Perl script

bioenvisage · 01-28-2010, 05:40 AM

Can any one help me with a perl script for removing the repeats in the reads , for eg i will paste the format of the seq below

HWI-EAS373:2:100:1792:1509#0/1 AAAAAAAAAAAAAAAAAACAACAAAAAAACAAAACAAAAACAAAACCAACACC ]_a`_Z_IT`b_\[_Ya\[\[]S\[RHUR^a^YY_V]aa^[TaW\Y\W_`^][aYR_BBBBBBBBBBBBBBBBBBB NF
HWI-EAS373:2:100:1792:1509#0/2 ACACACACATGGTCCACCATATTTTTTTACTTGGTTGTA aRaPZ__\__]VG[]RMGX\_Z_aa_P_NQ[_\VTFZTOa`R_[Q]ZZZXaBBBBBBBBBBBBBBBBBBBBBBBBB NF
HWI-EAS373:2:100:1792:1691#0/1 ACACACACAGTGTAGCTGGGGAGCAGGGATCCATTGATC abaa^]Waa]b_`Vb_b`aa[^`aa_aaXD^H]`]QWYa`ZaZaH]`TMS]`^BBBBBBBBBBBBBBBBBBBBBBB NF
HWI-EAS373:2:100:1792:1691#0/2 GGCTTTTTTGGTATCCTTTTCTCATGTTAGATGATGGGAGCATTTTTCTTCAGTgggatggatggtctggtagggc a^aY`_aaVa`UUabWaWa_bab_`a`b`aaOb``YN[a]GR`a`a`ba]_[J[XYBBBBBBBBBBBBBBBBBBBB NF
HWI-EAS373:2:100:1792:198#0/1 CGGCATTCCTTTTATTATAGCCCCTCTAGCTAGTTACAGTAGATAGGAACGtgcatgaatctntaaatggntgnan aZ]`]ab``aaab`a`]`YT`a^`aa`UZ\^X_Y]^Z^aYY[TYV[\XVLYBBBBBBBBBBBBBBBBBBBBBBBBB NF
HWI-EAS373:2:100:1792:198#0/2 agCTGATCTAGCGTCGTCTGCAACAACAACCGCGGGGGCGTCatcaacggcaagtgcggctcagcctcgggtgttg HOT_TTGYZGV_]GUQ_XNGSQZ\QIYTXT\_RKQGGL]O\ZBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB NF
HWI-EAS373:2:100:1793:876#0/1 CCNCTGCCTCTACCTCCACGCCCTCGGCCTCTGCCACGCCCGCGGCCTGTATCTccagtgctctactcgcacanan `WDV^`a``a`aa^a`_aa[a]aY[`a\][a`\^``\`\]\^^S]Z[ZXW]ZP\SQBBBBBBBBBBBBBBBBBBBB NF

maubp · 01-28-2010, 07:43 AM

I'm having trouble making out what the data should look like - try wrapping the example with code tags,
[ code ] sequence data [ /code ]

krobison · 01-28-2010, 08:14 AM

By repeats in the reads do you mean
(a) Within a read, the repetition of a single nucleotide or simple sequence
(b) For sets of reads which are identical (presumed PCR duplicates), report only one
(c) Something else

SAMTools will do (b)

Dave S. · 01-28-2010, 10:14 AM

If you just want to remove homopolymers of DNA of some arbitrary length, use something like:

Code:

$min = 4;

while (<>)
{
s/(G){$min,}|(A){$min,}|(T){$min,}|(C){$min,}/$1$2$3$4/g;
print;
}

You are probably better off determining where and when they occur before wiping them out, e.g. see http://www.bioperl.org/wiki/Finding_...hes_in_contigs

If your sequencing method is generating spurious homopolymers you will need a much more sophisticated approach to determining which ones are real.

bioenvisage · 01-28-2010, 12:25 PM

hi krobison ...iam telling about with in the read the repetation of single nucleotide and also simple repeats.

