在data.table :: fread中绕过"ghost"换行符或文件结尾(EOF)

Question

我正在加载从(可访问我)数据库导出的几个大的制表符分隔文本文件到R使用data.table::fread. fread处理大多数文件非常容易和速度,但其中一个文件正在生成一个定期报告的fread错误:

Error in fread(read_problem, encoding = "UTF-8", na.strings = "", header = TRUE,  : 
                   Expected sep ('  ') but new line or EOF ends field ...

此处提供了包含违规行的较小(2000行)版本的文件(RDS文件).

以下是我尝试诊断问题的方法:

library(data.table) # I'm using 1.9.7 development (same error with 1.9.6)
read_problem <- readRDS("read_problem.rds")
error <- fread(read_problem, encoding = "UTF-8", na.strings = "",
               header = TRUE, sep = "\t", 
               colClasses = rep("character", 44),  # For simplicity
               verbose = TRUE)

如果我删除违规行,问题就会消失:

cat(read_problem, file = "temp")   
string_vec <- readLines("temp")
clipped_vec <- string_vec[-1027] # Get rid of problem line 1027
restored <- paste(clipped_vec, collapse = "\n")
noerror <- fread(restored, encoding = "UTF-8", na.strings = "",
                 header = TRUE, sep = "\t", 
                 colClasses = rep("character", 44)) # For simplicity
class(noerror)
[1] "data.table" "data.frame"

dim(noerror) 
[1] 1999   44

错误消息似乎足够清楚:fread正在寻找一个"\ t",但在其位置找到了其他东西.

但是,仔细观察相对于周围环境的违规线,我没有发现任何明显的结果.

制表符的数量是相同的

sapply(gregexpr("\t", string_vec[1026:1028]), length)
[1] 43 43 43

换行信息似乎相同

unlist(gregexpr("\n", string_vec[1026:1028]))
[1] -1 -1 -1

以下是将违规行本身视为字符串:

string_vec[1027]
[1] "URN:CornellLabOfOrnithology:EBIRD:OBS132960387\t29816\tspecies\tNelson's Sparrow\tAmmodramus nelsoni\t\t\t1\t\t\tUnited States\tUS\tGeorgia\tUS-GA\tGlynn\tUS-GA-127\tUS-GA_3181\t\t\tJekyll Island\tL140461\tH\t31.0464993\t-81.4113007\t1990-11-03\t13:15:00\t\"Jekyll Island and Causeway. Partly cloudy, mild, NE wind 8-15 mph. Note: Did very little birding in upland habitats as time available was rather brief.\"  Data entered on behalf of Paul Sykes by Alison Huff (arhuff@uga.edu) on 12-15-11.\tListed on old Georgia Field Checklist as \"Sparrow, Sharp-tailed.\"\tobsr289931\tPaul\tSykes\tS9336358\teBird - Traveling Count\tEBIRD\t270\t8.047\t\t1\t1\t\t1\t0\t\t"

有什么建议可以解决这个问题而无需手动提取有问题的线路？

Answer 1

通过此提交,现在已在当前开发版本的v1.9.7中修复.因此,下一个稳定版本应该能够正确使用quote="".

require(data.table) #v1.9.7+
fread('"abcd efgh." ijkl.\tmnop "qrst uvwx."\t45\n', quote="")
#                    V1                V2 V3
# 1: "abcd efgh." ijkl. mnop "qrst uvwx." 45

在第1027行,最后"Sparrow, Sharp-tailed."只有一个标签.在其他行中,在该字段之后,在"obsr [0-9]"字段开始之前有两个.

选项卡的数量似乎匹配,因为在第1027行,在"在旧的Georgia Field上列出"而不是空格之前有一个选项卡.

因此,线1027只获得43个col而不是44.这似乎是个问题.

再看一遍,似乎Listed on old Georgia Field Checklist as "Sparrow, Sharp-tailed."应该作为一个单独的列阅读,而是与前一列一起阅读......

这是一个可重复的小例子:

# note that there are only 2 instead of 3 columns
fread('"abcd efgh." ijkl.\tmnop "qrst uvwx."\t45\n')
#                                     V1 V2
# 1: abcd efgh." ijkl.\tmnop "qrst uvwx. 45

# add a header column and it returns the same error
fread('a\tb\tc\n"abcd efgh." ijkl.\tmnop "qrst uvwx."\t45\n')
# Error in fread("a\tb\tc\n\"abcd efgh.\" ijkl.\tmnop \"qrst uvwx.\"\t45\n") : 
#   Expected sep (' ') but new line, EOF (or other non printing character) 
#   ends field 1 when detecting types (   first): "abcd efgh." ijkl.    mnop 
#   "qrst uvwx."    45

提起1367年.