OrthoFinder2で検出したsingle-copy orthologsのFASTAエントリを一括改名する

動機

系統樹を描くのに使うsingle-copy orthologsをOrthoFinder2で選抜した。
このときSingle_Copy_Orthologue_Sequencesフォルダに OG0000001.faのような名前のFASTA形式ファイルが保存される。

FASTAファイル内の各配列のタイトルはタンパク質そのもののIDとなっている。

>BDT62344.1
MENNSHDNVINTPFIDDDNVKNDIFINTSDDDDNNNSDNDSKGNSNNNSSNSSSSSSSSN
SSTTSEDIDNIDLDDYKSVLLLCKEEKIYNNQKNERVENKQFYPNKKKRKLNNIESPQPQ
PSLLSRLPTLSSSSSSSSSSSPSSPPPPSSPTLSVPPPSDDQPPLLITNCKEVVDIIYRH
ERQVMSDSELYLGYASTKMPKEFVECLLMFRDEMTLILQEYARLRRSQQLLGNFNTNSIN
YADEMVKKMIDIILRIDKNSMSVDKYRDVVREALYIYHLVVSKMTGPKHLKRLRTPELHF
DFCMLIALLSHNVENVKNISTKYRVSSIIQFVSALDCQWYLSVVPSILSVFNRSNSICHA
LSFSYMRHAQVNITLCLVFALTETNTTNLVLGVILYLFPESLESIKTNELIKDESLIIPL
CRKIKEHLRSQWIDRMDITNAAYLLLGSCTDGLDTIKVFKKHNYDKKIVAVSIMIQQKLK
QLNQSICFH
>BDT62474.1
MFDHFDPEHFLIVYSPIAFLSIITRNFALIREMSLQDDLYLSTSSDEIEDDNESEEEEDD
DDDYDDNGDSVNDKDDDDDVEFDPDKTNSTVLLTHVPRKGTYVSRIAHDESDSRGCSKSV
ISDTDSGSQTSSVSQSNEHRWRMSLRHQRKRFRHNNFDHHVRTTSPQMVVLSQPMNVLGA
LANEERTAMEVAEITLTQGSLAMSEPDREALLTFYREIKTIISAYLSLVHIQRTLNNYNT
NSINYPEGMVKKILSIIRQIPRHEMSMEKYNVVCRDALFLYYTIITRMTGPKHSKRLRTP
YWQFYFCGVLAMLVNDVPVASDLTVSGKETSLVQFASAVGNPAYQTAVHDISSVYNSSYS
VYKALGLSRSQLTDANMVLAILSARNTHLSDRKPRTMAQSALLYRNPDLIDRMRASGLVQ
DESSLGSTSRAVAAQLRVAGVSNQTLDDASHFLHGSYNQEGVTLRCFGSGQRDLKTVAAS
VLVTEDLRRRIRTTW
>BDV49871.1
MKYIFSDDDDDDNSTISNSNSSSNKSSDNSDIEDDEDDDNDEDLDNYQSILLMSKNDTNH
IIEKKFEHDNSIHSNNIDNKNIPFCSSFDMKETLEIKHDNTSKKNITYEYDSSNNRKDTE
EGQEDKRGPLLITNPKEVVDEILREEKKTSSETIIGYALSKYSKESVESLSMFKEEIILI
LQMYAKMKCRQQLLGNFNTNSTNYSEEMVKKMIEIISRIDKNSMALDKYRDVVREALYIY
HLVVSKMTGPKHLKRLRTPDLHFDFCVIVALLAHNIEVNKSNFSKYRATSLIQFVSALDC
QWYLSVVPNILSVFNSSSSICQIIGFSALKHAKINIILCLLFNIFEKKPNNLVLATILYL
YPESLNVIKQNGLIRDEASVIALSKKIKIHLDDYWIYQSDIHCAANLLIGQWTEGLNIIK
LFKKQHYDKKVIAISLLVQQRLKQLNQTVEYY

