[semna]

>q6gqm1_danre
mrecisvhvgqagvqignacwelyclehgiqadghmp-------sdhttsggdqsfntffsetgagkhvpravfvdleptvvdevrtgtyrqlfhpeqlitgkedaannyarghytigkeivdlvldrvrklcdqctglqgflifhsfgggtgsgfasllmerlsvdygkkaklefavypapqvstavvepynsiltthttlehsdcafmvdneaiydicrrnldierptytnlnrligqivssitaslrfdgalnvdltefqtnlvpyprihfplvtyapvisaekayheqlsvveitnacfepanqmvkcdprhgkymaccmlyrgdvvpkdvnaaigsiktkrtiqfvdwcptgfkvginyqpptvvpggdlakvqravcmlsnttaiaeawarldhkfdlmyakrafvhwyvgegmeegefaearedlaalekdyeevgvdtidgegeaegee
>tba3_drome
mrecisihvgqagvqignacwelyclehgiqpdgqmp-------sdktvgggddsfntffsetgagkhvpravfvdleptvvdevrtgtyrqlfhpeqlitgkedaannyarghytigkeivdlvldrirkladqctglqgflifhsfgggtgsgftsllmerlsvdygkksklefavypapqvstavvepynsiltthttlehsdcafmvdneaiydicrrnldierptytnlnrligqivssitaslrfdgalnvdltefqtnlvpyprihfplvtyapvisaekayheqlsvaeitnacfepanqmvkvdprhgkymaccmlyrgdvvpkdvnaaiatiktkrtiqfvdwcptgfkvginyqpptvvpggdlakvqravcmlsnttaiaeawarldhkfdlmyakrafvhwyvgegmeegefsearedlaalekdyeevgmdsgdgegegaeey
>tba3_arath
mreiisihigqagiqvgnscwelyclehgiqpdgmmp-------sdttvgvahdafntffsetgagkhvpravfvdleptvidevrtgtyrqlfhpeqlisgkedaannfarghytvgkeivdlcldrvrkladnctglqgflvfnavgggtgsglgslllerlsvdygkksklgftiypspqvstavvepynsvlsthsllehtdvavlldneaiydicrrsldierptytnlnrlisqiisslttslrfdgainvditefqtnlvpyprihfmlssyapvisaakayheqlsvpeitnavfepasmmakcdprhgkymacclmyrgdvvpkdvnaavgtiktkrtvqfvdwcptgfkcginyqpptvvpggdlakvqravcmisnntavaevfsridhkfdlmyakrafvhwyvgegmeegefsearedlaalekdyeevgaeggddeedegedy
>tba2_caeel
mrevisihvgqagvqignacwelyclehgiqpdgtmp-------tqstneg--esfttffsdtgsgryvprsifvdleptvvdeirtgtykklfhpeqmitgkedaannyarghytvgkelidtvldrirrladncsglqgffvfhsfgggtgsgftsllmerlsvdygkksklefsiypapqvstavvepynsiltthttlehsdcafmvdneaiydicrrnldverpsytnlnriisqvvssitaslrfdgalnvdlnefqtnlvpyprihfplaaytplisaekayhealsvsditnscfepanqmvkcdprhgkymavcllyrgdvvpkdvntaiaaiktkrtiqfvdwcptgfkvginyqpptvvpggdlakvpravcmlsnttaiaeawsrldykfdlmyakrafvhwyvgegmeegeftearedlaalekdyeevgadsneggeeegeey
>tba3_yeast
mrevisinvgqagcqignacwelyslehgikedghled------glskpkggeegfstffhetgygkfvpraiyvdlepnvidevrtgrfkelfhpeqlingkedaannyarghytvgreivdeveerirkmadqcdglqgflfthslgggtgsglgslllenlsyeygkksklefavypapqlstsvvepyntvltthttlehadctfmvdneaiydickrnlgisrpsfsnlngliaqvissvtaslrfdgslnvdlnefqtnlvpyprihfplvsyapilskkrathesnsvseitnacfepgnqmvkcdptkgkymancllyrgdvvtrdvqraveqvknkktvqmvdwcptgfkigicyeppsvipsselanvdravcmlsnttaiadawkridqkfdlmyakrafvhwyvgegmeegeftearedlaalerdyievgadsyaeef------
>tbal3_human
mreclsihigqagiqigdacwelyclehgiqpngvvldtqqdqlenakmehtnasfdtffcetragkhvpralfvdleptvidgirtgqhrslfhpeqllsgkedaannyargrysvgsevidlvlertrklaeqcgglqgflifrsfgggtgsgftsllmerltgeysrktklefsvypapristavvepynsvltthsttehtdctfmvdneavydichrklgvecpshasinrlvvqvvssitaslrfegplnvdliefqtnlvpyprihfpmtafapivsadkayheqfsvsdittacfessnqlvkcdprlgkymaccllyrgdvvpkevnaaiaatksrhsvqfvdwcptgfkvginnrpptvmpggdlakvhrsicmlsnttaiveawarldhkfdlmyakraflhwylregmeeaeflearedlaalerdyeevaqsf-----------
