SB Merge - mendessoares/BuddySuite GitHub Wiki

--merge, -mrg

Description

Merge multiple copies of sequence records together, combining their feature lists. This is particularly useful if you are combining genbank records from different sources.

Example

Input file 1: Panx_TMDs.gb

LOCUS       Mle-Panxα3               412 aa                     UNA 02-JAN-2015
DEFINITION  cDNA - ML036514a.
ACCESSION   Mle-Panxα3
VERSION     Mle-Panxα3
KEYWORDS    .
SOURCE      
  ORGANISM  . . . . .
            .
FEATURES             Location/Qualifiers
     TMD1            29..49
     TMD2            132..152
     TMD3            218..238
     TMD4            302..332
ORIGIN
        1 mlllgslgti knlsifkdls lddwldqmnr tfmflllcfm gtivavsqyt gkniscdgft
       61 kfgedfsqdy cwtqglytik eaydlpesqi pypgiipenv pacrehalkn ggkivcpped
      121 qvkpltrarh lwyqwipfyf wviapvfylp ymfvkrmgld rmkpllkims dyyhcttetp
      181 seeiivkcad wvynsivdrl segsswtswr nrhglglavl vskfmylggs vlvmmmttlm
      241 fqvgdfktyg iewlrqfpnp enystsvkhk lfpkmvacei krwgttglee engmcvlapn
      301 viyqyiflim wfalaitict nfgniffylf kltatrytyn klvatghfsh khpgwkfmyy
      361 rigtsgrvll nivaqntnpi ifgaimeklt psvikhlrig hvpgeyltdp a*
//
LOCUS       Mle-Panxα4               425 aa                     UNA 02-JAN-2015
DEFINITION  cDNA and genomic - ML129317a.
ACCESSION   Mle-Panxα4
VERSION     Mle-Panxα4
KEYWORDS    .
SOURCE      
  ORGANISM  . . . . .
            .
FEATURES             Location/Qualifiers
     TMD1            28..48
     TMD2            131..151
     TMD3            215..235
     TMD4            305..335
ORIGIN
        1 mviellagyk glspfkdatv ddswdqinrc yvfiamvvmg avttmrqysg tliacdgftk
       61 fhpqfaedyc wsigmytvre aydlpssmva ypgvipwdmp acvprllkng trtkcgsekd
      121 vmpsekiyhl wyqwasfyfw ivailyyapy imfkqlggge ykplikllcl asgspeqqmq
      181 diqervvkwl ffrfktyifa kgyyawlrkn sfsiaigvtk lsyllitilv fyltgfmfey
      241 gsntwyryga dwygtrfssy hetnnsitlt kdiifpkmva ceikrwgpsg ievetaqcvl
      301 apnvlyqylf lftwylliav fftnliscfl hisemffsng tynrmidqgm lpdkpsyryv
      361 fmnigaggre ivqiltdnsn pllfskifdd ltnllittsk nadvienlsk ldssvielgs
      421 kdsi*
//
LOCUS       Mle-Panxα5               406 aa                     UNA 02-JAN-2015
DEFINITION  cDNA - ML223536a.
ACCESSION   Mle-Panxα5
VERSION     Mle-Panxα5
KEYWORDS    .
SOURCE      
  ORGANISM  . . . .
            .
FEATURES             Location/Qualifiers
     TMD1            28..48
     TMD2            133..153
     TMD3            218..238
     TMD4            302..332
ORIGIN
        1 miywvwavfk rmapfkvvtl ddrwdqmnrs fmmpltmsfa ylidygiiag stikctgfed
       61 sfrseafvde ycwtqgiytl reaydlentk ipypgiipeg fpncmpyerw dgmkvecpke
      121 eqylkptrvy hlyyqhiqly fwlvctlfyl pymvgiclgf nytkplinll hnpltrdeee
      181 lealldkaar slrlrldiys dqkswfdlly rrhtmlyllf fiklqylgfs vailgltqak
      241 fkignfvtyg fewvgsqvpn gstytlvqhk lfpkmaacei krwgasgldv lrgmcvlpqn
      301 vsnsyiflvf wifllltilg nvigciltvk qylvksegys klvactfwnd wnlrhlywnv
      361 ggsgrvilhh ladnlhpctf eklirrywwl krneyvqyng hlkts*
//