系統解析する前に、配列名をもとの生物種名 (=input FASTAファイル名のbasename部分) に変更する必要が生じた。

>MelaMJNV
MENNSHDNVINTPFIDDDNVKNDIFINTSDDDDNNNSDNDSKGNSNNNSSNSSSSSSSSN
SSTTSEDIDNIDLDDYKSVLLLCKEEKIYNNQKNERVENKQFYPNKKKRKLNNIESPQPQ
PSLLSRLPTLSSSSSSSSSSSPSSPPPPSSPTLSVPPPSDDQPPLLITNCKEVVDIIYRH
ERQVMSDSELYLGYASTKMPKEFVECLLMFRDEMTLILQEYARLRRSQQLLGNFNTNSIN
YADEMVKKMIDIILRIDKNSMSVDKYRDVVREALYIYHLVVSKMTGPKHLKRLRTPELHF
DFCMLIALLSHNVENVKNISTKYRVSSIIQFVSALDCQWYLSVVPSILSVFNRSNSICHA
LSFSYMRHAQVNITLCLVFALTETNTTNLVLGVILYLFPESLESIKTNELIKDESLIIPL
CRKIKEHLRSQWIDRMDITNAAYLLLGSCTDGLDTIKVFKKHNYDKKIVAVSIMIQQKLK
QLNQSICFH
>MelaPMNV
MFDHFDPEHFLIVYSPIAFLSIITRNFALIREMSLQDDLYLSTSSDEIEDDNESEEEEDD
DDDYDDNGDSVNDKDDDDDVEFDPDKTNSTVLLTHVPRKGTYVSRIAHDESDSRGCSKSV
ISDTDSGSQTSSVSQSNEHRWRMSLRHQRKRFRHNNFDHHVRTTSPQMVVLSQPMNVLGA
LANEERTAMEVAEITLTQGSLAMSEPDREALLTFYREIKTIISAYLSLVHIQRTLNNYNT
NSINYPEGMVKKILSIIRQIPRHEMSMEKYNVVCRDALFLYYTIITRMTGPKHSKRLRTP
YWQFYFCGVLAMLVNDVPVASDLTVSGKETSLVQFASAVGNPAYQTAVHDISSVYNSSYS
VYKALGLSRSQLTDANMVLAILSARNTHLSDRKPRTMAQSALLYRNPDLIDRMRASGLVQ
DESSLGSTSRAVAAQLRVAGVSNQTLDDASHFLHGSYNQEGVTLRCFGSGQRDLKTVAAS
VLVTEDLRRRIRTTW
>MellatMJNV
MKYIFSDDDDDDNSTISNSNSSSNKSSDNSDIEDDEDDDNDEDLDNYQSILLMSKNDTNH
IIEKKFEHDNSIHSNNIDNKNIPFCSSFDMKETLEIKHDNTSKKNITYEYDSSNNRKDTE
EGQEDKRGPLLITNPKEVVDEILREEKKTSSETIIGYALSKYSKESVESLSMFKEEIILI
LQMYAKMKCRQQLLGNFNTNSTNYSEEMVKKMIEIISRIDKNSMALDKYRDVVREALYIY
HLVVSKMTGPKHLKRLRTPDLHFDFCVIVALLAHNIEVNKSNFSKYRATSLIQFVSALDC
QWYLSVVPNILSVFNSSSSICQIIGFSALKHAKINIILCLLFNIFEKKPNNLVLATILYL
YPESLNVIKQNGLIRDEASVIALSKKIKIHLDDYWIYQSDIHCAANLLIGQWTEGLNIIK
LFKKQHYDKKVIAISLLVQQRLKQLNQTVEYY

rename_single_copy_orthologs.py

Requirements

• Biopython

Usage

Outputディレクトリは事前に作成する必要がある。

 ./rename_single_copy_orthologs.py
usage: rename_single_copy_orthologs.py [-h] --input DIR --output DIR -t ORTHOGROUPS -s SINGLE_COPY_ORTHOLOGUES

Rename single-copy orthologue sequences identified by OrthoFinder2

optional arguments:
  -h, --help            show this help message and exit
  --input DIR, -i DIR, --in DIR
                        Single_Copy_Orthologue_Sequences directory
  --output DIR, -o DIR, --out DIR
                        output directory
  -t ORTHOGROUPS, --orthogroups ORTHOGROUPS
                        Orthogroups.tsv
  -s SINGLE_COPY_ORTHOLOGUES, --single_copy_orthologues SINGLE_COPY_ORTHOLOGUES
                        Orthogroups_SingleCopyOrthologues.txt

テーブルを複数指定する必要があるなど若干ぎこちない点があるが、問題なく作動するためよしとする。