SIF file format

[beyn...@gmail.com]

Greetings all,

I'm trying to subvert Cytoscape into helping me visualise a different problem.

Isoforms of proteins when digested, create peptides that are either common to multiple isoforms or unique. I have written a tool to create a SIF file to help me illustrate, visualise this.

But, although it has worked in the past, I can no longer import my home-crafted SIF file.

File/Import/Network/File...gives
'could not initialise preview'

The file format is simple:
three fields, each separated by a tab

e.g. peptide EASFER 866.367

with relationship formed from

ff
this protein

>ratMUP1_1_18340 Da

(pasted text from beginning of file below).

I am at a loss. The manual says if I use tabs, then spaces are allowed. So, this should not be an issue.

All help would be appreciated

Rob Beynon


EASFER 866.367 ff >ratMUP1_1_18340 Da
GNLDVDK 759.367 ff >ratMUP1_1_18340 Da
LNGDWFSIVVASDK 1549.768 ff >ratMUP1_1_18340 Da
IEENGSMR 934.408 ff >ratMUP1_1_18340 Da
VFVQHIDVLENSLGFTFR 2120.096 ff >ratMUP1_1_18340 Da
ENGVCTEFSLVADK 1567.717 ff >ratMUP1_1_18340 Da
DGEYFVEYDGENTFTILK 2138.959 ff >ratMUP1_1_18340 Da
TDYDNYVMFHLVNVNNGETFQLMELYGR 3381.534 ff >ratMUP1_1_18340 Da
DLSSDIK 776.382 ff >ratMUP1_1_18340 Da
LCVAHGITR 1025.542 ff >ratMUP1_1_18340 Da
DNIIDLTK 930.493 ff >ratMUP1_1_18340 Da
EEASFER 866.367 ff >ratMUP1_2_18553 Da
GNLDVDK 759.367 ff >ratMUP1_2_18553 Da
LNGDWFSIVVASDK 1549.768 ff >ratMUP1_2_18553 Da
IEENGSMR 934.408 ff >ratMUP1_2_18553 Da
VFVQHIDVLENSLGFTFR 2120.096 ff >ratMUP1_2_18553 Da
ENGVCTEFSLVADK 1567.717 ff >ratMUP1_2_18553 Da

[Alex Pico]

This should work fine. I copy/pasted your example into a file named test.sif and it imported without issue (attached here). I suspect your actual file has some hidden characters or something? Perhaps try saving from another text editor.

 - Alex

[beyn...@gmail.com]

Thanks Alex,
You surmised correctly.

When I open the file and save with UTF encoding, it reads fine. Something lurking in the file, obviously. Many thanks for your help
Rob