>q6dht2_danre
mgkekihinivvighvdsgkstttghliykcggidkrtiekfekeaaemgkgsfkyawvldklkaerergitidislwkfettkyyitiidapghrdfiknmitgtsqadcavlivaagvgefeagiskngqtrehallaytlgvkqlivavnkmdstepsysekrydeivkevsayikkigyspasvpfvpisgwhgdnmlepssnmpwfkgwkldrkehhaggvtllealdtimpptrptdkplrlplqdvykiggigtvpvgrvetgvlrpsmvvtfapvnittevksvemhheslsealpgdnvgfnvknvsvkdirrgnvcgdsksdppqeasgftaqviilnhpgqissgyspvidchtahiackfaelkekidrrsgkklednpkslksgdaaivdmipgkpmcvesfsqypplgrfavrdmrqtvavgviknvekkiggsgrvtksaqkaqkssk
>q6ips9_human
mgkekthinivvighvdsgkstttghliykcggidkrtiekfekeaaemgkgsfkyawvldklkaerergitidislwkfetskyyvtiidapghrdfiknmitgtsqadcavlivaagvgefeagiskngqtrehallaytlgvkqlivgvnkmdsteppysqkryeeivkevstyikkigynpdtvafvpisgwngdnmlepsanmpwfkgwkvtrkdgnasgttllealdcilpptrptdkplrlplqdvykiggigtvpvgrvetgvlkpgmvvtfapvnvttevksvemhhealsealpgdnvgfnvknvsvkdvrrgnvagdskndppmeaagftaqviilnhpgqisagyapvldchtahiackfaelkekidrrsgkkledgpkflksgdaaivdmvpgkpmcvesfsdypplgrfavrdmrqtvavgvikavdkkaagagkvtksaqkaqkak-
>a4v3q6_drome
mgkekihinivvighvdsgkstttghliykcggidkrtiekfekeaqemgkgsfkyawvldklkaerergitidialwkfetskyyvtiidapghrdfiknmitgtsqadcavlivaagtgefeagiskngqtrehallaftlgvkqlivgvnkmdsteppysearyeeikkevssyikkigynpasvafvpisgwhgdnmlepsekmpwfkgwsverkegkaegkclidaldailppqrptdkplrlplqdvykiggigtvpvgrvetgllkpgmvvnfapvnlvtevksvemhhealteampgdnvgfnvknvsvkelrrgyvagdsknnpprgaadftaqvivlnhpgqiangytpvldchtahiackfseikekcdrrtgkttetepkaiksgdaaiivlvpskplcvesfqefpplgrfavrdmrqtvavgviksvnfkettsgkvtkaaekaqkkk-
>ef1a_caeel
mgkekvhinivvighvdsgkstttghliykcggidkrtiekfekeaqemgkgsfkyawvldklkaerergitidialwkfetakyyitiidapghrdfiknmitgtsqadcavlvvacgtgefeagiskngqtrehallaqtlgvkqlivacnkmdsteppfsearfteitnevsgfikkigynpkavpfvpisgfngdnmlevssnmpwfkgwaverkegnasgktllealdsiippqrptdrplrlplqdvykiggigtvpvgrvetgiikpgmvvtfapqnvttevksvemhheslpeavpgdnvgfnvknvsvkdirrgsvcsdskqdpakeartfhaqviimnhpgqisngytpvldchtahiackfnelkekvdrrtgkkvedfpkflksgdagiveliptkplcvesftdyaplgrfavrdmrqtvavgviksveksdgssgkvtksaqkaapkkk
>ef1a_yeast
mgkekshinvvvighvdsgkstttghliykcggidkrtiekfekeaaelgkgsfkyawvldklkaerergitidialwkfetpkyqvtvidapghrdfiknmitgtsqadcailiiaggvgefeagiskdgqtrehallaftlgvrqlivavnkmdsvk--wdesrfqeivketsnfikkvgynpktvpfvpisgwngdnmieattnapwykgweketkagvvkgktlleaidaieqpsrptdkplrlplqdvykiggigtvpvgrvetgvikpgmvvtfapagvttevksvemhheqleqgvpgdnvgfnvknvsvkeirrgnvcgdakndppkgcasfnatvivlnhpgqisagyspvldchtahiacrfdellekndrrsgkkledhpkflksgdaalvkfvpskpmcveafseypplgrfavrdmrqtvavgviksvdktek-aakvtkaaqkaakk--
>ef1a_arath
mgkekfhinivvighvdsgkstttghliyklggidkrvierfekeaaemnkrsfkyawvldklkaerergitidialwkfettkyyctvidapghrdfiknmitgtsqadcavliidsttggfeagiskdgqtrehallaftlgvkqmicccnkmdattpkyskarydeiikevssylkkvgynpdkipfvpisgfegdnmierstnldwyk------------gptllealdqinepkrpsdkplrlplqdvykiggigtvpvgrvetgmikpgmvvtfaptglttevksvemhhesllealpgdnvgfnvknvavkdlkrgyvasnskddpakgaanftsqviimnhpgqigngyapvldchtshiavkfseiltkidrrsgkeiekepkflkngdagmvkmtptkpmvvetfseypplgrfavrdmrqtvavgviksvdkkdptgakvtkaavkkgak--
