How to redirect output to file to STDOUT?
Clash Royale CLAN TAG#URR8PPP
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Similar problem as here
How to redirect output from file to stdout?
However, the solution given there is not universal.
My problem: I have a command that produces output to STDOUT. At the same time, I can specify via arguments to produce another output that goes straight to a file.
tcsh$ hmmscan --domtblout FILEOUTPUT Pfam-A.hmm query.fasta
Pfam-A.hmm is a database file (input); query.fasta is also an input file
How can I redirect FILEOUTPUT to STDOUT ?
Background: I plan to use the command on thousands of inputs and I need to run it for each of them separately. The command is called within a Python script, and I would like to read its FILEOUTPUT directly into the memory/a variable using the subprocess module. I know how to get the STDOUT with the subprocess module; so if I could redirect FILEOUTPUT to STDOUT...
I tried already stuff like this (ended up with errors or created files):
tcsh$ hmmscan --domtblout >/dev/tty Pfam-A.hmm query.fasta
tcsh$ hmmscan --domtblout >(mypipe) Pfam-A.hmm query.fasta
tcsh$ hmmscan --domtblout >$ Pfam-A.hmm query.fasta
tcsh$ hmmscan --domtblout >($1) Pfam-A.hmm query.fasta
tcsh$ hmmscan --domtblout >cat Pfam-A.hmm query.fasta
tcsh$ hmmscan --domtblout test.tab Pfam-A.hmm query.fasta >/dev/tty
As you can likely see from my use of shell, I have no clue...
shell command-line io-redirection tcsh
New contributor
cytosine is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
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add a comment |Â
up vote
0
down vote
favorite
Similar problem as here
How to redirect output from file to stdout?
However, the solution given there is not universal.
My problem: I have a command that produces output to STDOUT. At the same time, I can specify via arguments to produce another output that goes straight to a file.
tcsh$ hmmscan --domtblout FILEOUTPUT Pfam-A.hmm query.fasta
Pfam-A.hmm is a database file (input); query.fasta is also an input file
How can I redirect FILEOUTPUT to STDOUT ?
Background: I plan to use the command on thousands of inputs and I need to run it for each of them separately. The command is called within a Python script, and I would like to read its FILEOUTPUT directly into the memory/a variable using the subprocess module. I know how to get the STDOUT with the subprocess module; so if I could redirect FILEOUTPUT to STDOUT...
I tried already stuff like this (ended up with errors or created files):
tcsh$ hmmscan --domtblout >/dev/tty Pfam-A.hmm query.fasta
tcsh$ hmmscan --domtblout >(mypipe) Pfam-A.hmm query.fasta
tcsh$ hmmscan --domtblout >$ Pfam-A.hmm query.fasta
tcsh$ hmmscan --domtblout >($1) Pfam-A.hmm query.fasta
tcsh$ hmmscan --domtblout >cat Pfam-A.hmm query.fasta
tcsh$ hmmscan --domtblout test.tab Pfam-A.hmm query.fasta >/dev/tty
As you can likely see from my use of shell, I have no clue...
shell command-line io-redirection tcsh
New contributor
cytosine is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
add a comment |Â
up vote
0
down vote
favorite
up vote
0
down vote
favorite
Similar problem as here
How to redirect output from file to stdout?
However, the solution given there is not universal.
My problem: I have a command that produces output to STDOUT. At the same time, I can specify via arguments to produce another output that goes straight to a file.
tcsh$ hmmscan --domtblout FILEOUTPUT Pfam-A.hmm query.fasta
Pfam-A.hmm is a database file (input); query.fasta is also an input file
How can I redirect FILEOUTPUT to STDOUT ?
Background: I plan to use the command on thousands of inputs and I need to run it for each of them separately. The command is called within a Python script, and I would like to read its FILEOUTPUT directly into the memory/a variable using the subprocess module. I know how to get the STDOUT with the subprocess module; so if I could redirect FILEOUTPUT to STDOUT...
I tried already stuff like this (ended up with errors or created files):
tcsh$ hmmscan --domtblout >/dev/tty Pfam-A.hmm query.fasta
tcsh$ hmmscan --domtblout >(mypipe) Pfam-A.hmm query.fasta
tcsh$ hmmscan --domtblout >$ Pfam-A.hmm query.fasta
tcsh$ hmmscan --domtblout >($1) Pfam-A.hmm query.fasta
tcsh$ hmmscan --domtblout >cat Pfam-A.hmm query.fasta
tcsh$ hmmscan --domtblout test.tab Pfam-A.hmm query.fasta >/dev/tty
As you can likely see from my use of shell, I have no clue...
shell command-line io-redirection tcsh
New contributor
cytosine is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
Similar problem as here
How to redirect output from file to stdout?
However, the solution given there is not universal.
My problem: I have a command that produces output to STDOUT. At the same time, I can specify via arguments to produce another output that goes straight to a file.
tcsh$ hmmscan --domtblout FILEOUTPUT Pfam-A.hmm query.fasta
Pfam-A.hmm is a database file (input); query.fasta is also an input file
How can I redirect FILEOUTPUT to STDOUT ?
Background: I plan to use the command on thousands of inputs and I need to run it for each of them separately. The command is called within a Python script, and I would like to read its FILEOUTPUT directly into the memory/a variable using the subprocess module. I know how to get the STDOUT with the subprocess module; so if I could redirect FILEOUTPUT to STDOUT...
I tried already stuff like this (ended up with errors or created files):
tcsh$ hmmscan --domtblout >/dev/tty Pfam-A.hmm query.fasta
tcsh$ hmmscan --domtblout >(mypipe) Pfam-A.hmm query.fasta
tcsh$ hmmscan --domtblout >$ Pfam-A.hmm query.fasta
tcsh$ hmmscan --domtblout >($1) Pfam-A.hmm query.fasta
tcsh$ hmmscan --domtblout >cat Pfam-A.hmm query.fasta
tcsh$ hmmscan --domtblout test.tab Pfam-A.hmm query.fasta >/dev/tty
As you can likely see from my use of shell, I have no clue...
shell command-line io-redirection tcsh
shell command-line io-redirection tcsh
New contributor
cytosine is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
New contributor
cytosine is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
New contributor
cytosine is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
asked 6 mins ago
cytosine
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New contributor
cytosine is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
New contributor
cytosine is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
cytosine is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
add a comment |Â
add a comment |Â
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cytosine is a new contributor. Be nice, and check out our Code of Conduct.
cytosine is a new contributor. Be nice, and check out our Code of Conduct.
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