使用 reticulate 将简单的 Python 代码块转换为 R

如何解决使用 reticulate 将简单的 Python 代码块转换为 R

这里有一个 R reticulate 新手问题。

我正在尝试将使用 python 将 biopython 文件解析为 genbank 的简单 R 代码使用 reticulate {{1} } 包。

这是 R 代码：

python

这是一个示例 from Bio import SeqIO filename = "example.protein.gpff" for record in SeqIO.parse(filename,"genbank"): for feature in record.features: if feature.type == "CDS": locus_tag = feature.qualifiers.get("locus_tag",["???"])[0] 文件，其中包含重复的 genbank（由 record 分隔），其中每个 // 都有一个 record 部分，其中有几个固定的字段，例如 FEATURES、source 和 CDS，引用特定于该 Region 的信息：

record

这是我对其 LOCUS NP_001346895 208 aa linear PRI 20-JAN-2018 DEFINITION intercellular adhesion molecule 2 precursor [Cercocebus atys]. ACCESSION NP_001346895 VERSION NP_001346895.1 DBSOURCE REFSEQ: accession NM_001359966.1 KEYWORDS RefSeq. SOURCE Cercocebus atys (sooty mangabey) ORGANISM Cercocebus atys Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Cercopithecidae; Cercopithecinae; Cercocebus. REFERENCE 1 (residues 1 to 208) AUTHORS Palesch D,Bosinger SE,Tharp GK,Vanderford TH,Paiardini M,Chahroudi A,Johnson ZP,Kirchhoff F,Hahn BH,Norgren RB,Patel NB,Sodora DL,Dawoud RA,Stewart CB,Seepo SM,Harris RA,Liu Y,Raveendran M,Han Y,English A,Thomas GWC,Hahn MW,Pipes L,Mason CE,Muzny DM,Gibbs RA,Sauter D,Worley K,Rogers J and Silvestri G. TITLE Sooty mangabey genome sequence provides insight into AIDS resistance in a natural SIV host JOURNAL Nature 553 (7686),77-81 (2018) PUBMED 29300007 COMMENT VALIDATED REFSEQ: This record has undergone validation or preliminary review. The reference sequence was derived from KY308194.1. ##Evidence-Data-START## Transcript exon combination :: KY308194.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMN02045730,SAMN03085078 [ECO:0000348] ##Evidence-Data-END## FEATURES Location/Qualifiers source 1..208 /organism="Cercocebus atys" /db_xref="taxon:9531" Protein 1..208 /product="intercellular adhesion molecule 2 precursor" /calculated_mol_wt=21138 sig_peptide 1..19 /inference="COORDINATES: ab initio prediction:SignalP:4.0" /calculated_mol_wt=1999 Region 24..109 /region_name="ICAM_N" /note="Intercellular adhesion molecule (ICAM),N-terminal domain; pfam03921" /db_xref="CDD:252248" Region 112..>167 /region_name="Ig" /note="Immunoglobulin domain; cl11960" /db_xref="CDD:325142" CDS 1..208 /gene="ICAM2" /coded_by="NM_001359966.1:1..627" /db_xref="GeneID:105590766" ORIGIN 1 mssfgfgtlt malfalvccs gsdekafevh mrleklivkp kesfevncst tcnqpevggl 61 etslnkilll eqtqwkhyli snishdtvlw chftcsgkqk smssnvsvyq pprqvfltlq 121 ptwvavgksf tiecrvpave pldsltlsll rgsetlhsqt frkaapalpv lrelgmkfiq 181 lcprrglagt mppsrpwcpa athwsqgc // LOCUS NP_001280013 406 aa linear MAM 22-JAN-2018 DEFINITION 26S proteasome regulatory subunit 8 [Dasypus novemcinctus]. ACCESSION NP_001280013 XP_004456848 VERSION NP_001280013.1 DBSOURCE REFSEQ: accession NM_001293084.1 KEYWORDS RefSeq. SOURCE Dasypus novemcinctus (nine-banded armadillo) ORGANISM Dasypus novemcinctus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Xenarthra; Cingulata; Dasypodidae; Dasypus. COMMENT VALIDATED REFSEQ: This record has undergone validation or preliminary review. The reference sequence was derived from AAGV03083693.1. On May 28,2014 this sequence version replaced XP_004456848.1. Sequence Note: The RefSeq transcript and protein were derived from genomic sequence to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on alignments. ##Evidence-Data-START## RNAseq introns :: mixed/partial sample support SAMN00668203,SAMN00744121 [ECO:0000350] ##Evidence-Data-END## FEATURES Location/Qualifiers source 1..406 /organism="Dasypus novemcinctus" /db_xref="taxon:9361" Protein 1..406 /product="26S proteasome regulatory subunit 8" /calculated_mol_wt=45495 Region 4..404 /region_name="RPT1" /note="ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification,protein turnover,chaperones]; COG1222" /db_xref="CDD:224143" CDS 1..406 /gene="PSMC5" /coded_by="NM_001293084.1:1..1221" /db_xref="GeneID:101445299" ORIGIN 1 maldgpeqme leegkagsgl rqyylskiee lqlivndksq nlrrlqaqrn elnakvrllr 61 eelqllqeqg syvgevvram dkkkvlvkvh pegkfvvdvd knidindvtp ncrvalrnds 121 ytlhkilpnk vdplvslmmv ekvpdstyem iggldkqike ikevielpvk hpelfealgi 181 aqpkgvllyg ppgtgktlla ravahhtdct firvsgselv qkfigegarm vrelfvmare 241 hapsiifmde idsigssrle ggsggdsevq rtmlellnql dgfeatknik vimatnridi 301 ldsallrpgr idrkiefppp neearldilk ihsrkmnltr ginlrkiael mpgasgaevk 361 gvcteagmya lrerrvhvtq edfemavakv mqkdseknms ikklwk // 翻译的失败尝试：

R

我得到的错误是：

library(reticulate)
si <- reticulate::import("Bio.SeqIO")
gb.fn <- "example.protein.gpff"
for(r in si$parse(gb.fn,"genbank")){
  for(f in r$features){
    if(f$type == "CDS"){
      locus.tag <- f$qualifiers$get("locus_tag",["???"])[0]
    }
  }
}

但是带有 Error in for (r in si$parse(gb.fn,"genbank")) { : invalid for() loop sequence 的行也是错误的，因为 locus.tag 将其标记为 RStudio 错误。

我正在尝试翻译成 syntax，因为我不精通 R，但是 this post 是我的 python 尝试解析这个文件，所以任何一个帮助都会很棒.