Input file 2: Panx_prosite_scan.gb

LOCUS       Mle-Panxα4               425 aa                     UNA 02-JAN-2015
DEFINITION  cDNA and genomic - ML129317a.
ACCESSION   Mle-Panxα4
VERSION     Mle-Panxα4
KEYWORDS    .
SOURCE      
  ORGANISM  . . . . . . . .
            .
FEATURES             Location/Qualifiers
     PANNEXIN        17..401
     MYRISTYL        41..45
     MYRISTYL        51..55
     CAMP_PHOSPHO_SI 209..211
     MYRISTYL        255..259
     MYRISTYL        420..424
ORIGIN
        1 mviellagyk glspfkdatv ddswdqinrc yvfiamvvmg avttmrqysg tliacdgftk
       61 fhpqfaedyc wsigmytvre aydlpssmva ypgvipwdmp acvprllkng trtkcgsekd
      121 vmpsekiyhl wyqwasfyfw ivailyyapy imfkqlggge ykplikllcl asgspeqqmq
      181 diqervvkwl ffrfktyifa kgyyawlrkn sfsiaigvtk lsyllitilv fyltgfmfey
      241 gsntwyryga dwygtrfssy hetnnsitlt kdiifpkmva ceikrwgpsg ievetaqcvl
      301 apnvlyqylf lftwylliav fftnliscfl hisemffsng tynrmidqgm lpdkpsyryv
      361 fmnigaggre ivqiltdnsn pllfskifdd ltnllittsk nadvienlsk ldssvielgs
      421 kdsi*
//
LOCUS       Mle-Panxα3               412 aa                     UNA 02-JAN-2015
DEFINITION  cDNA - ML036514a.
ACCESSION   Mle-Panxα3
VERSION     Mle-Panxα3
KEYWORDS    .
SOURCE      
  ORGANISM  . . . . . . . .
            .
FEATURES             Location/Qualifiers
     MYRISTYL        6..10
     MYRISTYL        9..13
     PANNEXIN        18..399
     MYRISTYL        42..46
     TYR_PHOSPHO_SIT 188..193
     MYRISTYL        204..208
     MYRISTYL        215..219
ORIGIN
        1 mlllgslgti knlsifkdls lddwldqmnr tfmflllcfm gtivavsqyt gkniscdgft
       61 kfgedfsqdy cwtqglytik eaydlpesqi pypgiipenv pacrehalkn ggkivcpped
      121 qvkpltrarh lwyqwipfyf wviapvfylp ymfvkrmgld rmkpllkims dyyhcttetp
      181 seeiivkcad wvynsivdrl segsswtswr nrhglglavl vskfmylggs vlvmmmttlm
      241 fqvgdfktyg iewlrqfpnp enystsvkhk lfpkmvacei krwgttglee engmcvlapn
      301 viyqyiflim wfalaitict nfgniffylf kltatrytyn klvatghfsh khpgwkfmyy
      361 rigtsgrvll nivaqntnpi ifgaimeklt psvikhlrig hvpgeyltdp a*
//