>q6nwb3_danre
------------maagpisernqdatvyvggldekvsepllwelflqagpvvnthmpkdrvtgqhqgygfveflseedadyaikimn-miklygkpirvnkasahnknldvg-----------anifignldpeidekllydtfsafgvilqtpkimrdpdtgnskgyafinfasfdasdaaieamngqylcnrpitvsyafkkdskg-erhgsaaerllaaqnplsqadrphqlfadappppsmptpvmtalgaampipgmpppgafpp-vpppgtmppgmppgmpmppapg---tpapqggggpppghp--------pfppagmhppgmphmpmpptgppgmvppppgppgsnqprapppp----qmppppmgvpprgp-fgppmgpp--mhpgmrgppppmpppgygagpprpppfgfqrgppmpprpp-----aprgpmrapaps
>sf3b4_human
------------maagpisernqdatvyvggldekvsepllwelflqagpvvnthmpkdrvtgqhqgygfveflseedadyaikimn-miklygkpirvnkasahnknldvg-----------anifignldpeidekllydtfsafgvilqtpkimrdpdtgnskgyafinfasfdasdaaieamngqylcnrpitvsyafkkdskg-erhgsaaerllaaqnplsqadrphqlfadappppsapnpvvsslgsglpppgmpppgsfpppvpppgalppgippamppppmppgaaghgppsagtpgaghpghghshphpfppggmphpgmsqmqlahhgphglghphagppgsggqppprpppgmphpgpppmgmpprgppfgspmghpgpmpphgmrgppplmpphgytgpprpppygyqrgplppprptprppvpprgplrgplpq
>q9w424_drome
------------maagpiaernqdatiyagglddkvsetllwelfvqagpvvnvhmpkdrvtqmhqgygfveflseedadygikimn-miklygkpirvnkasahqknldvg-----------anifignldvevdekllydtfsafgvilqtpkimrdpetgksksfafinfasfeasdaamdamngqylcnrpisvsyafkkdhkg-erhgsaaerllaaqnpsthadrphqlfadapvqtmmpqmpgqipaqmpgqmmpppmmappppvvpvsnnnmgmlappppvpqpapfpatipppplppmtggqp-------plppamgipppprmmqpnawappgmpappprppptnwrpppvpfpptpyarpyqpdgyqy----------------------------------------------------------------------
>sf3b4_caeel
------------msagpivernqdatiyvggldekvsesilwelmvqagpvvsvnmpkdrvtanhqgfgfvefmgeedadyaikiln-miklygkpikvnkasaheknmdvg-----------anifvgnldpevdekllydtfsafgvilqvpkimrdvdsgtskgfafinfasfeasdtaleamngqflcnraitvsyafkrdskg-erhgtaaermlaaqnplfpkdrphqvfsdvplgvpantplampgvhaaiaahatgrpgyqppplmgmaqsgyqgqyppvpppppsvtpmpppmpptpgmtprpp------pppssgmwppppppppgrtpgppgmpgmppppppsrfgppgmggmppppppgmrypggmpppppprypsagpgmypppppsrppappsghgmipppppps------------------------------
>q9zu66_arath
mttriapgvganllgqhsaernqdatvyvggldaqlseellwelfvqagpvvnvyvpkdrvtnlhqnygfieyrseedadyaikvln-miklhgkpirvnkasqdkksldvg-----------anlfignldpdvdekllydtfsafgviasnpkimrdpdtgnsrgfgfisydsfeasdaaiesmtgqylsnrqitvsyaykkdtkg-erhgtpaerllaatnptaqksrphtlfamgppssapqvnglprpfangsmqpvpipaprqppppppqvyqtqppswpsqpqqhsmvpppmqfrppqgmppppppqflnhqqgfggprpppppqamgmhqhggwppqhmqqqggppqqqqppyqhhhmsmppppphqg-------------------------------------------------------------------------
>hsh49_yeast
----------------mnysadsgntvyvgnidpritkeqlyelfiqinpvlrikypkdkvlqayqgyafiefynqgdaqyaikimnntvrlydrlikvrqvtnstgttnlpsniskdmilpiaklfiknladsidsdqlvkifnkfgklirepeifylsng--klkcayvyfedfekadlaikslnnqlvannritvdyafkengkgnakygddvdrllnkealkhnmlk--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

