ptt and rnt files that were created from assembly rather than a genome

Question

[langziv]

Hi

In order to use Rockhopper I created ptt and rnt files from the GenBank file of the bacterium's strain I work with. Since this strain has an assembly instead of a genome, the ptt and rnt files are created differently than files that are created from a genome, and have a different format.

When I run Rockhopper with these files error messages were printed. Here are some example lines:

Error - expecting 9 columns of gene information but found less than 9:  278..1100       +       822     -       AFK73_25870     AFK73_25870     -       hypothetical protein
Error - expecting 9 columns of gene information but found less than 9:  1494..1980      -       486     -       AFK73_25875     AFK73_25875     -       lytic transglycosylase
Error - expecting 9 columns of gene information but found less than 9:  2413..2806      +       393     -       AFK73_25880     AFK73_25880     -       conjugal transfer protein TraM

I tried creating the files with the script that's in this post, as well as with Edge-pro's documentation. Did anyone face this problem and managed to solve it?

Answer 1

[shelkmike]

You need to add an additional column with "-" before the last column. For example, here are the first 10 lines of my .ptt file which I successfully used with Rockhopper:

NS - 1..5637360
5427 proteins
Location    Strand  Length  PID Gene    Synonym Code    COG Product
2816432..2818867    +   812 -   -   KR76_13805  -   -   Membrane alanine aminopeptidase N
1408840..1410318    -   493 -   -   KR76_06980  -   -   hypothetical protein
704477..705019  +   181 -   -   KR76_03405  -   -   putative multidomain membrane protein
1..1623 +   541 -   -   KR76_00005  -   -   Chromosomal replication initiator protein DnaA
2108..3166  +   353 -   -   KR76_00010  -   -   DNA polymerase III beta subunit
3246..4127  +   294 -   -   KR76_00015  -   -   6-phosphogluconate dehydrogenase,decarboxylating
4128..4541  -   138 -   -   KR76_00020  -   -   hypothetical protein

[langziv]

Thanks. I'll try. I'm very skeptic because of the the files' structure. For instance:

Klebsiella pneumoniae strain B199 plasmid unnamed 4 scaffold_39, whole genome shotgun sequence 
- 0..10952
10 proteins
Location    Strand  Length  PID Gene    Synonym Code    COG Product
0..194  -   194 -   AFK73_28005 AFK73_28005 -   transposase
472..1132   +   660 -   AFK73_28010 AFK73_28010 -   chloramphenicol acetyltransferase
1332..1710  -   378 -   AFK73_28015 AFK73_28015 -   acetyltransferase
2020..3025  -   1005    -   AFK73_28020 AFK73_28020 -   transposase
3103..6070  -   2967    -   AFK73_28025 AFK73_28025 -   transposase
6072..6633  -   561 -   AFK73_28030 AFK73_28030 -   hypothetical protein
6758..7037  -   279 -   AFK73_28035 AFK73_28035 -   transposase
7173..7353  +   180 -   AFK73_28040 AFK73_28040 -   transcriptional regulator
7311..8292  -   981 -   AFK73_28045 AFK73_28045 -   integrase
8689..10039 -   1350    -   AFK73_28055 AFK73_28055 -   DNA polymerase
Klebsiella pneumoniae strain B199 plasmid unnamed 5 scaffold_45, whole genome shotgun sequence - 0..5834
9 proteins
Location    Strand  Length  PID Gene    Synonym Code    COG Product
717..1089   -   372 -   AFK73_28270 AFK73_28270 -   hypothetical protein
1483..1828  +   345 -   AFK73_28275 AFK73_28275 -   mobilization protein
2009..2255  -   246 -   AFK73_28280 AFK73_28280 -   hypothetical protein
2505..3015  +   510 -   AFK73_28285 AFK73_28285 -   mobilization protein
3021..3234  +   213 -   AFK73_28290 AFK73_28290 -   mobilization protein
4108..4375  +   267 -   AFK73_28295 AFK73_28295 -   addiction module toxin RelE
4444..4795  -   351 -   AFK73_28300 AFK73_28300 -   hypothetical protein
4860..5406  -   546 -   AFK73_28305 AFK73_28305 -   hypothetical protein
5431..5758  -   327 -   AFK73_28310 AFK73_28310 -   hypothetical protein

As can be seen, there are multiple entrees instead of one long table (due to the reference being an assembly rather than a genome).