Usage example

$: sb Panx_TMDs.gb Panx_prosite_scan.gb -mrg

Output

LOCUS       Mle-Panxα3               412 aa                     UNA 02-JAN-2015
DEFINITION  cDNA - ML036514a.
ACCESSION   Mle-Panxα3
VERSION     Mle-Panxα3
KEYWORDS    .
SOURCE      
  ORGANISM  .
            .
FEATURES             Location/Qualifiers
     MYRISTYL        6..10
     MYRISTYL        9..13
     PANNEXIN        18..399
     TMD1            29..49
     MYRISTYL        42..46
     TMD2            132..152
     TYR_PHOSPHO_SIT 188..193
     MYRISTYL        204..208
     MYRISTYL        215..219
     TMD3            218..238
     TMD4            302..332
ORIGIN
        1 mlllgslgti knlsifkdls lddwldqmnr tfmflllcfm gtivavsqyt gkniscdgft
       61 kfgedfsqdy cwtqglytik eaydlpesqi pypgiipenv pacrehalkn ggkivcpped
      121 qvkpltrarh lwyqwipfyf wviapvfylp ymfvkrmgld rmkpllkims dyyhcttetp
      181 seeiivkcad wvynsivdrl segsswtswr nrhglglavl vskfmylggs vlvmmmttlm
      241 fqvgdfktyg iewlrqfpnp enystsvkhk lfpkmvacei krwgttglee engmcvlapn
      301 viyqyiflim wfalaitict nfgniffylf kltatrytyn klvatghfsh khpgwkfmyy
      361 rigtsgrvll nivaqntnpi ifgaimeklt psvikhlrig hvpgeyltdp a*
//
LOCUS       Mle-Panxα4               425 aa                     UNA 02-JAN-2015
DEFINITION  cDNA and genomic - ML129317a.
ACCESSION   Mle-Panxα4
VERSION     Mle-Panxα4
KEYWORDS    .
SOURCE      
  ORGANISM  .
            .
FEATURES             Location/Qualifiers
     PANNEXIN        17..401
     TMD1            28..48
     MYRISTYL        41..45
     MYRISTYL        51..55
     TMD2            131..151
     CAMP_PHOSPHO_SI 209..211
     TMD3            215..235
     MYRISTYL        255..259
     TMD4            305..335
     MYRISTYL        420..424
ORIGIN
        1 mviellagyk glspfkdatv ddswdqinrc yvfiamvvmg avttmrqysg tliacdgftk
       61 fhpqfaedyc wsigmytvre aydlpssmva ypgvipwdmp acvprllkng trtkcgsekd
      121 vmpsekiyhl wyqwasfyfw ivailyyapy imfkqlggge ykplikllcl asgspeqqmq
      181 diqervvkwl ffrfktyifa kgyyawlrkn sfsiaigvtk lsyllitilv fyltgfmfey
      241 gsntwyryga dwygtrfssy hetnnsitlt kdiifpkmva ceikrwgpsg ievetaqcvl
      301 apnvlyqylf lftwylliav fftnliscfl hisemffsng tynrmidqgm lpdkpsyryv
      361 fmnigaggre ivqiltdnsn pllfskifdd ltnllittsk nadvienlsk ldssvielgs
      421 kdsi*
//
LOCUS       Mle-Panxα5               406 aa                     UNA 02-JAN-2015
DEFINITION  cDNA - ML223536a.
ACCESSION   Mle-Panxα5
VERSION     Mle-Panxα5
KEYWORDS    .
SOURCE      
  ORGANISM  .
            .
FEATURES             Location/Qualifiers
     TMD1            28..48
     TMD2            133..153
     TMD3            218..238
     TMD4            302..332
ORIGIN
        1 miywvwavfk rmapfkvvtl ddrwdqmnrs fmmpltmsfa ylidygiiag stikctgfed
       61 sfrseafvde ycwtqgiytl reaydlentk ipypgiipeg fpncmpyerw dgmkvecpke
      121 eqylkptrvy hlyyqhiqly fwlvctlfyl pymvgiclgf nytkplinll hnpltrdeee
      181 lealldkaar slrlrldiys dqkswfdlly rrhtmlyllf fiklqylgfs vailgltqak
      241 fkignfvtyg fewvgsqvpn gstytlvqhk lfpkmaacei krwgasgldv lrgmcvlpqn
      301 vsnsyiflvf wifllltilg nvigciltvk qylvksegys klvactfwnd wnlrhlywnv
      361 ggsgrvilhh ladnlhpctf eklirrywwl krneyvqyng hlkts*
//