[zee]

OK try this

#!/bin/sh
#save as split2.sh

perl -e '$count=0; $len=0; while(<>) {s/\r?\n//; s/\t/ /g; if (s/^>//) { if ($. != 1) {print "\n"} s/ |$/\t/; $count++; $_ .= "\t";} else {s/ //g; $len += length($_)};print }'  $1 | perl -lane '$species=$1 if $F[0] =~ /_(\S+)/; $h{$species}.="$F[1]\n"; END { print ">$_\n$h{$_}" for keys %h  }  '

bash split2.sh <input file>

[semna]

It works great but it will be great if coonect the last letter of first part to the first letter to next part
like:
AAA
BBB
be like AAABBB
tanks so much for your help

[zee]

This should do it.

#!/bin/sh

#split3.sh

 perl -e '$count=0; $len=0; while(<>) {s/\r?\n//; s/\t/ /g; if (s/^>//) { if ($. != 1) {print "\n"} s/ |$/\t/; $count++; $_ .= "\t";} else {s/ //g; $len += length($_)};print }'  $1  | perl -lane '$species=$1 if $F[0] =~ /_(\S+)/; $h{$species}.="$F[1]"; END { print ">$_\n$h{$_}" for keys %h  }  '

[semna]

Hi Zee,
Thanks so much for your help