how can I pass over a string on several txt files
Clash Royale CLAN TAG#URR8PPP
0
I have a data like this but much bigger. So I have a df1.txt as follow
sp|O15304|SIVA_HUMAN MPKRSCPFADVAPLQLKVRVSQRELSRGVCAERYSQEVFEKTKRLLFLGAQAYLDHVWDEGCAVVHLPESPKPGPTGAPRAARGQMLIGPDGRLIRSLGQASEADPSGVASIACSSCVRAVDGKAVCGQCERALCGQCVRTCWGCGSVACTLCGLVDCSDMYEKVLCTSCAMFET
tr|A0A1B1L9R9|A0A1B1L9R9_BACTU MNKQLFLASLKETQKSILSYACGAALYLWLLIWIFPSMVSAKGLNELIAAMPDSVKKIVGMESPIQNVMDFLAGEYYSLLFIIILTIFCVTVATHLIARHVDKGAMAYLLATPVSRVQIAITQATVLILGLLIIVSVTYVAGLVGAEWFLQDNNLNKELFLKINIVGGLIFLVVSAYSFFFSCICNDERKALSYSASLTILFFVLDMVGKLSDKLEWMKNLSLFTLFRPKEIAEGAYNIWPVSIGLIAGALCIFIVAIVVFKKRDLPL
and I have df2.txt as follow
sp|O15304|SIVA_HUMAN IGPDGR
I am trying to join them both together so I do the following
join df1.txt df2.txt | awk 'gsub($3, tolower($3), $2) ; print $1 "t" $2' > out.txt
I expect to have this
sp|O15304|SIVA_HUMAN MPKRSCPFADVAPLQLKVRVSQRELSRGVCAERYSQEVFEKTKRLLFLGAQAYLDHVWDEGCAVVHLPESPKPGPTGAPRAARGQMLigpdgrLIRSLGQASEADPSGVASIACSSCVRAVDGKAVCGQCERALCGQCVRTCWGCGSVACTLCGLVDCSDMYEKVLCTSCAMFET
tr|A0A1B1L9R9|A0A1B1L9R9_BACTU MNKQLFLASLKETQKSILSYACGAALYLWLLIWIFPSMVSAKGLNELIAAMPDSVKKIVGMESPIQNVMDFLAGEYYSLLFIIILTIFCVTVATHLIARHVDKGAMAYLLATPVSRVQIAITQATVLILGLLIIVSVTYVAGLVGAEWFLQDNNLNKELFLKINIVGGLIFLVVSAYSFFFSCICNDERKALSYSASLTILFFVLDMVGKLSDKLEWMKNLSLFTLFRPKEIAEGAYNIWPVSIGLIAGALCIFIVAIVVFKKRDLPL
but instead I am having this
sp|O15304|SIVA_HUMAN MPKRSCPFADVAPLQLKVRVSQRELSRGVCAERYSQEVFEKTKRLLFLGAQAYLDHVWDEGCAVVHLPESPKPGPTGAPRAARGQMLigpdgrLIRSLGQASEADPSGVASIACSSCVRAVDGKAVCGQCERALCGQCVRTCWGCGSVACTLCGLVDCSDMYEKVLCTSCAMFET
, how can I solve it?
