remove maxquant MBR rows #229
Conversation
| @@ -11,6 +12,8 @@ | |||
| psm_reader_yaml, | |||
| ) | |||
|
|
|||
| warnings.filterwarnings("always") | |||
There was a problem hiding this comment.
could the scope of this be reduced, e.g. to a specific code block and/or specific warnings?
There was a problem hiding this comment.
Maybe you know more about this.
This code is needed to enforce that warning are shown because it's somehow not happening.
So it's not removing warnings but showing them.
There was a problem hiding this comment.
ah, I misinterprested this as "filter always" .. then it's fine, maybe add the information that warnings are otherwise not shown as a comment ..
| ) | ||
| df = df[~no_ms2_mask] | ||
| df.reset_index(drop=True, inplace=True) | ||
| df[scan_num_col] = df[scan_num_col].astype(int) |
There was a problem hiding this comment.
if we don't hit the if "scan_num" in mapped_columns: block: will the type of scan_num_col still be int?
or turning it around: we should make sure all columns' dtypes are consistent, and independent of the inner logic of the reader.
| if "scan_num" in mapped_columns: | ||
| scan_num_col = mapped_columns["scan_num"] | ||
| no_ms2_mask = df[scan_num_col] == "" | ||
| if np.sum(no_ms2_mask) > 0: |
There was a problem hiding this comment.
(nit)
if (num_no_ms2_mask := np.sum(no_ms2_mask)) > 0:
currently alphabase fails for maxquant output which contains MBR PSMs.
This removes MBR PSMs and prints an explicit warning