Skip to content

Commit

Permalink
Merge pull request #7 from aweimann/master
Browse files Browse the repository at this point in the history 
v1.1.1
  • Loading branch information
aweimann authored Jul 25, 2016
2 parents 01b1694 + e1ee7a3 commit bdd39bb
Show file tree
Hide file tree
Showing 115 changed files with 19,854 additions and 14,193 deletions.
3 changes: 3 additions & 0 deletions MANIFEST.in
View file
Original file line number Diff line number Diff line change
@@ -1,2 +1,5 @@
include README.md
recursive-include traitar *
recursive-exclude traitar config.json
recursive-exclude traitar *.pyc
recursive-exclude traitar *.swp
2 changes: 1 addition & 1 deletion README.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -96,5 +96,5 @@ which will take ~30 minutes. Note there is a problem with parallel usage so -c o
If you use Traitar in your research, please cite our preprint:

**From genomes to phenotypes: Traitar, the microbial trait analyzer**
Aaron Weimann, Jeremy Frank, Phillip B Pope, Andreas Bremges, Alice C McHardy
Aaron Weimann, Kyra Mooren, Jeremy Frank, Phillip B Pope, Andreas Bremges, Alice C McHardy
*bioRxiv* (2016) doi:[10.1101/043315](http://dx.doi.org/10.1101/043315)
96 changes: 72 additions & 24 deletions README.rst
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3,31 +3,33 @@ Traitar – the microbial trait analyzer

Traitar is a software for characterizing microbial samples from
nucleotide or protein sequences. It can accurately phenotype `67 diverse
traits <https://github.com/hzi-bifo/traitar/blob/master/traits.tsv>`__.
Please take a look at the `gitHub repository <https://github.com/hzi-bifo/traitar/>`__ for further information.
traits`_.

Table of Contents
~~~~~~~~~~~~~~~~~

| `Installation <#installation>`__
| `Basic usage <#basic-usage>`__
| `Results <#results>`__
| `Installation`_
| `Basic usage`_
| `Results`_
| `Docker`_
| `Citing Traitar`_
Installation
============

Please see `INSTALL.md <https://github.com/hzi-bifo/traitar/blob/master/INSTALL.md>`__ for installation instructions.
Please see `INSTALL.md`_ for installation instructions.

Basic usage
===========

``traitar phenotype <in dir> <sample file> from_nucleotides <out_dir>``

will trigger the standard `workflow <https://raw.githubusercontent.com/hzi-bifo/traitar/master/workflow.png>`__ of Traitar, which is to predict open
will trigger the standard `workflow <https://raw.githubusercontent.com/hzi-bifo/traitar/master/workflow.png>`__ of Traitar, which is to predict open
reading frames with Prodigal, annotate the coding sequences provided as
nucleotide FASTAs in the for all samples in with Pfam families using
HMMer and finally predict phenotypes from the models for the 67 traits.


The sample file has one column for the sample file names and one for the
names as specified by the user. You can also specify a grouping of the
samples in the third column, which will be shown in the generated plots.
Expand All @@ -36,7 +38,7 @@ also take a look at the sample file for the packaged example data:

| sample\_file\_name{tab}sample\_name{tab}category
| sample1\_file\_name{tab}sample1\_name[{tabl}sample\_category1]
| sample2\_file\_name{tab}sample2\_name[{tabl}sample\_category2]
sample2\_file\_name{tab}sample2\_name[{tabl}sample\_category2]
``traitar phenotype <in dir> <sample file> from_genes <out_dir>``

Expand All @@ -56,6 +58,19 @@ the number of processes used e.g. ``-c 2`` for using two processes

This requires installing GNU parallel as noted above.

Inspect phenotype classification models
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Traitar can be used to inspect the protein families in each phenotype
model:

``traitar show 'Glucose fermenter``

will show the majority features i.e. the Pfam families that contribute
to the assignment of the trait Glucose fermenter with *phypat*
classifier to some genome sequence. Via –predictor the user may specify
the classifier (phypat, phypat+PGL).

Run Traitar with packaged sample data
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Expand All @@ -64,11 +79,8 @@ will trigger phenotyping of *Listeria grayi DSM\_20601* and *Listeria
ivanovii WSLC3009*. Computation should be done within 5 minutes. You can
find out ``<traitar_dir>`` by running

::

python
>>> import traitar
>>> traitar.__path__
\`\`\` python
python >>> import traitar >>> traitar.\ **path** \`\`\`

Results
=======
Expand All @@ -84,15 +96,14 @@ Heatmaps
The phenotype prediction is summarized in heatmaps individually for the
phyletic pattern classifier in ``heatmap_phypat.png``, for the
phylogeny-aware classifier in ``heatmap_phypat_ggl.png`` and for both
classifiers `combined <https://github.com/aweimann/traitar/blob/master/traitar/data/sample_data/traitar_out/phenotype_prediction/heatmap_combined.png?raw=true>`__
in ``heatmap_comb.png`` and provide hierarchical
classifiers `combined <https://github.com/aweimann/traitar/blob/master/traitar/data/sample_data/traitar_out/phenotype_prediction/heatmap_combined.png?raw=true>`__ in ``heatmap_comb.png`` and provide hierarchical
clustering dendrograms for phenotypes and the samples.

Phenotype prediction - Tables and flat files
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

These heatmaps are based on tab separated text files e.g.
``predictions_majority-votes_combined.txt``. A negative prediction is
``predictions_majority-vote_combined.txt``. A negative prediction is
encoded as 0, a prediction made only by the pure phyletic classifier as
1, one made by the phylogeny-aware classifier by 2 and a prediction
supported by both algorithms as 3.
Expand All @@ -101,14 +112,16 @@ of this table with one prediction per row. The expert user might also
want to access the individual results for each algorithm in the
respective sub folders ``phypat`` and ``phypat+PGL``.

Feature tracks
~~~~~~~~~~~~~~
Phenotype-relevant protein families and feature tracks
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