text-processing paste
edited Dec 20 '18 at 23:49
Jeff Schaller
38.8k1053125
asked Dec 20 '18 at 23:03
Learner
1082
add a comment |
0
I have a data like this but much bigger. So I have a df1.txt as follow
sp|O15304|SIVA_HUMAN MPKRSCPFADVAPLQLKVRVSQRELSRGVCAERYSQEVFEKTKRLLFLGAQAYLDHVWDEGCAVVHLPESPKPGPTGAPRAARGQMLIGPDGRLIRSLGQASEADPSGVASIACSSCVRAVDGKAVCGQCERALCGQCVRTCWGCGSVACTLCGLVDCSDMYEKVLCTSCAMFET
tr|A0A1B1L9R9|A0A1B1L9R9_BACTU MNKQLFLASLKETQKSILSYACGAALYLWLLIWIFPSMVSAKGLNELIAAMPDSVKKIVGMESPIQNVMDFLAGEYYSLLFIIILTIFCVTVATHLIARHVDKGAMAYLLATPVSRVQIAITQATVLILGLLIIVSVTYVAGLVGAEWFLQDNNLNKELFLKINIVGGLIFLVVSAYSFFFSCICNDERKALSYSASLTILFFVLDMVGKLSDKLEWMKNLSLFTLFRPKEIAEGAYNIWPVSIGLIAGALCIFIVAIVVFKKRDLPL
and I have df2.txt as follow
sp|O15304|SIVA_HUMAN IGPDGR
I am trying to join them both together so I do the following
join df1.txt df2.txt | awk 'gsub($3, tolower($3), $2) ; print $1 "t" $2' > out.txt
I expect to have this
sp|O15304|SIVA_HUMAN MPKRSCPFADVAPLQLKVRVSQRELSRGVCAERYSQEVFEKTKRLLFLGAQAYLDHVWDEGCAVVHLPESPKPGPTGAPRAARGQMLigpdgrLIRSLGQASEADPSGVASIACSSCVRAVDGKAVCGQCERALCGQCVRTCWGCGSVACTLCGLVDCSDMYEKVLCTSCAMFET
tr|A0A1B1L9R9|A0A1B1L9R9_BACTU MNKQLFLASLKETQKSILSYACGAALYLWLLIWIFPSMVSAKGLNELIAAMPDSVKKIVGMESPIQNVMDFLAGEYYSLLFIIILTIFCVTVATHLIARHVDKGAMAYLLATPVSRVQIAITQATVLILGLLIIVSVTYVAGLVGAEWFLQDNNLNKELFLKINIVGGLIFLVVSAYSFFFSCICNDERKALSYSASLTILFFVLDMVGKLSDKLEWMKNLSLFTLFRPKEIAEGAYNIWPVSIGLIAGALCIFIVAIVVFKKRDLPL
but instead I am having this
sp|O15304|SIVA_HUMAN MPKRSCPFADVAPLQLKVRVSQRELSRGVCAERYSQEVFEKTKRLLFLGAQAYLDHVWDEGCAVVHLPESPKPGPTGAPRAARGQMLigpdgrLIRSLGQASEADPSGVASIACSSCVRAVDGKAVCGQCERALCGQCVRTCWGCGSVACTLCGLVDCSDMYEKVLCTSCAMFET
, how can I solve it?
text-processing paste
edited Dec 20 '18 at 23:49
Jeff Schaller
38.8k1053125
asked Dec 20 '18 at 23:03
Learner
1082
Why would you expect to have thetrline in the output? The only way I can see of obtaining your desired output from the two example files iscat df1.txt, which presumably isn't what you're intending.
– roaima
Dec 21 '18 at 20:48
@roaima I want to have all the ones that are in the df1.txt, just modify by the df2.txt
– Learner
Dec 21 '18 at 20:52
And the others passed through unchanged?
