How to determine variables between two lines of input?
In my project, I have to iterate through files using Java. The idea of it is processing genome data and outputting it to a new file.
Here is an example from a couple lines of data we have to go through:
cure for cancer protein
ATGCCACTATGGTAG
captain picard hair growth protein
ATgCCAACATGgATGCCcGATAtGGATTgA
bogus protein
CCATt-AATgATCa-CAGTt
I am struggling on how one would logically decipher between the name for the region ("cure for cancer protein") and the following sequence of characters. I can get the file to display all info easily, but I need to process the sequence of characters differently than the region name and I can't figure out how to logically determine if the line is a region name or a sequence.
Any help would be greatly appreciated.
java string file loops
edited Nov 24 '18 at 17:20
oleg.cherednik
6,98421118
asked Nov 24 '18 at 16:51
N.SpiessN.Spiess
244
add a comment |
In my project, I have to iterate through files using Java. The idea of it is processing genome data and outputting it to a new file.
Here is an example from a couple lines of data we have to go through:
cure for cancer protein
ATGCCACTATGGTAG
captain picard hair growth protein
ATgCCAACATGgATGCCcGATAtGGATTgA
bogus protein
CCATt-AATgATCa-CAGTt
I am struggling on how one would logically decipher between the name for the region ("cure for cancer protein") and the following sequence of characters. I can get the file to display all info easily, but I need to process the sequence of characters differently than the region name and I can't figure out how to logically determine if the line is a region name or a sequence.
Any help would be greatly appreciated.
java string file loops
edited Nov 24 '18 at 17:20
oleg.cherednik
6,98421118
asked Nov 24 '18 at 16:51
N.SpiessN.Spiess
244
1
Based on your example, the names appear on even line numbers, and the proteins appear on odd line numbers. The names start with a lowercase, not the sequences. The names contain spaces, not the sequences.
– JB Nizet
Nov 24 '18 at 16:56
Ah, the spaces. I didn't think of that. Thank you!!
– N.Spiess
Nov 24 '18 at 16:59
1
Either you find a rigid way of distinguishing them (even f it requires reworking some files by hand, and imposing stricter formatting rules for future files), or you're forced to use heuristics. Frankly, using such a loosely defined file format for a system dealing with "cure for cancer proteins" is scary. Why not use a well-defined file format, like JSON, XML, or even simpler conventions like starting a name by#?
– JB Nizet
Nov 24 '18 at 17:02
You can split the file into lines
– preciousbetine
Nov 24 '18 at 18:59
add a comment |
In my project, I have to iterate through files using Java. The idea of it is processing genome data and outputting it to a new file.
Here is an example from a couple lines of data we have to go through:
cure for cancer protein
ATGCCACTATGGTAG
captain picard hair growth protein
ATgCCAACATGgATGCCcGATAtGGATTgA
bogus protein
CCATt-AATgATCa-CAGTt
I am struggling on how one would logically decipher between the name for the region ("cure for cancer protein") and the following sequence of characters. I can get the file to display all info easily, but I need to process the sequence of characters differently than the region name and I can't figure out how to logically determine if the line is a region name or a sequence.
Any help would be greatly appreciated.
java string file loops
edited Nov 24 '18 at 17:20
oleg.cherednik
6,98421118
asked Nov 24 '18 at 16:51
N.SpiessN.Spiess
244
In my project, I have to iterate through files using Java. The idea of it is processing genome data and outputting it to a new file.
Here is an example from a couple lines of data we have to go through:
cure for cancer protein
ATGCCACTATGGTAG
captain picard hair growth protein
ATgCCAACATGgATGCCcGATAtGGATTgA
bogus protein
CCATt-AATgATCa-CAGTt
I am struggling on how one would logically decipher between the name for the region ("cure for cancer protein") and the following sequence of characters. I can get the file to display all info easily, but I need to process the sequence of characters differently than the region name and I can't figure out how to logically determine if the line is a region name or a sequence.
Any help would be greatly appreciated.
java string file loops
java string file loops
edited Nov 24 '18 at 17:20
oleg.cherednik
6,98421118
asked Nov 24 '18 at 16:51
N.SpiessN.Spiess
244
edited Nov 24 '18 at 17:20
oleg.cherednik
6,98421118
asked Nov 24 '18 at 16:51
N.SpiessN.Spiess
244
edited Nov 24 '18 at 17:20
oleg.cherednik
6,98421118
edited Nov 24 '18 at 17:20
oleg.cherednik
6,98421118
edited Nov 24 '18 at 17:20
oleg.cherednik
6,98421118
6,98421118
asked Nov 24 '18 at 16:51
N.SpiessN.Spiess
244
asked Nov 24 '18 at 16:51
N.SpiessN.Spiess
244
asked Nov 24 '18 at 16:51
N.SpiessN.Spiess
244
244
1
Based on your example, the names appear on even line numbers, and the proteins appear on odd line numbers. The names start with a lowercase, not the sequences. The names contain spaces, not the sequences.
– JB Nizet
Nov 24 '18 at 16:56
Ah, the spaces. I didn't think of that. Thank you!!
