Using fix_targetfile messes up with the target file

[josh3397]

Hi,

I've been reading the section on improving the target file using fix_targetfile option by removing low complexity regions. I noticed that using this option is messing up with the fasta file headers in my target protein dataset. Anybody else faced this issue?

[chrisjackson-pellicle]

Hi @josh3397,

Can you provide more details on this, please? An example of your input, and the incorrect output?

Cheers,

Chris

[josh3397]

Hello,

My input protein targets look like this -

Bombyx_mori-BGIBMGA010725
VLASLHNGVIQLWDYRMCTLLEKFDEHDGPVRGICFHIQQPLFVSGGDDYKIKVWNYKQRRCLFTLLGHLDYIRTTFFHHEYPWILSASDDQTIRIWNWQSRQCISVLTGHNHYVMCAQFHPTEDLLVSASLDQSVRVWDFSGLRKKSVAPGPAGLTEHLRNPQATDLFG-----QADAVVKHVLEGHDRGVNWACFHPTLPLIASAADDRQVKLWRMNDSKAWEVDTCRGHYNNVSCVLFHAKHELIISNSEDLYIRVWDMSKRTLLQSFRREHERH----------------------------------------------LRKLDMLTNRDAPVMHLSKGGGRQQPYS------------------------------------MSLNHAEWCVLVTWRNG---ENCSYELYAAPRD--HSGAVPEGTEPARGQATTAIW--------------LVIRNLKNEVSKKISTPTCEEIMYAGTGMLLLREADSVQLLDVQQKRTIASVKVSKCRYAIWNTDMSIVALLGKHTVTLCTKKLEQLCCITEGARVKSGAFDDSTPQPVFIYTTANHIKYCCKDGDYGIIRTLDVPVYAVRVLS-----TETGARVVCLDRECRPKVLNIDPTEY-RFKLALVTRQYDQVLHMVRTAKLVGQSIIAYLQEKGYPEVALHFVKDSRTRLSLALQCGNIEVALEAAKSLDEPAAWDQLAKAALTTGNHQIVEMCYQRTKNFDKLSFLYLVTGNLEKLRKMMKIAEIRKDTSAQFQGALLLGDVGERIRLLRNSGQLSLAYLTAINHKQVEEAEQLKAALEAAGMPVPEANPDAVFLRPPLPIQRNQPNWPLLAVSKSFFEVAGQARAAAEGSGSAVAAA-LDEPLEAAGAWGDDDVL----PDHKEEGEEEIMEDACEDGGWDVGDEDLELPEELAPVSADMGAAEDSEQYFVAPTRGASAPLAARLRTAHDHVATGQFEAAMRLLNEQVGIVNFAPYESVFAEMFAHARVTFGALPSLPALTAYLHRNWKEATGKDLLPVITLKLSDLVSQLQQSYQLTTAGRFPEAIERLQGVAQRVPLLLVDSKAELSEAQQLLAVCRDYLVGLAMETARKAMPKNTVDEQKRTCEMAAYFTHCKLQPVHQILTLRTALNMFFKLKNYRTAASFARRLLELGPRPEVAQQARKILQACEKTPTDEHQLLYDEHNPFSVCGISYKPIYRGKPEEKCSLCAASFMPEHKGKLCPVCGVAEIGKDALGLRICPLQFNR
--
Bombyx_mori-BGIBMGA000829
-------------------------------------MYLYNLTLQGSSAITHAVHGNFSGTKQQEIIISRGKTLELLRPDPNTGKVHTFMKIEIFGVVRSIMAFRLTGGTKDYIVVGSDSGRIIILEYIPTKNILEKVHQETFGKSGCRRIVPGQYLSIDPKGRAVMIGAIEKQKLVYILNRDAEARLTISSPLEAHKSNTLVYHMVGVDVGFENPMFACLEIDYEEADSDPTGEAAQKTQQTLTFYELDLGLNHVVRKYSEPLEEHANFLITVPGGNDGPSGVLICSENYLTYKNLGDQHDIRCPIPRRRNDLDDPERGMIFVCSATHKTKSMFFFLAQTEQGDIFKITIETDEDMVTEIKLKYFDTVPVATSMCVLKTGFLFVACEFGNHYLYQIAHLGDEDDEPEFSSAMPLEEGDTFFFAPRPLRNLVLVDEMDSLSPILACHVADLAGEDTPQVYLACGRGPRSSLRALRHGLEVAEMAVSELPGSPNAVWTVRRNKDEEYDSYIIVSFVNATLVLSIGETVEEVTDSGFLGTTPTLSCHAMGNDALVQVYPDGIRHIRADKRVNEWKAPGKKSIVRCAVNQRQVVIALTGGELVYFEMDPTGQLNEYTERKKLSSDVCCMALGSVAAGEQRAWFLAVGLNDNTVRIISLDPADCLSPRSMQALPAGAESLCIIEQPFESGAKSALHLNIGLSNGVLLRTTLDSVSGDLADTRTRYLGSRPVKLFKVRVQAAEAVLAVSSRTWLGYHYQNRFHLTPLSYECLEYAAGFSSEQCTEGIVAISSNTLRILALEKLGAVFNQTFVPLEYTPRKFIINSDNNHIIVLETDHNAYTEEMKKH-RRIQMAQEMREAAA-GGAPEEQQLANEMADAFLSDTLPEYIFSSPKAGAGMWASLIRVVDMGIGGG--QPNTLFRL-PLEQNEAAVSLCIVRWAAHAEHAQPHLVVGVAKDL-ILSPRSCTEGSLHVYKIYGNTGKLELVHKTPVDEYPGAIAAFNGRLLAGVGRMLRLYDIGRRKLLRKCENRHIPNLIADIKTIGQRIFVSDVQESVFCVKHKKRENQLIIFADDTNPRWITNSCILDYDTIAVSDKFGNVAIMRLPQSVSDDVDEDPTGNKALWDRGLLNGASQKGDVVVNFHVGETVTSLQRATLIPGGSEALLYATISGSLGVLLPFTSREDHDFFQHLEMHMRSENSPLCGRDHLSFRSYYYPVKNVIDGDLCEQFNSLDPGKQKAIAGDLERTPAEVSKKLEDIRTRYAF
--