– roaima
Dec 21 '18 at 20:54
add a comment |
0
0
0
I have a data like this but much bigger. So I have a df1.txt as follow
sp|O15304|SIVA_HUMAN MPKRSCPFADVAPLQLKVRVSQRELSRGVCAERYSQEVFEKTKRLLFLGAQAYLDHVWDEGCAVVHLPESPKPGPTGAPRAARGQMLIGPDGRLIRSLGQASEADPSGVASIACSSCVRAVDGKAVCGQCERALCGQCVRTCWGCGSVACTLCGLVDCSDMYEKVLCTSCAMFET
tr|A0A1B1L9R9|A0A1B1L9R9_BACTU MNKQLFLASLKETQKSILSYACGAALYLWLLIWIFPSMVSAKGLNELIAAMPDSVKKIVGMESPIQNVMDFLAGEYYSLLFIIILTIFCVTVATHLIARHVDKGAMAYLLATPVSRVQIAITQATVLILGLLIIVSVTYVAGLVGAEWFLQDNNLNKELFLKINIVGGLIFLVVSAYSFFFSCICNDERKALSYSASLTILFFVLDMVGKLSDKLEWMKNLSLFTLFRPKEIAEGAYNIWPVSIGLIAGALCIFIVAIVVFKKRDLPL
and I have df2.txt as follow
sp|O15304|SIVA_HUMAN IGPDGR
I am trying to join them both together so I do the following
join df1.txt df2.txt | awk 'gsub($3, tolower($3), $2) ; print $1 "t" $2' > out.txt
I expect to have this
sp|O15304|SIVA_HUMAN MPKRSCPFADVAPLQLKVRVSQRELSRGVCAERYSQEVFEKTKRLLFLGAQAYLDHVWDEGCAVVHLPESPKPGPTGAPRAARGQMLigpdgrLIRSLGQASEADPSGVASIACSSCVRAVDGKAVCGQCERALCGQCVRTCWGCGSVACTLCGLVDCSDMYEKVLCTSCAMFET
tr|A0A1B1L9R9|A0A1B1L9R9_BACTU MNKQLFLASLKETQKSILSYACGAALYLWLLIWIFPSMVSAKGLNELIAAMPDSVKKIVGMESPIQNVMDFLAGEYYSLLFIIILTIFCVTVATHLIARHVDKGAMAYLLATPVSRVQIAITQATVLILGLLIIVSVTYVAGLVGAEWFLQDNNLNKELFLKINIVGGLIFLVVSAYSFFFSCICNDERKALSYSASLTILFFVLDMVGKLSDKLEWMKNLSLFTLFRPKEIAEGAYNIWPVSIGLIAGALCIFIVAIVVFKKRDLPL
but instead I am having this
sp|O15304|SIVA_HUMAN MPKRSCPFADVAPLQLKVRVSQRELSRGVCAERYSQEVFEKTKRLLFLGAQAYLDHVWDEGCAVVHLPESPKPGPTGAPRAARGQMLigpdgrLIRSLGQASEADPSGVASIACSSCVRAVDGKAVCGQCERALCGQCVRTCWGCGSVACTLCGLVDCSDMYEKVLCTSCAMFET
, how can I solve it?
text-processing paste
edited Dec 20 '18 at 23:49
Jeff Schaller
38.8k1053125
asked Dec 20 '18 at 23:03
Learner
1082
I have a data like this but much bigger. So I have a df1.txt as follow
sp|O15304|SIVA_HUMAN MPKRSCPFADVAPLQLKVRVSQRELSRGVCAERYSQEVFEKTKRLLFLGAQAYLDHVWDEGCAVVHLPESPKPGPTGAPRAARGQMLIGPDGRLIRSLGQASEADPSGVASIACSSCVRAVDGKAVCGQCERALCGQCVRTCWGCGSVACTLCGLVDCSDMYEKVLCTSCAMFET
tr|A0A1B1L9R9|A0A1B1L9R9_BACTU MNKQLFLASLKETQKSILSYACGAALYLWLLIWIFPSMVSAKGLNELIAAMPDSVKKIVGMESPIQNVMDFLAGEYYSLLFIIILTIFCVTVATHLIARHVDKGAMAYLLATPVSRVQIAITQATVLILGLLIIVSVTYVAGLVGAEWFLQDNNLNKELFLKINIVGGLIFLVVSAYSFFFSCICNDERKALSYSASLTILFFVLDMVGKLSDKLEWMKNLSLFTLFRPKEIAEGAYNIWPVSIGLIAGALCIFIVAIVVFKKRDLPL
and I have df2.txt as follow
sp|O15304|SIVA_HUMAN IGPDGR
I am trying to join them both together so I do the following
join df1.txt df2.txt | awk 'gsub($3, tolower($3), $2) ; print $1 "t" $2' > out.txt
I expect to have this
sp|O15304|SIVA_HUMAN MPKRSCPFADVAPLQLKVRVSQRELSRGVCAERYSQEVFEKTKRLLFLGAQAYLDHVWDEGCAVVHLPESPKPGPTGAPRAARGQMLigpdgrLIRSLGQASEADPSGVASIACSSCVRAVDGKAVCGQCERALCGQCVRTCWGCGSVACTLCGLVDCSDMYEKVLCTSCAMFET