– N.Spiess
Nov 24 '18 at 16:59
1
Either you find a rigid way of distinguishing them (even f it requires reworking some files by hand, and imposing stricter formatting rules for future files), or you're forced to use heuristics. Frankly, using such a loosely defined file format for a system dealing with "cure for cancer proteins" is scary. Why not use a well-defined file format, like JSON, XML, or even simpler conventions like starting a name by#?
– JB Nizet
Nov 24 '18 at 17:02
You can split the file into lines
– preciousbetine
Nov 24 '18 at 18:59
add a comment |
1
Based on your example, the names appear on even line numbers, and the proteins appear on odd line numbers. The names start with a lowercase, not the sequences. The names contain spaces, not the sequences.
– JB Nizet
Nov 24 '18 at 16:56
Ah, the spaces. I didn't think of that. Thank you!!
– N.Spiess
Nov 24 '18 at 16:59
1
Either you find a rigid way of distinguishing them (even f it requires reworking some files by hand, and imposing stricter formatting rules for future files), or you're forced to use heuristics. Frankly, using such a loosely defined file format for a system dealing with "cure for cancer proteins" is scary. Why not use a well-defined file format, like JSON, XML, or even simpler conventions like starting a name by#?
– JB Nizet
Nov 24 '18 at 17:02
You can split the file into lines
– preciousbetine
Nov 24 '18 at 18:59
1
1
Based on your example, the names appear on even line numbers, and the proteins appear on odd line numbers. The names start with a lowercase, not the sequences. The names contain spaces, not the sequences.
– JB Nizet
Nov 24 '18 at 16:56
Based on your example, the names appear on even line numbers, and the proteins appear on odd line numbers. The names start with a lowercase, not the sequences. The names contain spaces, not the sequences.
– JB Nizet
Nov 24 '18 at 16:56
Ah, the spaces. I didn't think of that. Thank you!!
– N.Spiess
Nov 24 '18 at 16:59
Ah, the spaces. I didn't think of that. Thank you!!
– N.Spiess
Nov 24 '18 at 16:59
1
1
Either you find a rigid way of distinguishing them (even f it requires reworking some files by hand, and imposing stricter formatting rules for future files), or you're forced to use heuristics. Frankly, using such a loosely defined file format for a system dealing with "cure for cancer proteins" is scary. Why not use a well-defined file format, like JSON, XML, or even simpler conventions like starting a name by
#?– JB Nizet
Nov 24 '18 at 17:02
Either you find a rigid way of distinguishing them (even f it requires reworking some files by hand, and imposing stricter formatting rules for future files), or you're forced to use heuristics. Frankly, using such a loosely defined file format for a system dealing with "cure for cancer proteins" is scary. Why not use a well-defined file format, like JSON, XML, or even simpler conventions like starting a name by
#?– JB Nizet
Nov 24 '18 at 17:02
You can split the file into lines
– preciousbetine
Nov 24 '18 at 18:59
You can split the file into lines
– preciousbetine
Nov 24 '18 at 18:59
add a comment |
1 Answer
1
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What about using RegExp? I think you can define is your line contains [ATGC-] only.
answered Nov 24 '18 at 18:23
oleg.cherednikoleg.cherednik
6,98421118
add a comment |
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What about using RegExp? I think you can define is your line contains [ATGC-] only.
answered Nov 24 '18 at 18:23
oleg.cherednikoleg.cherednik
6,98421118
add a comment |
What about using RegExp? I think you can define is your line contains [ATGC-] only.
answered Nov 24 '18 at 18:23
oleg.cherednikoleg.cherednik
6,98421118
add a comment |
What about using RegExp? I think you can define is your line contains [ATGC-] only.
answered Nov 24 '18 at 18:23
oleg.cherednikoleg.cherednik
6,98421118
What about using RegExp? I think you can define is your line contains [ATGC-] only.
answered Nov 24 '18 at 18:23
oleg.cherednikoleg.cherednik
6,98421118
answered Nov 24 '18 at 18:23
oleg.cherednikoleg.cherednik
6,98421118
answered Nov 24 '18 at 18:23
oleg.cherednikoleg.cherednik
6,98421118
answered Nov 24 '18 at 18:23
oleg.cherednikoleg.cherednik
6,98421118
6,98421118
add a comment |
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Based on your example, the names appear on even line numbers, and the proteins appear on odd line numbers. The names start with a lowercase, not the sequences. The names contain spaces, not the sequences.
– JB Nizet
Nov 24 '18 at 16:56
Ah, the spaces. I didn't think of that. Thank you!!
– N.Spiess
Nov 24 '18 at 16:59
1
Either you find a rigid way of distinguishing them (even f it requires reworking some files by hand, and imposing stricter formatting rules for future files), or you're forced to use heuristics. Frankly, using such a loosely defined file format for a system dealing with "cure for cancer proteins" is scary. Why not use a well-defined file format, like JSON, XML, or even simpler conventions like starting a name by
#?– JB Nizet
Nov 24 '18 at 17:02
You can split the file into lines
– preciousbetine
Nov 24 '18 at 18:59