input files for add-methylation-level about methylpy HOT 9 CLOSED

Hi, it is possible to run methylpy with the 3 columns missing but they need to be filled with appropriate values. I would suggest "+" for strand, "CGN" for sequence context and "1" for methylated. Please let me know if it works.

Yupeng

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Hi, Yupeng, thanks very much for your quick reply and your suggestion.

Yes, it works! I am just wondering if it is reasonable to have more than 95% ( 225901/27751) "NA" in the output?

I also got another little question. I compress all the cell allc files into only ONE .tgz files, is it possible for "add-methylation-level" to take .tgz (compressed file) and recognize it as several allc input files? Since I have tried one .tgz file, it seemed that the program never ends.

Thanks again!

from methylpy.

You may want to check whether the tsv file is sorted by coordinates. Otherwise, the values you got are probably not correct.

Thanks for the suggestion but taking a tar ball as input is not supported by methylpy yet.

Yupeng

from methylpy.

Hi, Yupeng, thank you for your reply.

May I know further what "tsv file is sorted by corordinates" means? Does it mean for every chromosome, I need to sort the positions from least number to largest number?

Thanks in advance!

from methylpy.

Exactly. You can use the below command to do that.

tail -n +2 TSV_FILE|sort -k 1,1 -k 2,2g -k 3,3g |cat header - > TSV_FILE_REFORMATTED
rm header

from methylpy.

Hi, Yupeng, thank you for the further suggestion, and it really helps! After sorting the coordinates, the results become more reasonable.

Thanks again for your time and valuable advice!

from methylpy.

Hi, Yupeng. Sorry to bother you again.

Now I am running "add-methylation_level" for 52 samples, and I got an error message as below.

rm: cannot remove ‘March15_HSC_methy_gene_level_cmp_0_D2_1_R2_allc_reformed_temp_methylation_levels.tsv’: No such file or directory
Traceback (most recent call last):
File "/home/wangwujiaxuan/.local/bin/methylpy", line 5, in
parse_args()
File "/home/wangwujiaxuan/.local/lib/python2.7/site-packages/methylpy/parser.py", line 270, in parse_args
input_no_header=args.input_no_header)
File "/home/wangwujiaxuan/.local/lib/python2.7/site-packages/methylpy/DMRfind.py", line 888, in get_methylation_levels_DMRfind
subprocess.check_call(shlex.split("rm "+output.replace(".tsv","")+"_"+sample+"_temp_methylation_levels.tsv"))
File "/usr/lib64/python2.7/subprocess.py", line 542, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['rm', 'March15_HSC_methy_gene_level_cmp_0_D2_1_R2_allc_reformed_temp_methylation_levels.tsv']' returned non-zero exit status 1

FYI, 'March15_HSC_methy_gene_level_cmp.tsv' is my output file name, and 'CMP_50_D2_1_R2_allc_reformed.tsv' is my input allc filename.

Since I have 'CMP_50_D2_1_R2_allc_reformed.tsv' and 'CMP_10_D2_1_R2_allc_reformed.tsc', according to the output name, these two will share the same name "March15_HSC_methy_gene_level_cmp_0_D2_1_R2_allc_reformed_temp_methylation_levels.tsv". Is this the reason which causes the error? If it is, is it possible to output full allc filename to avoid this kind of confusion? If it is not, may I know is there any way to deal with it?

Thank in advance! Looking forward to your reply!

from methylpy.

Hi, the naming of allc files look like the cause. I would recommend changing the names of the allc files such that they have different basename (e.g. "CMP_50_D2_1_R2_allc_reformed_1" and "CMP_50_D2_1_R2_allc_reformed_2") and the same suffix ".tsv".

Yupeng

from methylpy.

Hi, Yupeng.

Sure, I have already changed the name. Thanks again for your continuous help!

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