apraga/org - Change OA2LY3TCTCUBN67P57P5NNM2INIMEZ56H76UFLFM43SK5PHWCICAC

Avancement mustard

Created by Alexis Praga on August 4, 2022

OA2LY3TCTCUBN67P57P5NNM2INIMEZ56H76UFLFM43SK5PHWCICAC

Dependencies

In channels

main

Change contents

Insertion in projects.org at line 308 [3.123895]

[2.1892]


def getExome(root, dna, p):
    # Merge exome and sample
    e = readExome(root)
    d = dna.set_index("sampleID").join(e.set_index("specimenID"),
                                    how="inner",
                                    lsuffix="dna", rsuffix="exome")
    d2 = d.set_index('patientIDdna').join(p.set_index("patientID"),
                                        how="inner")
    # Reorder columns
    d2 = cleanExome(d2)
    d2.to_excel(root / "exome dijons.xlsx")
def getPanel(root, dna, p):
    # Merge exome and sample
    e = readExome(root)
    d = dna.set_index("sampleID").join(e.set_index("specimenID"),
                                    how="inner",
                                    lsuffix="dna", rsuffix="exome")
    d2 = d.set_index('patientIDdna').join(p.set_index("patientID"),
                                        how="inner")
    # Reorder columns
    d2 = cleanExome(d2)
    d2.to_excel(root / "exome dijons.xlsx")

Deletion in projects.org at line 335 [3.123895]
B:BD[4.124] → [2.1894:1914]
```
e = readExome(root)
```

Replacement in projects.org at line 338 [3.123895]

∅:D[2.1958] → [5.393:480]

B:BD[5.393] → [5.393:480]

B:BD[5.480] → [2.1959:2267]

# Merge exome and sample
d = dna.set_index("sampleID").join(e.set_index("specimenID"),
                                   how="inner",
                                   lsuffix="dna", rsuffix="exome")
d2 = d.set_index('patientIDdna').join(p.set_index("patientID"),
                                      how="inner")
# Reorder columns
d2 = cleanExome(d2)
d2.to_excel(root / "exome dijons.xlsx")

[2.1958]

[2.2267]

# getExome(root, dna, p)
getPanel(root, dna, p)

Deletion in projects.org at line 347 [3.123895]
B:BD[2.2437] → [2.2437:2439]
```
:
```

Replacement in projects.org at line 1581 [3.123895]

B:BD[6.439] → [6.439:496]

**** TODO Refaire export csv
SCHEDULED: <2022-07-24 Sun>

[7.23689]

[8.10917]


**** DONE Fusionner exome dijon format CSV
CLOSED: [2022-08-04 Thu 17:42]
**** DONE Fusionner panels dijon format CSV