unable to parse MiTCR outputs about tcr

[vadimnazarov]

Hello Joon,

It's unexpected that MiTCR output do not have the first line with metadata. The MiTCR parser function tries to skip first line and then starts to read column names and rows. Have you removed somehow the very first line from the MiTCR output and then tried to parse it?

Anyway, you could use this function to parse MiTCR files without skipping the first line:
https://gist.github.com/vadimnazarov/1b438863748fdc3bccf1

[joonlee3]

First of all, thank you so much for your quick reply.

No. I ran MiTCR with one of the output format options '-level=2'.

It seems that the first line with metadata is added to the output when -level=3. Can these parse functions work with level 3 MiTCR outputs?

[vadimnazarov]

I just realised that this file structure could be due to the MiTCR run parameters. If you run MiTCR with -level 3 parameter then parse.mitcr should work. I will try to fix this issue with the first line in the couple of days.

[vadimnazarov]

Yes!

[vadimnazarov]

I will post in this topic when I fix this issue to let you know about this update. Please let me know about any issues with parse.mitcr with -level 3 and/or other bugs, I would greatly appreciate this.

[joonlee3]

It works well with level 3 data set. Thank you so much for your support.

[vadimnazarov]

Dear Joon,

I've just added the feature to parse different levels of MiTCR's output to the parse.mitcr function. If you would like to use it, please let me know if it works for you.

[joonlee3]

Thanks a lot. I'll try later and let you know. ^^

[juni-juli]

Dear Vadim,

I have the same problem as Joon, except that using level 3 output does not fix my problem:

Error in [.data.frame(df, , make.names(c(.barcodes, .umi.prop, .reads, :
undefined columns selected

My first line contains metadata:

MiTCRFullExportV1.1 HomoSapiens TRB /media/sf_VMdata/mitcr/file1.fastq.gz 1.01.0.3TRBHomoSapiens25both-41123both-14122310010both0.153oneMismatch0.33
Read count Percentage CDR3 nucleotide sequence CDR3 nucleotide quality Min quality CDR3 amino acid sequence V alleles V segments J alleles J segments D alleles D segments Last V nucleotide position First D nucleotide position Last D nucleotide position First J nucleotide position VD insertions DJ insertions Total insertions
5888 0.014855894293045634 TGTGCCAGCAGTGATTCGCGCGTCCAAGGGGCCAACGTCCTGACTTTC HHHHHHHHGHHIHIIHIHGGGGGGGGHHGGGGGGHGGHHGGHHHHHHH 38 CASSDSRVQGANVLTF TRBV6-1_01 TRBV6-1 TRBJ2-6_01 TRBJ2-6 TRBD1_01, TRBD2_02, TRBD2_01 TRBD1, TRBD2 13 21 24 27 7 2 9
4048 0.010213427326468873 TGTGCCAGCAACCCTGCGGGACAGTCAAAGGGACAGCAGTTCTTC HHHHHHHHGHHHHGHHHHGGGGHGHHHHHHHGHGGGHHHHHHHHH 38 CASNPAGQSKGQQFF TRBV6-1_01 TRBV6-1 TRBJ2-1_01 TRBJ2-1 TRBD1_01 TRBD1 9 17 23 34 7 10 17

Do you have any idea what might cause this?
Thanks in advance!

[vadimnazarov]

Hi!

Could you please update to the latest development version via

install.packages("devtools")
devtools::install_github("imminfo/tcR", build_vignettes = FALSE, ref = "develop")

and try to parse files again?

[juni-juli]

Hi, thanks for the quick response!
The installation failed with this message:

library(devtools)
devtools::install_github("imminfo/tcR", build_vignettes = FALSE, ref = "develop")
Downloading github repo imminfo/tcR@develop
Installing tcR
"C:/PROGRA1/R/R-321.1/bin/x64/R" --no-site-file --no-environ --no-save --no-restore CMD INSTALL
"C:/Users/WSUser/AppData/Local/Temp/RtmpS4Ig9x/devtools1e445fbb3a1a/imminfo-tcr-3a98516"
--library="C:/Users/WSUser/Documents/R/win-library/3.2" --install-tests

• installing source package 'tcR' ...
  ** libs

*** arch - i386
Warnung: Ausführung von Kommando 'make -f "Makevars" -f "C:/PROGRA1/R/R-321.1/etc/i386/Makeconf" -f "C:/PROGRA1/R/R-321.1/share/make/winshlib.mk" CXX='$(CXX1X) $(CXX1XSTD)' CXXFLAGS='$(CXX1XFLAGS)' CXXPICFLAGS='$(CXX1XPICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX1XLDFLAGS)' SHLIB_LD='$(SHLIB_CXX1XLD)' SHLIB="tcR.dll" OBJECTS="RcppExports.o neighbour.search.o"' ergab Status 127
ERROR: compilation failed for package 'tcR'

• removing 'C:/Users/WSUser/Documents/R/win-library/3.2/tcR'
• restoring previous 'C:/Users/WSUser/Documents/R/win-library/3.2/tcR'
  Error: Command failed (1)

[vadimnazarov]

Hi,

could you please install Rtools (http://cran.r-project.org/bin/windows/Rtools/) for Windows, that is needed to build packages?