCACTCACAAG
ACTGCTTCTAAGCTTAAGAGTATAATAGCTGAAGCTTCAACTCTCATTGAGGAAAATAATCA
GGAGAAATCAACTGGCACCATCTGCAGATTGGATACTATCAAGGATATTCTTGACATTGTTT
TCAGGGATGGAAGAACTTCTCATGCTAAATACTATCGTGTAAGTTTTGAATTATCGTTTACA
CTTCAGTGGATTGATTTTGTTTGTCTTGTTGCTTCC


$ cat n.fa | sed -e 's/_ORF.*//' > new.fa

$ more listfile # This file should contain only fasta header remove `>` from header
MSTRG.944.3_j

$ ./faSomeRecords -exclude new.fa listfile wanted.fa

$ more wanted.fa
>MSTRG.942.2_j
TAACTGTTGAGTATAGATTCCTTTTTCACTCAgtaagcaaaaaaaaaagtagatctGAAACCCAT
CTTTCTATCAAGAACCCCCAGCTCCATTTCCACGCCCCATCTCCGGCCTCCGCGACACATAT
ATCCATTTTCGTGCTCTTCATCTCCTAAGCTTTCATTTGAACCGAATAAATCAACTTTTGAA
GCAACTTCGTGGTCAACCCATTTTCTTCCCTTCCCGGTAATACTCTTTTTCCGGTCACCTTT
CCTCTTTTCTTCCTTCTCTCTTACCtatttattccttttttttgtctttcaaaACTGTAGTT
TTTgtcctttttattttcttcttctagaTGCATTTTTTATTCCT

[CHINMAYA]

if i converted two fasta file into txt and use

diff a.txt b.txt|grep ">"|cut -c 3- > foo.txt

can it work?

[GenoMax]

Fasta files are plain text. I demonstrated how to make this work (with your own data) in example above.

[CHINMAYA]

it is normal confussion in my mind like

in FASTA sequence if one header file contain one or two ORF from some postion to another, so i delete whole header or that position only?

Answer 1

[GenoMax]

Use faSomeRecords utility from Jim Kent (Linux version linked). Add execute permissions after downloading (chmod a+x faSomeRecords).

faSomeRecords - Extract multiple fa records
usage:
   faSomeRecords in.fa listFile out.fa
options:
   -exclude - output sequences not in the list file.

So you can do

faSomeRecords -exclude normal.fasta orfs.fa wanted.fa

[CHINMAYA]

i download and give the permission but after running it say

faSomeRecords: command not found

[GenoMax]

If the program is in current directory where you have all files then use

./faSomeRecords -exclude normal.fasta orfs.fa wanted.fa