GenBank下载的cds和gff格式更改为MCscan(jcv

作者: SnorkelingFan凡潜 | 来源:发表于2021-08-30 22:35 被阅读0次

GenBank下载的cds和gff格式更改为MCscan(jcv
几种绘制基因组共线图的方法
基因家族分析十（基因家族加倍分析）
gbff 文件
Biostar handbook学习笔记四
技巧 | GenBank/EMBL 转换为 GFF 格式
gff to cds/pep
GenBank部分基因组.gff信息存在的小问题：UTR注释不全
练习：基因家族
gffread处理工具

#先重新生成初步的cds文件
perl /ldfssz1/MS_OP/USER/00.genome/06.GenomeAnnotation/02.gene/01.StructuralAnnotation/00.gene/03.maker/getGene.pl GCA_019343175.1_Ogib_1.0_genomic.gff GCA_019343175.1_Ogib_1.0_genomic.fna > Ogib-raw.cds

#再利用原有的gff得到初步的bed文件，注意 这个的key为ID
python3 -m jcvi.formats.gff bed --type=mRNA --key=ID GCA_019343175.1_Ogib_1.0_genomic.gff -o Ogib-raw.bed

#然后再处理初步的raw.cds
/ldfssz1/MS_OP/USER/seqkit grep -f <(cut -f 4 Ogib-raw.bed) Ogib-raw.cds | /ldfssz1/MS_OP/USER/seqkit seq -i > Ogib.cds

#最后替换掉不要的字符ID
vi Ogib.cds # :%s/rna-gnl|WGS:JAFNEN|//g
vi Ogib.raw.bed # :%s/rna-gnl|WGS:JAFNEN|//g > mv Ogib.raw.bed Ogib.bed

修改前gff：

##gff-version 3
#!gff-spec-version 1.21
#!processor NCBI annotwriter
#!genome-build Ogib_1.0
#!genome-build-accession NCBI_Assembly:GCA_019343175.1
##sequence-region CM033270.1 1 49491545
##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=931172
CM033270.1      Genbank region  1       49491545        .       +       .       ID=CM033270.1:1..49491545;Dbxref=taxon:931172;Name=LG01;collected-by=Frederik Hendrickx;collection-date=2019-03-27;country=Belgium: Tielt-Winge%2C Walenbos;dev-stage=adult;gbkey=Src;genome=chromosome;identified-by=Hendrickx Frederik;isolate=W744_W776;isolation-source=pool of 12 gibbosus (Gg) and 6 tuberosus (gg) offspring of W744 (f%2C Gg) x W776 (m%2C gg) cross;linkage-group=LG01;mol_type=genomic DNA;tissue-type=whole body
CM033270.1      Genbank gene    115832  120915  .       +       .       ID=gene-JTE90_000925;Name=JTE90_000925;gbkey=Gene;gene_biotype=protein_coding;locus_tag=JTE90_000925
CM033270.1      Genbank mRNA    115832  120915  .       +       .       ID=rna-gnl|WGS:JAFNEN|g932.t1;Parent=gene-JTE90_000925;gbkey=mRNA;locus_tag=JTE90_000925;orig_protein_id=gnl|WGS:JAFNEN|g932.t1.CDS4;orig_transcript_id=gnl|WGS:JAFNEN|g932.t1;product=hypothetical protein
CM033270.1      Genbank exon    115832  116130  .       +       .       ID=exon-gnl|WGS:JAFNEN|g932.t1-1;Parent=rna-gnl|WGS:JAFNEN|g932.t1;gbkey=mRNA;locus_tag=JTE90_000925;orig_protein_id=gnl|WGS:JAFNEN|g932.t1.CDS4;orig_transcript_id=gnl|WGS:JAFNEN|g932.t1;product=hypothetical protein
CM033270.1      Genbank exon    116676  117024  .       +       .       ID=exon-gnl|WGS:JAFNEN|g932.t1-2;Parent=rna-gnl|WGS:JAFNEN|g932.t1;gbkey=mRNA;locus_tag=JTE90_000925;orig_protein_id=gnl|WGS:JAFNEN|g932.t1.CDS4;orig_transcript_id=gnl|WGS:JAFNEN|g932.t1;product=hypothetical protein
CM033270.1      Genbank exon    119917  120174  .       +       .       ID=exon-gnl|WGS:JAFNEN|g932.t1-3;Parent=rna-gnl|WGS:JAFNEN|g932.t1;gbkey=mRNA;locus_tag=JTE90_000925;orig_protein_id=gnl|WGS:JAFNEN|g932.t1.CDS4;orig_transcript_id=gnl|WGS:JAFNEN|g932.t1;product=hypothetical protein
CM033270.1      Genbank exon    120634  120915  .       +       .       ID=exon-gnl|WGS:JAFNEN|g932.t1-4;Parent=rna-gnl|WGS:JAFNEN|g932.t1;gbkey=mRNA;locus_tag=JTE90_000925;orig_protein_id=gnl|WGS:JAFNEN|g932.t1.CDS4;orig_transcript_id=gnl|WGS:JAFNEN|g932.t1;product=hypothetical protein
CM033270.1      Genbank CDS     115832  116130  .       +       0       ID=cds-KAG8178410.1;Parent=rna-gnl|WGS:JAFNEN|g932.t1;Dbxref=NCBI_GP:KAG8178410.1;Name=KAG8178410.1;gbkey=CDS;locus_tag=JTE90_000925;orig_transcript_id=gnl|WGS:JAFNEN|g932.t1;product=hypothetical protein;protein_id=KAG8178410.1
CM033270.1      Genbank CDS     116676  117024  .       +       1       ID=cds-KAG8178410.1;Parent=rna-gnl|WGS:JAFNEN|g932.t1;Dbxref=NCBI_GP:KAG8178410.1;Name=KAG8178410.1;gbkey=CDS;locus_tag=JTE90_000925;orig_transcript_id=gnl|WGS:JAFNEN|g932.t1;product=hypothetical protein;protein_id=KAG8178410.1