tr|A0A1B1L9R9|A0A1B1L9R9_BACTU MNKQLFLASLKETQKSILSYACGAALYLWLLIWIFPSMVSAKGLNELIAAMPDSVKKIVGMESPIQNVMDFLAGEYYSLLFIIILTIFCVTVATHLIARHVDKGAMAYLLATPVSRVQIAITQATVLILGLLIIVSVTYVAGLVGAEWFLQDNNLNKELFLKINIVGGLIFLVVSAYSFFFSCICNDERKALSYSASLTILFFVLDMVGKLSDKLEWMKNLSLFTLFRPKEIAEGAYNIWPVSIGLIAGALCIFIVAIVVFKKRDLPL
but instead I am having this
sp|O15304|SIVA_HUMAN MPKRSCPFADVAPLQLKVRVSQRELSRGVCAERYSQEVFEKTKRLLFLGAQAYLDHVWDEGCAVVHLPESPKPGPTGAPRAARGQMLigpdgrLIRSLGQASEADPSGVASIACSSCVRAVDGKAVCGQCERALCGQCVRTCWGCGSVACTLCGLVDCSDMYEKVLCTSCAMFET
, how can I solve it?
text-processing paste
text-processing paste
edited Dec 20 '18 at 23:49
Jeff Schaller
38.8k1053125
asked Dec 20 '18 at 23:03
Learner
1082
edited Dec 20 '18 at 23:49
Jeff Schaller
38.8k1053125
asked Dec 20 '18 at 23:03
Learner
1082
edited Dec 20 '18 at 23:49
Jeff Schaller
38.8k1053125
edited Dec 20 '18 at 23:49
Jeff Schaller
38.8k1053125
edited Dec 20 '18 at 23:49
Jeff Schaller
38.8k1053125
38.8k1053125
asked Dec 20 '18 at 23:03
Learner
1082
asked Dec 20 '18 at 23:03
Learner
1082
asked Dec 20 '18 at 23:03
Learner
1082
1082
Why would you expect to have thetrline in the output? The only way I can see of obtaining your desired output from the two example files iscat df1.txt, which presumably isn't what you're intending.
– roaima
Dec 21 '18 at 20:48
@roaima I want to have all the ones that are in the df1.txt, just modify by the df2.txt
– Learner
Dec 21 '18 at 20:52
And the others passed through unchanged?
– roaima
Dec 21 '18 at 20:54
add a comment |
Why would you expect to have thetrline in the output? The only way I can see of obtaining your desired output from the two example files iscat df1.txt, which presumably isn't what you're intending.
– roaima
Dec 21 '18 at 20:48
@roaima I want to have all the ones that are in the df1.txt, just modify by the df2.txt
– Learner
Dec 21 '18 at 20:52
And the others passed through unchanged?
– roaima
Dec 21 '18 at 20:54
Why would you expect to have the
tr line in the output? The only way I can see of obtaining your desired output from the two example files is cat df1.txt, which presumably isn't what you're intending.– roaima
Dec 21 '18 at 20:48
Why would you expect to have the
tr line in the output? The only way I can see of obtaining your desired output from the two example files is cat df1.txt, which presumably isn't what you're intending.– roaima
Dec 21 '18 at 20:48
@roaima I want to have all the ones that are in the df1.txt, just modify by the df2.txt
– Learner
Dec 21 '18 at 20:52
@roaima I want to have all the ones that are in the df1.txt, just modify by the df2.txt
– Learner
Dec 21 '18 at 20:52
And the others passed through unchanged?
– roaima
Dec 21 '18 at 20:54
And the others passed through unchanged?
– roaima
Dec 21 '18 at 20:54
add a comment |
1 Answer
1
active
oldest
votes
2
The problem is in the join command. You need to use -a 1.