If Traitar is run from\_nucleotides it will generate a link between the
Prodigal gene prediction and predicted phenotypes in
``phypat/feat_gffs`` and ``phypat+PGL/feat_gffs`` (no example in the
sample data). The user can visualize gene prediction phenotype-specific
Pfam annotations tracks via GFF files.
Traitar will link the protein families and predicted phenotypes. The
results can be found in ``phypat/feat_gffs`` and
\`\ ``phypat+PGL/feat_gffs``. If the user picked the ‘from nucleotides’
option, Traitar will also generate GFF files that link the genes called
by Prodidgal with the important protein families. The phenotype-specific
protein family annotations tracks can be visualized via GFF files in a
genome browser of choice.

Feature tracks with *from\_genes* option (experimental feature)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Expand All @@ -117,9 +130,44 @@ If the *from\_genes* option is set, the user may specify gene GFF files
via an additional column called gene\_gff in the sample file. As gene
ids are not consistent across gene GFFs from different sources e.g. img,
RefSeq or Prodigal the user needs to specify the origin of the gene gff
file via the -g / --gene\_gff\_type parameter. Still there is no
file via the -g / –gene\_gff\_type parameter. Still there is no
guarantee that this works currently. Using samples\_gene\_gff.txt as the
sample file in the above example will generate phenotype-specific Pfam
tracks for the two genomes.

``traitar phenotype . samples_gene_gff.txt from_genes traitar_out -g refseq``

Docker
======

There is a Docker container available for Traitar. Pull by

``docker pull aweimann/traitar``

To run traitar for the sample data execute

``docker run -v <traitar_dir>/data/sample_data:/mnt 1445e6c01992 bash -c 'traitar phenotype /mnt/ /mnt/samples.txt from_nucleotides /mnt/traitar_out'``,

which will take ~30 minutes. Note there is a problem with parallel usage
so -c option is not guaranteed to work. The output will be owned by
root. So currently you still need root access to your machine to inspect
the traitar\_out folder.

Citing Traitar
==============

If you use Traitar in your research, please cite our preprint:

| **From genomes to phenotypes: Traitar, the microbial trait analyzer**
| Aaron Weimann, Jeremy Frank, Phillip B Pope, Andreas Bremges, Alice C
McHardy
| *bioRxiv* (2016) doi:\ `10.1101/043315`_
.. _10.1101/043315: http://dx.doi.org/10.1101/043315
.. _67 diverse traits: traits.tsv
.. _Installation: #installation
.. _Basic usage: #basic-usage
.. _Results: #results
.. _Docker: #docker
.. _Citing Traitar: #citing-traitar
.. _INSTALL.md: INSTALL.md
2 changes: 1 addition & 1 deletion traitar/_version.py
View file
Original file line number Diff line number Diff line change
@@ -1 +1 @@
__version__ = "1.1.0"
__version__ = "1.1.1"
1 change: 0 additions & 1 deletion traitar/config.json.backup
View file

This file was deleted.

