Check if a nucleotide matches in CDS (from GenBank)

Question

[pablo]

Hello,

I have a list.txt of nucleotides positions :

260
269
601
1411
1502
1516
1819
2103
2113
2227

I have a GenBank file :

CDS             complement(358..468)
                 /locus_tag="ADGNGPNM_00001"
                 /inference="ab initio prediction:Prodigal:002006"
                 /codon_start=1
                 /transl_table=11
                 /product="hypothetical protein"
                 /translation="MSWTMIFKKFEFPVLKVPVGNKVYIWLKKNINLLRV"
 CDS             complement(446..2329)
                 /locus_tag="ADGNGPNM_00002"
                 /inference="ab initio prediction:Prodigal:002006"
                 /codon_start=1
                 /transl_table=11
                 /product="hypothetical protein"
                 /translation="MQIEKLTKETILEDTTFEEIIDEKDEIYRQRLINDLTDRAAELG
                 VKTKFTSLLKAYQKEEKKMLQEQKKQLQEQNRARILQNLDRRTEFGSECYPDLRCGNW
                 FADETGIRTFGMFGEVQACYHPILPVERFTNLETGDEKIKLAFKKGERWKEIICDKDL
                 IASSTKIISLANSGVAVTSENAKYLVRYLADVENFNMDLLPEWVSTSKLGWHGENAIK
                 EFVPYCSNIVFDGDVRFRNVYGDIRQCGNEKKWDAFVKKVRAEGRIEPRIMMAASFAS
                 VIIKMCNALPFFVHLHGQSEGGKTLCLMLAASIWGNPSMESAFTGDFLSTQTAIEVRA
                 DMLNHLPYIMDDTAQVMEKYKGDFSTLIYTMCSGNGKDRSNRSLGLNRNYNWHCAFLT
                 TGELPITKEYSQAGAANRVIEVEAGYSKIFENGIEVARTLNENFGFAGKRFIEILQNI
                 GAEEVCRIQGELLAEIEKSGKMQKQSISLSLILTADRIATDCLFEDGVYLSIEETAAM
                 LKSEKEISENERCYEFIQGEIVRNNHRFKQEGDEFFPTECWGVREKNYTYIIKNVFDQ
                 MCRDCNYNGTAFLKWADLKGLIQCNEGRKTKKKKINGASAWTVCLKNMQEIEGFNELD
                 DDF"
 CDS             complement(2344..2907)
                 /locus_tag="ADGNGPNM_00003"
                 /inference="ab initio prediction:Prodigal:002006"
                 /codon_start=1
                 /transl_table=11
                 /product="hypothetical protein"
                 /translation="MTTKEKADLIKATLTMREILGMYGLGSNARHHRIPCPIHDGKDR
                 NFSFTDFGFRCFVCGAEGGLVHFVELYRGLSFEAALEEINGHFRLWEDYPELESAESS
                 RNQHKKDSAFRSRRAIAKLRHERRTADREKEKAEEIRMTLLEELWRLDANKIKYAPKS
                 EDEPFHPLYVEACHKLEYQQYLVESIV"

I need to know if the nucleotide matches with the CDS coordinates. Is there a tool to do that or do I need to create a script with an output like that :

260 0
269 0
601 1
1411 1 
1502 1

with 0 for no and 1 for yes.

Best

[lieven.sterck]

bedtools intersect 

you will need to do some format changes/parsing though to make it to work.