#375 Add allow-dups option to tide-index

[William S Noble]

The new --allow-dups option will toggle allowing duplicate peptides into the target and decoy databases. The default value will be F, and will use a "set" data structure to keep track of potential duplicates. This is the current behavior. When set to "T", the program will save memory by not keeping the set data structure.

Here is the documentation string:

--allow-dups T|F - Prevent duplicate peptides between the target and decoy databases. When set to "F", the program keeps all target and previously generated decoy peptides in memory. A shuffled decoy will be re-shuffled multiple times to avoid duplication. If a non-duplicated peptide cannot be generated, the decoy is skipped entirely. When set to "T", every decoy is added to the database without checking for duplication. This option reduces the memory requirements significantly. Default = F.

[William S Noble]

What is the status of this issue? Has it passed code review?

[Zijin Zhang]

Sent from my iPhone

On Mar 18, 2016, at 09:23, William S Noble wsnoble@users.sf.net wrote:

What is the status of this issue? Has it passed code review?

[issues:#375] Add allow-dups option to tide-index

Status: open
Milestone: post v2.0
Created: Wed Mar 02, 2016 05:27 PM UTC by William S Noble
Last Updated: Wed Mar 02, 2016 05:27 PM UTC
Owner: Zijin Zhang

The new --allow-dups option will toggle allowing duplicate peptides into the target and decoy databases. The default value will be F, and will use a "set" data structure to keep track of potential duplicates. This is the current behavior. When set to "T", the program will save memory by not keeping the set data structure.

Here is the documentation string:

--allow-dups T|F - Prevent duplicate peptides between the target and decoy databases. When set to "F", the program keeps all target and previously generated decoy peptides in memory. A shuffled decoy will be re-shuffled multiple times to avoid duplication. If a non-duplicated peptide cannot be generated, the decoy is skipped entirely. When set to "T", every decoy is added to the database without checking for duplication. This option reduces the memory requirements significantly. Default = F.

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[Zijin Zhang]

There is some repeated code in my previous version, so I am rewriting a new one.

Please ignore the previous email, I sent it by mistake.

Thanks,
Zijin

On Mar 18, 2016, at 09:23, William S Noble <wsnoble@users .sf.net> wrote:

What is the status of this issue? Has it passed code review?

[issues:#375] Add allow-dups option to tide-index

Status: open
Milestone: post v2.0
Created: Wed Mar 02, 2016 05:27 PM UTC by William S Noble
Last Updated: Wed Mar 02, 2016 05:27 PM UTC
Owner: Zijin Zhang

The new --allow-dups option will toggle allowing duplicate peptides into the target and decoy databases. The default value will be F, and will use a "set" data structure to keep track of potential duplicates. This is the current behavior. When set to "T", the program will save memory by not keeping the set data structure.

Here is the documentation string:

--allow-dups T|F - Prevent duplicate peptides between the target and decoy databases. When set to "F", the program keeps all target and previously generated decoy peptides in memory. A shuffled decoy will be re-shuffled multiple times to avoid duplication. If a non-duplicated peptide cannot be generated, the decoy is skipped entirely. When set to "T", every decoy is added to the database without checking for duplication. This option reduces the memory requirements significantly. Default = F.

Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/cruxtoolkit/issues/375/

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[William S Noble]

OK, thanks for the update.

On Thu, Mar 17, 2016 at 6:48 PM, Zijin Zhang zijinzhang@users.sf.net
wrote:

There is some repeated code in my previous version, so I am rewriting a
new one.

Please ignore the previous email, I sent it by mistake.

Thanks,
Zijin

On Mar 18, 2016, at 09:23, William S Noble <wsnoble@users .sf.net="">
wrote:

What is the status of this issue? Has it passed code review?

[issues:#375] https://sourceforge.net/p/cruxtoolkit/issues/375/ Add
allow-dups option to tide-index

Status: open
Milestone: post v2.0
Created: Wed Mar 02, 2016 05:27 PM UTC by William S Noble
Last Updated: Wed Mar 02, 2016 05:27 PM UTC
Owner: Zijin Zhang

The new --allow-dups option will toggle allowing duplicate peptides into
the target and decoy databases. The default value will be F, and will use a
"set" data structure to keep track of potential duplicates. This is the
current behavior. When set to "T", the program will save memory by not
keeping the set data structure.

Here is the documentation string:

--allow-dups T|F - Prevent duplicate peptides between the target and decoy
databases. When set to "F", the program keeps all target and previously
generated decoy peptides in memory. A shuffled decoy will be re-shuffled
multiple times to avoid duplication. If a non-duplicated peptide cannot be
generated, the decoy is skipped entirely. When set to "T", every decoy is
added to the database without checking for duplication. This option reduces
the memory requirements significantly. Default = F.

Sent from sourceforge.net because you indicated interest in
https://sourceforge.net/p/cruxtoolkit/issues/375/

To unsubscribe from further messages, please visit
https://sourceforge.net/auth/subscriptions/

---

• [issues:#375] https://sourceforge.net/p/cruxtoolkit/issues/375/ Add
  allow-dups option to tide-index*

Status: open
Milestone: post v2.0
Created: Wed Mar 02, 2016 05:27 PM UTC by William S Noble
Last Updated: Fri Mar 18, 2016 12:23 AM UTC
Owner: Zijin Zhang

The new --allow-dups option will toggle allowing duplicate peptides into
the target and decoy databases. The default value will be F, and will use a
"set" data structure to keep track of potential duplicates. This is the
current behavior. When set to "T", the program will save memory by not
keeping the set data structure.

Here is the documentation string:

--allow-dups T|F - Prevent duplicate peptides between the target and decoy
databases. When set to "F", the program keeps all target and previously
generated decoy peptides in memory. A shuffled decoy will be re-shuffled
multiple times to avoid duplication. If a non-duplicated peptide cannot be
generated, the decoy is skipped entirely. When set to "T", every decoy is
added to the database without checking for duplication. This option reduces
the memory requirements significantly. Default = F.

---

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