After using fix_targetfile to remove low complexity regions, I get the output where fasta headers of many sequences is messed up like this:

Heliconius_melpomene-HMEL007836
ADLVVIGSGPGGYVAAIKAAQLGLKTISVEKDPSLGGTCLNVGCIPSKALLHNSHLY>He
liconius_melpomene-HMAKHDFKHRGIDVGEVKFDFDAMMAYKSNAVKGLTGGIAM
LFNKNKVQLVRGVGSVVAPNKVEVQGEKG-VETINTKNIIIASGSEVTPFPGVTFDEQQI
ITSTGALSLSKVPKKMLVIGAGVIGLELGSVYQRLGADVTAIEFLESIGGIGIDGEVSKT
LQKILTKQGMKFKLGTKVTAVKKEGGVVKIEVEAAKGGNKETLDCDVVLISIGRRPYTKG
LGLEKVGIALDDRGRIPVNNKFQTTIPGIYAIGDVIHGPMLAHKAEDEGIVCVEGIKGMP
VHFNYDAIPSVIYTSPEVGWVGKSEEDLKK-EGRAYKVGKFPFMANSRAKTNGEPEGFVK

Heliconius_melpomene-HMEL010336
CPYLDTINRHVLDFDFEKLCSISLTRINVYACLVCGKYFQGRGTNTHAYTHSVADGHHVF
LNLHTLKFYCLPDNYEVIDSSLNDIKYVLNPIFTPEQIKQLDENTKMSRAIDGTMYMPGI
VGLNNIKANDYCNVILQCLSQVRPLRNYFLREENYADVKRPPGDSSFLLVQRFGELIRKL
WNPRAFKAHVSPHEMLQAVVLWSKKRFQFIKQSDPIDFLSWFLNSLHLALNGTKKP-NSS
IIYKSFLG>Heliconius_melpomene-HMRIYTRKLPPPDADDAAKVDLSSEEYNEM
ITESPFLYLTCDLPPTPLFTDEFRENIIPQVNLYQLLSKFNGQTSKEYKTYKENFMKRFE
ITQLPPYLILYIKRFTKNTFFVEKNPTVVNFPVKNVDFGDILTPEVKAKHNGKTTYELVG
NIVHDGTPEKGTYRAHVLHTPTQQWYEMQDLHVTSILPQMITLTEAYIQIYELKQD--

Regards,
Mukta

[chrisjackson-pellicle]

Hi Mukta,

It looks like your target file contains alignments, rather that unaligned sequences?

Can you upload your target file, and paste the hybpiper check_targetfile and hybpiper_fix_targetfile you used?

Cheers,

Chris