From man join
-a FILENUM
also print unpairable lines from file FILENUM, where
FILENUM is 1 or 2, corresponding to FILE1 or FILE2
i.e. the final command is
join -a 1 df1.txt df2.txt | awk 'gsub($3, tolower($3), $2) ; print $1 "t" $2' > out.txt
Background
When troubleshooting, you should test each part of the pipe sequentially. join df1.txt df2.txt only outputs lines that are in both files. To include lines in df1.txt that have no match in df2.txt, use -a 1 as above.
answered Dec 21 '18 at 0:02
Sparhawk
9,27863991
I have a MAC, should still this work? because when I run it it seems I have a syntax issue
– Learner
Dec 21 '18 at 0:44
It does give me output with I use without a but as soon as I add -a 1 or 2, it gives me likeusage: join [-a fileno | -v fileno ] [-e string] [-1 field] [-2 field] [-o list] [-t char] file1 file2
– Learner
Dec 21 '18 at 0:55
@Learner I've changed the position of the option. Could you please try again? (Often OS X ships very old versions of command line tools, because Apple doesn't like the open-source GPL licence. As an aside, I'd recommend installing from an unofficial repository.)
– Sparhawk
Dec 21 '18 at 0:56
add a comment |
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1 Answer
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1 Answer
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active
oldest
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2
The problem is in the join command. You need to use -a 1.
From man join
-a FILENUM
also print unpairable lines from file FILENUM, where
FILENUM is 1 or 2, corresponding to FILE1 or FILE2
i.e. the final command is
join -a 1 df1.txt df2.txt | awk 'gsub($3, tolower($3), $2) ; print $1 "t" $2' > out.txt
Background
When troubleshooting, you should test each part of the pipe sequentially. join df1.txt df2.txt only outputs lines that are in both files. To include lines in df1.txt that have no match in df2.txt, use -a 1 as above.
answered Dec 21 '18 at 0:02
Sparhawk
9,27863991
I have a MAC, should still this work? because when I run it it seems I have a syntax issue
– Learner
Dec 21 '18 at 0:44
It does give me output with I use without a but as soon as I add -a 1 or 2, it gives me likeusage: join [-a fileno | -v fileno ] [-e string] [-1 field] [-2 field] [-o list] [-t char] file1 file2
– Learner
Dec 21 '18 at 0:55
@Learner I've changed the position of the option. Could you please try again? (Often OS X ships very old versions of command line tools, because Apple doesn't like the open-source GPL licence. As an aside, I'd recommend installing from an unofficial repository.)
– Sparhawk
Dec 21 '18 at 0:56
add a comment |
2
The problem is in the join command. You need to use -a 1.
From man join
-a FILENUM
also print unpairable lines from file FILENUM, where
FILENUM is 1 or 2, corresponding to FILE1 or FILE2
i.e. the final command is
join -a 1 df1.txt df2.txt | awk 'gsub($3, tolower($3), $2) ; print $1 "t" $2' > out.txt
Background
When troubleshooting, you should test each part of the pipe sequentially. join df1.txt df2.txt only outputs lines that are in both files. To include lines in df1.txt that have no match in df2.txt, use -a 1 as above.
answered Dec 21 '18 at 0:02
Sparhawk
9,27863991
I have a MAC, should still this work? because when I run it it seems I have a syntax issue
– Learner
Dec 21 '18 at 0:44
It does give me output with I use without a but as soon as I add -a 1 or 2, it gives me likeusage: join [-a fileno | -v fileno ] [-e string] [-1 field] [-2 field] [-o list] [-t char] file1 file2
– Learner
Dec 21 '18 at 0:55
@Learner I've changed the position of the option. Could you please try again? (Often OS X ships very old versions of command line tools, because Apple doesn't like the open-source GPL licence. As an aside, I'd recommend installing from an unofficial repository.)
– Sparhawk
Dec 21 '18 at 0:56
add a comment |
2
2
2
The problem is in the join command. You need to use -a 1.
From man join
-a FILENUM
also print unpairable lines from file FILENUM, where
FILENUM is 1 or 2, corresponding to FILE1 or FILE2
i.e. the final command is
join -a 1 df1.txt df2.txt | awk 'gsub($3, tolower($3), $2) ; print $1 "t" $2' > out.txt
Background
When troubleshooting, you should test each part of the pipe sequentially. join df1.txt df2.txt only outputs lines that are in both files. To include lines in df1.txt that have no match in df2.txt, use -a 1 as above.
answered Dec 21 '18 at 0:02
Sparhawk
9,27863991
The problem is in the join command. You need to use -a 1.
