Link to problematic files

[nchenche]

Issue created to add input files orftrack wrongly handles (preferentially link to files to avoid huge files to be stored here)

[nchenche]

Hi paul,

I received your mail and the problematic files :

1. PNL4-3XCS.fa & PNL4-3XCS.gff3
2. Spar.fna & Spar.gff
3. Oryza_sativa.fna & Oryza_sativa.gff

Case 1:

The error was due to an inconsistent chromosome name between the fasta (chr name: PNL4-3XCS) and the gff (chr name: chrVIH) file. If the chromosome name don't match, the process is stopped and a message is written in the ouput:

# PARSING GFF FILE
------------------

Checking chromosome IDs consistency between GFF and fasta file...

      Chromosome ids              in GFF            in fasta
------------------------------------------------------------
           PNL4-3XCS                   -                   X
              chrVIH                   X                   -

Chromosomes are not consistent between GFF and fasta files.

Case 2:

No problem identified neither with orftrack nor with orfget.

Case 3:

Orfget stops with the following error:

  File "/home/nchenche/projects/ORFmine/orftrack/orftrack/scripts/ORFget.py", line 248, in write_multifastas
    aa_seq = dico_info[gene]['AA_seq']
KeyError: 'AA_seq'

Orftrack runs until the end without any raised error. However the output looks strange at the first sight since for each chromosome only one type of ORF is found:

chr	ORF type	qty	avg length (aa)
1	nc_intergenic	1340250	46.29
10	nc_intergenic	717431	46.16
11	nc_intergenic	900540	45.53
12	nc_intergenic	856175	45.52
2	nc_intergenic	1117788	45.81
3	nc_intergenic	1132103	46.09
4	nc_intergenic	1096840	46.68
5	nc_intergenic	927312	46.36
6	nc_intergenic	968303	46.07
7	nc_intergenic	920731	46
8	nc_intergenic	881891	45.86
9	nc_intergenic	713027	46.05
AC155918	nc_ovp_opp-scaffold	1033	47.74
AC156495	nc_ovp_opp-scaffold	2694	49.73
AC160949	nc_ovp_opp-scaffold	3942	46.05
AC174930	nc_ovp_opp-scaffold	482	43.78
AP008246	nc_ovp_opp-scaffold	6367	45.13
AP008247	nc_ovp_opp-scaffold	4775	47.98
Mt	nc_intergenic	16576	42.2
Pt	nc_intergenic	4310	42.87
Syng_TIGR_002	nc_ovp_opp-scaffold	473	43.33
Syng_TIGR_004	nc_ovp_opp-scaffold	631	39.41
Syng_TIGR_005	nc_ovp_opp-scaffold	634	53.61
Syng_TIGR_007	nc_ovp_opp-scaffold	181	72.8
Syng_TIGR_008	nc_ovp_opp-scaffold	504	42.51
Syng_TIGR_009	nc_ovp_opp-scaffold	297	56.61
Syng_TIGR_010	nc_ovp_opp-scaffold	482	48.22
Syng_TIGR_011	nc_ovp_opp-scaffold	337	44.83
Syng_TIGR_012	nc_ovp_opp-scaffold	502	50.45
Syng_TIGR_013	nc_ovp_opp-scaffold	312	52.78
Syng_TIGR_014	nc_ovp_opp-scaffold	675	42.52
Syng_TIGR_015	nc_ovp_opp-scaffold	310	48.15
Syng_TIGR_016	nc_ovp_opp-scaffold	428	39.91
Syng_TIGR_019	nc_ovp_opp-scaffold	333	42.69
Syng_TIGR_020	nc_ovp_opp-scaffold	323	50.13
Syng_TIGR_021	nc_ovp_opp-scaffold	537	42.74
Syng_TIGR_022	nc_ovp_opp-scaffold	294	52.86
Syng_TIGR_023	nc_ovp_opp-scaffold	789	45.39
Syng_TIGR_024	nc_ovp_opp-scaffold	298	53.4
Syng_TIGR_026	nc_ovp_opp-scaffold	640	43.09
Syng_TIGR_027	nc_ovp_opp-scaffold	354	43.81
Syng_TIGR_028	nc_ovp_opp-scaffold	978	43.5
Syng_TIGR_029	nc_ovp_opp-scaffold	375	51.91
Syng_TIGR_030	nc_ovp_opp-scaffold	330	48.55
Syng_TIGR_031	nc_ovp_opp-scaffold	218	76.23
Syng_TIGR_032	nc_ovp_opp-scaffold	297	46.67
Syng_TIGR_033	nc_ovp_opp-scaffold	334	52.03
Syng_TIGR_034	nc_ovp_opp-scaffold	253	70.8
Syng_TIGR_035	nc_ovp_opp-scaffold	360	43.19
Syng_TIGR_036	nc_ovp_opp-scaffold	316	48.67
Syng_TIGR_037	nc_ovp_opp-scaffold	422	42.04
Syng_TIGR_038	nc_ovp_opp-scaffold	258	49.55
Syng_TIGR_039	nc_ovp_opp-scaffold	207	45.76
Syng_TIGR_041	nc_ovp_opp-scaffold	299	48.11
Syng_TIGR_042	nc_ovp_opp-scaffold	131	73.92
Syng_TIGR_043	nc_ovp_opp-scaffold	93	83.63
Syng_TIGR_044	nc_ovp_opp-scaffold	192	41.58
Syng_TIGR_045	nc_ovp_opp-scaffold	670	51.9
Syng_TIGR_046	nc_ovp_opp-scaffold	366	44.58
Syng_TIGR_047	nc_ovp_opp-scaffold	651	45.27
Syng_TIGR_048	nc_ovp_opp-scaffold	199	53.76
Syng_TIGR_049	nc_ovp_opp-scaffold	166	60.4
Syng_TIGR_050	nc_ovp_opp-scaffold	280	47.08

[nchenche]

Case 3 issue from orftrack has been fixed in the recent push (see commit Fix bug when '#' is found in gff between different features in same chr).