Palmprint/PalmID Integration into RdRP Explorer

[binoyskumar92]

preview link

This pull request addresses issue #158

Summary of changes

• Added a new table in the explorer page to show plamprints for a specific run
• Added a analyze button in the table to directly go to palm id page with fastaInput

Post-merge

• [ ] Create issue for "Click a family heatmap to view sequence-level matches" placement (ref)

[ababaian]

In the Analyze palmprint link the URL path does not parse the input sequence correctly, see: https://158-palmprint-palmid-integration-into-rdp-explorer.serratus.io/palmid?fastaInput=ERR2756788_1_u21405MGWDYPKCDRALPSMIRMISAMILGSKHVTCCTASDKYYRLCNELAQVLTEVVYSNGGFYFKPGGTTSGDATTAYANSVFNIFQAVSANINRLLTVDSYAIHNESVKSLQRQLYDNCYRATSVDATFVSDYYQFLRKHFSMMILSDDGVV

Which as a parsed input gives

>Serratus_palmid
ERRUMGWDYPKCDRALPSMIRMISAMILGSKHVTCCTASDKYYRLCNELA
QVLTEVVYSNGGFYFKPGGTTSGDATTAYANSVFNIFQAVSANINRLLTV
DSYAIHNESVKSLQRQLYDNCYRATSVDATFVSDYYQFLRKHFSMMILSD
DGVV

Where it should be

>ERR2756788_1_u21405
MGWDYPKCDRALPSMIRMISAMILGSKHVTCCTASDKYYRLCNELAQVLT
EVVYSNGGFYFKPGGTTSGDATTAYANSVFNIFQAVSANINRLLTVDSYA
IHNESVKSLQRQLYDNCYRATSVDATFVSDYYQFLRKHFSMMILSDDGVV

---

The corrected URL should use URL escape characters for > (%3E) and newline (%0A) like so:

https://158-palmprint-palmid-integration-into-rdp-explorer.serratus.io/palmid?fastaInput=%3EERR2756788_1_u21405%0AMGWDYPKCDRALPSMIRMISAMILGSKHVTCCTASDKYYRLCNELAQVLTEVVYSNGGFYFKPGGTTSGDATTAYANSVFNIFQAVSANINRLLTVDSYAIHNESVKSLQRQLYDNCYRATSVDATFVSDYYQFLRKHFSMMILSDDGVV

[binoyskumar92]

Thanks. good catch.

[binoyskumar92]

Updated

[ababaian]

@binoyskumar92 think you can clean this up and get it done?

I forgot you had this almost done and I took a stab at it: https://github.com/serratus-bio/serratus.io/pull/188

One suggestion is to not use > and \n in the URL parsing, instead pass the header and the sequence as two parameters: head and seq. This simplifies dealing with the special escape characters we can use some boilerplate header if one is not included, the requirement really is a sequence. Take a look at my PR above, it's not good (bit buggy on clear), but the idea is there.

[binoyskumar92]

Sure. I kinda assumed these changes were merged after 1st round of review. Did not keep track of second round of review from victor.