From man join
-a FILENUM
also print unpairable lines from file FILENUM, where
FILENUM is 1 or 2, corresponding to FILE1 or FILE2
i.e. the final command is
join -a 1 df1.txt df2.txt | awk 'gsub($3, tolower($3), $2) ; print $1 "t" $2' > out.txt
Background
When troubleshooting, you should test each part of the pipe sequentially. join df1.txt df2.txt only outputs lines that are in both files. To include lines in df1.txt that have no match in df2.txt, use -a 1 as above.
answered Dec 21 '18 at 0:02
Sparhawk
9,27863991
edited Dec 21 '18 at 0:55
answered Dec 21 '18 at 0:02
Sparhawk
9,27863991
answered Dec 21 '18 at 0:02
Sparhawk
9,27863991
answered Dec 21 '18 at 0:02
Sparhawk
9,27863991
9,27863991
I have a MAC, should still this work? because when I run it it seems I have a syntax issue
– Learner
Dec 21 '18 at 0:44
It does give me output with I use without a but as soon as I add -a 1 or 2, it gives me likeusage: join [-a fileno | -v fileno ] [-e string] [-1 field] [-2 field] [-o list] [-t char] file1 file2
– Learner
Dec 21 '18 at 0:55
@Learner I've changed the position of the option. Could you please try again? (Often OS X ships very old versions of command line tools, because Apple doesn't like the open-source GPL licence. As an aside, I'd recommend installing from an unofficial repository.)
– Sparhawk
Dec 21 '18 at 0:56
add a comment |
I have a MAC, should still this work? because when I run it it seems I have a syntax issue
– Learner
Dec 21 '18 at 0:44
It does give me output with I use without a but as soon as I add -a 1 or 2, it gives me likeusage: join [-a fileno | -v fileno ] [-e string] [-1 field] [-2 field] [-o list] [-t char] file1 file2
– Learner
Dec 21 '18 at 0:55
@Learner I've changed the position of the option. Could you please try again? (Often OS X ships very old versions of command line tools, because Apple doesn't like the open-source GPL licence. As an aside, I'd recommend installing from an unofficial repository.)
– Sparhawk
Dec 21 '18 at 0:56
I have a MAC, should still this work? because when I run it it seems I have a syntax issue
– Learner
Dec 21 '18 at 0:44
I have a MAC, should still this work? because when I run it it seems I have a syntax issue
– Learner
Dec 21 '18 at 0:44
It does give me output with I use without a but as soon as I add -a 1 or 2, it gives me like
usage: join [-a fileno | -v fileno ] [-e string] [-1 field] [-2 field] [-o list] [-t char] file1 file2– Learner
Dec 21 '18 at 0:55
It does give me output with I use without a but as soon as I add -a 1 or 2, it gives me like
usage: join [-a fileno | -v fileno ] [-e string] [-1 field] [-2 field] [-o list] [-t char] file1 file2– Learner
Dec 21 '18 at 0:55
@Learner I've changed the position of the option. Could you please try again? (Often OS X ships very old versions of command line tools, because Apple doesn't like the open-source GPL licence. As an aside, I'd recommend installing from an unofficial repository.)
– Sparhawk
Dec 21 '18 at 0:56
@Learner I've changed the position of the option. Could you please try again? (Often OS X ships very old versions of command line tools, because Apple doesn't like the open-source GPL licence. As an aside, I'd recommend installing from an unofficial repository.)
– Sparhawk
Dec 21 '18 at 0:56
add a comment |
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Why would you expect to have the
trline in the output? The only way I can see of obtaining your desired output from the two example files iscat df1.txt, which presumably isn't what you're intending.– roaima
Dec 21 '18 at 20:48
@roaima I want to have all the ones that are in the df1.txt, just modify by the df2.txt
– Learner
Dec 21 '18 at 20:52
And the others passed through unchanged?
– roaima
Dec 21 '18 at 20:54