修改前cds:

>lcl|CM033270.1_cds_KAG8178410.1_1 [protein=hypothetical protein] [protein_id=KAG8178410.1] [location=join(115832..116130,116676..117024,119917..120174,120634..120915)] [gbkey=CDS]
ATGTACGACGAGGGTGACTACATGAACATCGAGGCGGAGGTGGTGGACCCGCCCCCTCTGGCCACGCCCACCTCTATGCT
CCGCCTACTCCTCAACGACTCCTCCTACAACACCTGCCTCAACGCGTCCGGAAACGCCTCCGACTGCCTCGTCA

>lcl|CM033270.1_cds_KAG8178411.1_2 [protein=hypothetical protein] [protein_id=KAG8178411.1] [location=complement(join(274090..274182,276089..276244,277270..277335,280085..280129,283091..283189,283731..283826))] [gbkey=CDS]

修改中的bed:

CM033270.1      115831  120915  rna-gnl|WGS:JAFNEN|g932.t1      0       +
CM033270.1      274089  283826  rna-gnl|WGS:JAFNEN|g933.t1      0       -
CM033270.1      296836  313992  rna-gnl|WGS:JAFNEN|g934.t1      0       +
CM033270.1      314014  349328  rna-gnl|WGS:JAFNEN|g935.t1      0       +
CM033270.1      392062  406150  rna-gnl|WGS:JAFNEN|g936.t1      0       -
CM033270.1      406800  411410  rna-gnl|WGS:JAFNEN|g937.t1      0       +
CM033270.1      415405  464590  rna-gnl|WGS:JAFNEN|g938.t1      0       -

修改后bed:

CM033270.1      115831  120915  g932.t1 0       +
CM033270.1      274089  283826  g933.t1 0       -
CM033270.1      296836  313992  g934.t1 0       +
CM033270.1      314014  349328  g935.t1 0       +
CM033270.1      392062  406150  g936.t1 0       -
CM033270.1      406800  411410  g937.t1 0       +
CM033270.1      415405  464590  g938.t1 0       -
CM033270.1      415405  464590  g938.t2 0       -
CM033270.1      415405  464590  g938.t3 0       -
CM033270.1      467143  468161  g939.t1 0       -
CM033270.1      487031  490127  g940.t1 0       -
CM033270.1      490836  505647  g941.t1 0       +
CM033270.1      514650  515337  g942.t1 0       +
CM033270.1      568169  568409  g943.t1 0       +
CM033270.1      586980  591160  g944.t1 0       -

修改后cds:

>g10347.t1
ATGGAAATTATAACGGGCTCCTTTGAGGTACTTCTCATTCACCGATTCCCGCATGAGAGG
TGTATGAAGCACAAATCTCTCTCCGATGCCGACGTGGTGTACGGCCACATGGTGTTTACC
CCTTCCCCTTACCACAACGACAGCGTAGGGGGTGGAGGGTGGGAAGAAGATTTGGAGGAA
ATTCTGCGCAAGGAGGGCTGCTTCCACCCGGACGCTGCTTTTCCTAGCCAACTGCACCAC
ATGAACGATCATGACAGCCTAGAGATAGAAGGTGAGAGGAGTCACCTTAAATCTGCTTTA
TACCAGAGAAGAGCTAAACTAATTTGA
>g10348.t1