convert a text file in fasta with decollpasing

Giorgio C · 03-28-2013, 10:53 AM

Hi all,

I have this file:

TGAGGTAGTAGATTGTATAGTT 424866
TAGCTTATCAGACTGATGTTGA 359141
TAGCTTATCAGACTGATGTTGAC 276052
TGAGGTAGTAGGTTGTATAGTT 268735
ACAGTAGTCTGCACATTGGTT 209280
ACAGTAGTCTGCACATTGGTTA 178652
TAGCTTATCAGACTGATGTTG 166159
TGAGGTAGTAGGTTGTGTGGTT 105275
TGAGGTAGTAGGTTGTATGGTT 102447
AGCAGCATTGTACAGGGCTATGA 91296
TGAGGTAGTAGGTTGTGTGGTTT 63300
TGAGGTAGTAGTTTGTACAGTT 61604
TGAGGTAGTAGATTGTATAGT 61492
TAGCACCATCTGAAATCGGTTA 60637
TTCAAGTAATCCAGGATAGGCT 52300
TGAGGTAGTAGATTGTATAGTTA 50905
TGAGGTAGTAGGTTGTATAGT 48150
TACAGTAGTCTGCACATTGGTT 47534
TCTACAGTCCGACGATC 45803
................

They are sequences and the numbers are the respective occurrences. I would like to convert that file in a fasta format, decollapsing the sequences and giving a name like that:

>Sample1_0
TGAGGTAGTAGATTGTATAGTT
>Sample1_1
TGAGGTAGTAGATTGTATAGTT
>Sample1_2
TGAGGTAGTAGATTGTATAGTT
.....
for 424866 times.
>Sample1_424666
TGAGGTAGTAGATTGTATAGTT

then
>Sample1_424667
TAGCTTATCAGACTGATGTTGA (the second sequences)

The same for the other sequences in series. Is there any scripts for that purpose?

Thanks in advance,
Giorgio

vivek_ · 03-28-2013, 01:07 PM

Code:

awk '{for(i=0;i<=($2-1);i++) print ">Sample"NR"_"i"\n"$1}' file.txt

This might work!

Giorgio C · 03-28-2013, 01:49 PM

Thanks vivek it works great!

maasha · 03-29-2013, 11:48 AM

This can also be done with Biopieces (www.biopieces.org):

Code:

read_tab -i in.tab -k SEQ,COUNT | duplicate_record -k COUNT | add_ident -k SEQ_NAME -p Sample1_ | write_fasta -x

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03-28-2013, 10:53 AM	#1
Giorgio C Member Location: ITALY Join Date: Oct 2010 Posts: 89	convert a text file in fasta with decollpasing Hi all, I have this file: TGAGGTAGTAGATTGTATAGTT 424866 TAGCTTATCAGACTGATGTTGA 359141 TAGCTTATCAGACTGATGTTGAC 276052 TGAGGTAGTAGGTTGTATAGTT 268735 ACAGTAGTCTGCACATTGGTT 209280 ACAGTAGTCTGCACATTGGTTA 178652 TAGCTTATCAGACTGATGTTG 166159 TGAGGTAGTAGGTTGTGTGGTT 105275 TGAGGTAGTAGGTTGTATGGTT 102447 AGCAGCATTGTACAGGGCTATGA 91296 TGAGGTAGTAGGTTGTGTGGTTT 63300 TGAGGTAGTAGTTTGTACAGTT 61604 TGAGGTAGTAGATTGTATAGT 61492 TAGCACCATCTGAAATCGGTTA 60637 TTCAAGTAATCCAGGATAGGCT 52300 TGAGGTAGTAGATTGTATAGTTA 50905 TGAGGTAGTAGGTTGTATAGT 48150 TACAGTAGTCTGCACATTGGTT 47534 TCTACAGTCCGACGATC 45803 ................ They are sequences and the numbers are the respective occurrences. I would like to convert that file in a fasta format, decollapsing the sequences and giving a name like that: >Sample1_0 TGAGGTAGTAGATTGTATAGTT >Sample1_1 TGAGGTAGTAGATTGTATAGTT >Sample1_2 TGAGGTAGTAGATTGTATAGTT ..... for 424866 times. >Sample1_424666 TGAGGTAGTAGATTGTATAGTT then >Sample1_424667 TAGCTTATCAGACTGATGTTGA (the second sequences) The same for the other sequences in series. Is there any scripts for that purpose? Thanks in advance, Giorgio

03-28-2013, 01:07 PM	#2
vivek_ PhD Student Location: Denmark Join Date: Jul 2012 Posts: 164	Code: awk '{for(i=0;i<=($2-1);i++) print ">Sample"NR"_"i"\n"$1}' file.txt This might work!

03-29-2013, 11:48 AM	#4
maasha Senior Member Location: Denmark Join Date: Apr 2009 Posts: 153	This can also be done with Biopieces (www.biopieces.org): Code: read_tab -i in.tab -k SEQ,COUNT \| duplicate_record -k COUNT \| add_ident -k SEQ_NAME -p Sample1_ \| write_fasta -x

03-28-2013, 01:49 PM	#3
Giorgio C Member Location: ITALY Join Date: Oct 2010 Posts: 89	Thanks vivek it works great!