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What kind of error should be checked by a validator while validating biological file formats like GFF and FASTA
The 2019 Stack Overflow Developer Survey Results Are InEfficient file buffering & scanning methods for large files in pythonUsing a .fasta file to compute relative content of sequencesPerl program printing full .fasta file sequences to file, but trying to achieve specific nucleotide count with respect to genesHow to add snp/indels from a CSV file to a FASTA file using Biopython?DNAStringSet Error Biostrings in RPrinting a sequence from a fasta fileHow to retrieve all fasta records that contain any of a list of strings in the headerReplace multiple lines in one file with the same lines at the same line numbers in another file?Renaming files according to fasta headerPerl6 : What is the best way for dealing with very big files?
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I'm working on a project to create a library(in Java) that can validate various biological file formats like GFF, FASTA, OBO etc.
But as I'm not from this field, So I'm little confused about what kind of validation should be performed by the validator program.
There are some online tools like Genome Tools that can validate GFF file format, So can anyone help me understand what kind of validation rules should be applied on easy of these files.
fasta gff
asked Mar 22 at 4:52
Deepak SinghDeepak Singh
11
add a comment |
I'm working on a project to create a library(in Java) that can validate various biological file formats like GFF, FASTA, OBO etc.
But as I'm not from this field, So I'm little confused about what kind of validation should be performed by the validator program.
There are some online tools like Genome Tools that can validate GFF file format, So can anyone help me understand what kind of validation rules should be applied on easy of these files.
fasta gff
asked Mar 22 at 4:52
Deepak SinghDeepak Singh
11
There are two kinds of validations: format validations and data validations. First of all, you should search for the documentation of those formats and make sure the files comply with them (format validation). Second, you should check for the validity of the contents. In that case, better ask a bioinformatic or biologist about which are the suitable contents (like DNA must be formed with [ATGC], or the ranges of the exons must be in the ranges of the chromosome). The second part is the difficult one.
– Poshi
Mar 22 at 10:22
@Posh thanks for your response, yes I really want information about the second type(validity of content), Do any know any resource where I can look for this kind of Information Or correct place to ask this question?
– Deepak Singh
Mar 22 at 17:25
It all depends on the kind of file you are processing. The best source, your local bioinformatic. You can read biology books, but there are some details that are not covered because are related to technical issues.
– Poshi
Mar 22 at 17:27
add a comment |
I'm working on a project to create a library(in Java) that can validate various biological file formats like GFF, FASTA, OBO etc.
But as I'm not from this field, So I'm little confused about what kind of validation should be performed by the validator program.
There are some online tools like Genome Tools that can validate GFF file format, So can anyone help me understand what kind of validation rules should be applied on easy of these files.
fasta gff
asked Mar 22 at 4:52
Deepak SinghDeepak Singh
11
I'm working on a project to create a library(in Java) that can validate various biological file formats like GFF, FASTA, OBO etc.
But as I'm not from this field, So I'm little confused about what kind of validation should be performed by the validator program.
There are some online tools like Genome Tools that can validate GFF file format, So can anyone help me understand what kind of validation rules should be applied on easy of these files.
fasta gff
fasta gff
asked Mar 22 at 4:52
Deepak SinghDeepak Singh
11
asked Mar 22 at 4:52
Deepak SinghDeepak Singh
11
asked Mar 22 at 4:52
Deepak SinghDeepak Singh
11
asked Mar 22 at 4:52
Deepak SinghDeepak Singh
11
asked Mar 22 at 4:52
Deepak SinghDeepak Singh
11
11
There are two kinds of validations: format validations and data validations. First of all, you should search for the documentation of those formats and make sure the files comply with them (format validation). Second, you should check for the validity of the contents. In that case, better ask a bioinformatic or biologist about which are the suitable contents (like DNA must be formed with [ATGC], or the ranges of the exons must be in the ranges of the chromosome). The second part is the difficult one.
– Poshi
Mar 22 at 10:22
@Posh thanks for your response, yes I really want information about the second type(validity of content), Do any know any resource where I can look for this kind of Information Or correct place to ask this question?
– Deepak Singh
Mar 22 at 17:25
It all depends on the kind of file you are processing. The best source, your local bioinformatic. You can read biology books, but there are some details that are not covered because are related to technical issues.
– Poshi
Mar 22 at 17:27
add a comment |
There are two kinds of validations: format validations and data validations. First of all, you should search for the documentation of those formats and make sure the files comply with them (format validation). Second, you should check for the validity of the contents. In that case, better ask a bioinformatic or biologist about which are the suitable contents (like DNA must be formed with [ATGC], or the ranges of the exons must be in the ranges of the chromosome). The second part is the difficult one.
– Poshi
Mar 22 at 10:22
@Posh thanks for your response, yes I really want information about the second type(validity of content), Do any know any resource where I can look for this kind of Information Or correct place to ask this question?
– Deepak Singh
Mar 22 at 17:25
It all depends on the kind of file you are processing. The best source, your local bioinformatic. You can read biology books, but there are some details that are not covered because are related to technical issues.
– Poshi
Mar 22 at 17:27
There are two kinds of validations: format validations and data validations. First of all, you should search for the documentation of those formats and make sure the files comply with them (format validation). Second, you should check for the validity of the contents. In that case, better ask a bioinformatic or biologist about which are the suitable contents (like DNA must be formed with [ATGC], or the ranges of the exons must be in the ranges of the chromosome). The second part is the difficult one.
– Poshi
Mar 22 at 10:22
There are two kinds of validations: format validations and data validations. First of all, you should search for the documentation of those formats and make sure the files comply with them (format validation). Second, you should check for the validity of the contents. In that case, better ask a bioinformatic or biologist about which are the suitable contents (like DNA must be formed with [ATGC], or the ranges of the exons must be in the ranges of the chromosome). The second part is the difficult one.
– Poshi
Mar 22 at 10:22
@Posh thanks for your response, yes I really want information about the second type(validity of content), Do any know any resource where I can look for this kind of Information Or correct place to ask this question?
– Deepak Singh
Mar 22 at 17:25
@Posh thanks for your response, yes I really want information about the second type(validity of content), Do any know any resource where I can look for this kind of Information Or correct place to ask this question?
– Deepak Singh
Mar 22 at 17:25
It all depends on the kind of file you are processing. The best source, your local bioinformatic. You can read biology books, but there are some details that are not covered because are related to technical issues.
– Poshi
Mar 22 at 17:27
It all depends on the kind of file you are processing. The best source, your local bioinformatic. You can read biology books, but there are some details that are not covered because are related to technical issues.
– Poshi
Mar 22 at 17:27
add a comment |
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There are two kinds of validations: format validations and data validations. First of all, you should search for the documentation of those formats and make sure the files comply with them (format validation). Second, you should check for the validity of the contents. In that case, better ask a bioinformatic or biologist about which are the suitable contents (like DNA must be formed with [ATGC], or the ranges of the exons must be in the ranges of the chromosome). The second part is the difficult one.
– Poshi
Mar 22 at 10:22
@Posh thanks for your response, yes I really want information about the second type(validity of content), Do any know any resource where I can look for this kind of Information Or correct place to ask this question?
– Deepak Singh
Mar 22 at 17:25
It all depends on the kind of file you are processing. The best source, your local bioinformatic. You can read biology books, but there are some details that are not covered because are related to technical issues.
– Poshi
Mar 22 at 17:27