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Perl script to convert BAM to BED?	rebrendi	Bioinformatics	3	03-22-2012 10:34 PM
just perl script	semna	Bioinformatics	3	07-02-2011 08:42 AM
vcftools perl script	weiyulin	Bioinformatics	6	12-09-2010 02:13 PM
perl script	bioenvisage	Bioinformatics	5	02-01-2010 08:11 AM
perl script	bioenvisage	Bioinformatics	0	02-01-2010 07:23 AM

01-28-2010, 05:40 AM	#1
bioenvisage Member Location: it Join Date: Oct 2009 Posts: 40	Perl script Can any one help me with a perl script for removing the repeats in the reads , for eg i will paste the format of the seq below HWI-EAS373:2:100:1792:1509#0/1 AAAAAAAAAAAAAAAAAACAACAAAAAAACAAAACAAAAACAAAACCAACACC ]_a`_Z_IT`b_\[_Ya\[\[]S\[RHUR^a^YY_V]aa^[TaW\Y\W_`^][aYR_BBBBBBBBBBBBBBBBBBB NF HWI-EAS373:2:100:1792:1509#0/2 ACACACACATGGTCCACCATATTTTTTTACTTGGTTGTA aRaPZ__\__]VG[]RMGX\_Z_aa_P_NQ[_\VTFZTOa`R_[Q]ZZZXaBBBBBBBBBBBBBBBBBBBBBBBBB NF HWI-EAS373:2:100:1792:1691#0/1 ACACACACAGTGTAGCTGGGGAGCAGGGATCCATTGATC abaa^]Waa]b_`Vb_b`aa[^`aa_aaXD^H]`]QWYa`ZaZaH]`TMS]`^BBBBBBBBBBBBBBBBBBBBBBB NF HWI-EAS373:2:100:1792:1691#0/2 GGCTTTTTTGGTATCCTTTTCTCATGTTAGATGATGGGAGCATTTTTCTTCAGTgggatggatggtctggtagggc a^aY`_aaVa`UUabWaWa_bab_`a`b`aaOb``YN[a]GR`a`a`ba]_[J[XYBBBBBBBBBBBBBBBBBBBB NF HWI-EAS373:2:100:1792:198#0/1 CGGCATTCCTTTTATTATAGCCCCTCTAGCTAGTTACAGTAGATAGGAACGtgcatgaatctntaaatggntgnan aZ]`]ab``aaab`a`]`YT`a^`aa`UZ\^X_Y]^Z^aYY[TYV[\XVLYBBBBBBBBBBBBBBBBBBBBBBBBB NF HWI-EAS373:2:100:1792:198#0/2 agCTGATCTAGCGTCGTCTGCAACAACAACCGCGGGGGCGTCatcaacggcaagtgcggctcagcctcgggtgttg HOT_TTGYZGV_]GUQ_XNGSQZ\QIYTXT\_RKQGGL]O\ZBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB NF HWI-EAS373:2:100:1793:876#0/1 CCNCTGCCTCTACCTCCACGCCCTCGGCCTCTGCCACGCCCGCGGCCTGTATCTccagtgctctactcgcacanan `WDV^`a``a`aa^a`_aa[a]aY[`a\][a`\^``\`\]\^^S]Z[ZXW]ZP\SQBBBBBBBBBBBBBBBBBBBB NF Last edited by bioenvisage; 01-28-2010 at 05:43 AM.

01-28-2010, 10:14 AM	#4
Dave S. Junior Member Location: SF Bay Area Join Date: Jan 2010 Posts: 4	If you just want to remove homopolymers of DNA of some arbitrary length, use something like: Code: $min = 4; while (<>) { s/(G){$min,}\|(A){$min,}\|(T){$min,}\|(C){$min,}/$1$2$3$4/g; print; } You are probably better off determining where and when they occur before wiping them out, e.g. see http://www.bioperl.org/wiki/Finding_...hes_in_contigs If your sequencing method is generating spurious homopolymers you will need a much more sophisticated approach to determining which ones are real.

01-28-2010, 07:43 AM	#2
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,543	I'm having trouble making out what the data should look like - try wrapping the example with code tags, [ code ] sequence data [ /code ]

01-28-2010, 08:14 AM	#3
krobison Senior Member Location: Boston area Join Date: Nov 2007 Posts: 747	By repeats in the reads do you mean (a) Within a read, the repetition of a single nucleotide or simple sequence (b) For sets of reads which are identical (presumed PCR duplicates), report only one (c) Something else SAMTools will do (b)

01-28-2010, 12:25 PM	#5
bioenvisage Member Location: it Join Date: Oct 2009 Posts: 40	hi krobison ...iam telling about with in the read the repetation of single nucleotide and also simple repeats.