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fasta sequence manupulation

i have fasta file like this:

>1001796365 4.F.1.1.5
MDSIRPATFQIPAAVRELGWAALLLFFVLLSVHEWFSPPGWFGLLAILIFATQGALILTR
WPARQNFGWANRTTLLRSILVVSLVAWAPFLPAADSSALWIYGVACLIALILDGVDGKVA
>1002048002 2.A.4.2.8
MSPSRTARLYFLLVLDLLFFVLEISIGYAVGSLALVADSFHMLNDVVSLIIALYAIKLAA
SSTPTTRYSYGWHRAEILAALVNGVFLLALCFTITLEALERFFSTPEISNPKLIVLVGSL
>1002048004 2.A.4.5.2
IASDIRRILHRHGIHSSTIQPEYHPVRDTILEERSKDVNCLISCPPDSACCEVQACCPSY
AGT

header order in fasta sequence : 

 >+first_id then+\t+second_id

i want my sequence in this formate:

 >4.F.1.1.5
MDSIRPATFQIPAAVRELGWAALLLFFVLLSVHEWFSPPGWFGLLAILIFATQGALILTR
WPARQNFGWANRTTLLRSILVVSLVAWAPFLPAADSSALWIYGVACLIALILDGVDGKVA
 >2.A.4.2.8
MSPSRTARLYFLLVLDLLFFVLEISIGYAVGSLALVADSFHMLNDVVSLIIALYAIKLAA
SSTPTTRYSYGWHRAEILAALVNGVFLLALCFTITLEALERFFSTPEISNPKLIVLVGSL
 >2.A.4.5.2
IASDIRRILHRHGIHSSTIQPEYHPVRDTILEERSKDVNCLISCPPDSACCEVQACCPSY
AGT

only 

 >+second_id+\n+sequence
sequence alignment
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updated by Daniel Daniel • written by poonam.bi01 • poonam.bi01
  1. No greater-than sign means that it's not fasta
  2. The format you request looks very random in your example
• 1 views • link
written by 5heikki 5heikki

The greater-than sign gets auto-formatted I think, so I guess the post doesn't reflect what OP had in mind.

• 1 views • link
written by WouterDeCoster WouterDeCoster

2 answers

To code golf-ify the answer, you could do it in fewer keystrokes with sed:

# 21 Keystrokes (+infile.fa)
sed -i 's/^>.\+ />/g' infile.fa

EDIT: Golfing harder:

# 19 Keystrokes (+infile.fa)
sed -i 's/>.\+ />/' infile.fa
• 1 views • link
written by Daniel Daniel

If I understand it properly, something like this should work.

cat file.fa | paste - - | awk '{print ">"$2"\n"$3}' > new_file.fa

PS: When I copy paste your sequence, there is a gap in the sequence. If it is a formatting problem, it is ok, if not make sure nothing is going wrong.

After reformatting (by genomax2), first linearize the fasta file and use the above.

• 1 views • link
written by venu venu

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