[Seqinr-forum] read.fasta fails to read a gzipped compressed file from a ftp server

Jean Lobry jean.lobry at univ-lyon1.fr
Sat Apr 21 20:02:02 CEST 2018 

Dear all,

I was able to reproduce the well documented faulty behaviour as follows:

-------------------------- BEGIN ------------------------------------
$ R --quiet
 > library("seqinr")
 > filename <- 
"ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/008/865/GCF_000008865.1_ASM886v1/GCF_000008865.1_ASM886v1_rna_from_genomic.fna.gz"
 > ld <- read.fasta(file = filename)
Error in substr(lines, 1L, 1L) :
   chaîne de charactères multioctets incorrecte à 
'<aa><89><b4>b<68><8d><a4>c0<ed><B$<97>	O<eb>3:<d2>ڀR 
46<a4>L<9b><91>d<ba><b2>9<a6><c4>k!<d2>z<a6>G<8d>4<bb> 
פa0>2H[<ac>X<d2>VP<b0>a<d2>tj<84><e6><99>&<95><8e><86>Kt<ac>OHZ:@<d7>.
 
|Sэ<e8><81>#<e9><ae><9a><9f>ab><bb>b<ac>ab>W<d7>W<8c><95><93><8d><d5><d0>/<8c><d5>]6<?<fb><cd><f5>ա<8d>\e5><86>a<b2>Qw<b0>Q<b4><90>` 
<8e>#-M<a8><9d<f5><db><9a>
                                                  z
 
d$|<8a>4r<dc>¥<d7><f3><eb><e7><ae>a<d7>p<8c>+\??<c2>5<e8><8e>p<f9><d6><e1>!<aa><94>"`E2<a1>iR<ab><88><e6><89>'
De plus : There were 27 warnings (use warnings() to see them)
 > sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: 
/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: 
/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] seqinr_3.4-5

loaded via a namespace (and not attached):
[1] compiler_3.4.1 ade4_1.7-8
 > q()
Save workspace image? [y/n/c]: n

-------------------------- END ------------------------------------

Rings a bell to me, I'll post a solution asap.

Best,

JLO


-------- Message transféré --------
Sujet : 	Re: Error in library(help=seqinr)
Date : 	Sun, 22 Apr 2018 02:21:23 +0900
De : 	Haruo Suzuki <haruo at sfc.keio.ac.jp>
Pour : 	Simon Penel <simon.penel at univ-lyon1.fr>
Copie à : 	jean.lobry at univ-lyon1.fr



Dear Simon,

The `read.fasta` function of seqinr package failed to load the gzipped 
FASTA file directly from the ftp site, simply by specifying a full URL, 
as shown in attachment.

Yours sincerely,
Haruo Suzuki
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> 
> library("seqinr")
> filename <- "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/008/865/GCF_000008865.1_ASM886v1/GCF_000008865.1_ASM886v1_rna_from_genomic.fna.gz"
> ld <- read.fasta(file = filename)
Error in substr(lines, 1L, 1L) : 
  invalid multibyte string at '<aa><89><b4>b<68><8d><a4>c0<ed><B$<97>	O<eb>3:<d2>ڀR	46<a4>L<9b><91>d<ba><b2>9<a6><c4>k!<d2>z<a6>G<8d>4<bb>	פ<a0>2H[<ac>X<d2>VP<b0>a<d2>tj<84><e6><99>&<95><8e><86>Kt<ac>OHZ:@<d7>.
|Sэ<e8><81>#<e9><ae><9a><9f><ab><bb>b<ac><ab>W<d7>W<8c><95><93><8d><d5><d0>/<8c><d5>]6<?<fb><cd><f5>ա<8d>\<e5><86>a<b2>Qw<b0>Q<b4><90>` <8e>#-M<a8><9d<f5><db><9a>
z
d$|<8a>4r<dc>¥<d7><f3><eb><e7><ae>a<d7>p<8c>+\??<c2>5<e8><8e>p<f9><d6>
<e1>!<aa><94>"`E2<a1>iR<ab><88><e6><89>'
In addition: There were 27 warnings (use warnings() to see them)
> 
> warnings()
Warning messages:
1: In readLines(file) : line 1 appears to contain an embedded nul
2: In readLines(file) : line 3 appears to contain an embedded nul
3: In readLines(file) : line 4 appears to contain an embedded nul
4: In readLines(file) : line 9 appears to contain an embedded nul
5: In readLines(file) : line 10 appears to contain an embedded nul
6: In readLines(file) : line 13 appears to contain an embedded nul
7: In readLines(file) : line 15 appears to contain an embedded nul
8: In readLines(file) : line 17 appears to contain an embedded nul
9: In readLines(file) : line 22 appears to contain an embedded nul
10: In readLines(file) : line 28 appears to contain an embedded nul
11: In readLines(file) : line 30 appears to contain an embedded nul
12: In readLines(file) : line 32 appears to contain an embedded nul
13: In readLines(file) : line 34 appears to contain an embedded nul
14: In readLines(file) : line 40 appears to contain an embedded nul
15: In readLines(file) : line 46 appears to contain an embedded nul
16: In readLines(file) : line 50 appears to contain an embedded nul
17: In readLines(file) : line 52 appears to contain an embedded nul
18: In readLines(file) : line 53 appears to contain an embedded nul
19: In readLines(file) : line 54 appears to contain an embedded nul
20: In readLines(file) : line 70 appears to contain an embedded nul
21: In readLines(file) : line 71 appears to contain an embedded nul
22: In readLines(file) :
  incomplete final line found on 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/008/865/GCF_000008865.1_ASM886v1/GCF_000008865.1_ASM886v1_rna_from_genomic.fna.gz'
23: In grep("^;", lines) : input string 1 is invalid in this locale
24: In grep("^;", lines) : input string 2 is invalid in this locale
25: In grep("^;", lines) : input string 4 is invalid in this locale
26: In grep("^;", lines) : input string 5 is invalid in this locale
27: In grep("^;", lines) : input string 6 is invalid in this locale
> sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X Mavericks 10.9.5

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] seqinr_3.4-6

loaded via a namespace (and not attached):
[1] MASS_7.3-45 ade4_1.7-10
> 
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