4 changes: 4 additions & 0 deletions traitar/data/sample_data/traitar_out/phenotype_prediction/feature_track_commands.txt
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
hmm2gff.py traitar_out/annotation/pfam/Listeria_ivanovii_WSLC3009_filtered_best.dat traitar_out/phenotype_prediction/phypat/feat_gffs/ Listeria_ivanovii_WSLC3009 /home/aaron/traitar/traitar/data/models/phypat.tar.gz 8556,8567,8549,8548,8558,8489,8536,8537,8540,8550,8545,8530,8566,8563,8510,8488,8477,8524,8534,8517,8498,8486,8562,8478 --gene_gff ./1457190.3.RefSeq.gff --gene_gff_type refseq
hmm2gff.py traitar_out/annotation/pfam/Listeria_ivanovii_WSLC3009_filtered_best.dat traitar_out/phenotype_prediction/phypat/feat_gffs/ Listeria_ivanovii_WSLC3009 /home/aaron/traitar/traitar/data/models/phypat+PGL.tar.gz 8556,8567,8549,8548,8558,8489,8536,8537,8540,8550,8545,8530,8566,8563,8510,8488,8477,8524,8534,8517,8498,8486,8562,8478 --gene_gff ./1457190.3.RefSeq.gff --gene_gff_type refseq
hmm2gff.py traitar_out/annotation/pfam/Listeria_grayi_DSM_20601_filtered_best.dat traitar_out/phenotype_prediction/phypat/feat_gffs/ Listeria_grayi_DSM_20601 /home/aaron/traitar/traitar/data/models/phypat.tar.gz 8556,8567,8494,8549,8548,8558,8489,8537,8526,8540,8550,8530,8533,8547,8563,8510,8488,8477,8524,8534,8498,8486,8562,8478 --gene_gff ./525367.9.RefSeq.gff --gene_gff_type refseq
hmm2gff.py traitar_out/annotation/pfam/Listeria_grayi_DSM_20601_filtered_best.dat traitar_out/phenotype_prediction/phypat/feat_gffs/ Listeria_grayi_DSM_20601 /home/aaron/traitar/traitar/data/models/phypat+PGL.tar.gz 8556,8567,8494,8549,8548,8558,8489,8537,8526,8540,8550,8530,8533,8547,8563,8510,8488,8477,8524,8534,8498,8486,8562,8478 --gene_gff ./525367.9.RefSeq.gff --gene_gff_type refseq
Binary file modified traitar/data/sample_data/traitar_out/phenotype_prediction/heatmap_combined.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified traitar/data/sample_data/traitar_out/phenotype_prediction/heatmap_phypat+PGL.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified traitar/data/sample_data/traitar_out/phenotype_prediction/heatmap_phypat.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
6 changes: 6 additions & 0 deletions .../phypat+PGL/feat_gffs/Listeria_grayi_DSM_20601_Acetate_utilization_important_features.gff
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
##gff-version 3
accn|NZ_GG692933 HMMER phypat+PGL 185775 185970 5.1e-10 + . Parent=HMPREF0556_0273;Name=PF06779;Note=DUF1228;Description=Protein of unknown function (DUF1228)
accn|NZ_GG692933 HMMER phypat+PGL 249098 249422 1.3e-17 + . Parent=HMPREF0556_0335;Name=PF02517;Note=Abi;Description=CAAX protease self-immunity
accn|NZ_GG692933 HMMER phypat+PGL 492426 492687 8.8000000000000009e-23 - . Parent=HMPREF0556_0581;Name=PF02517;Note=Abi;Description=CAAX protease self-immunity
accn|NZ_GG692932 HMMER phypat+PGL 378393 378651 9.4999999999999999e-14 - . Parent=HMPREF0556_1276;Name=PF02517;Note=Abi;Description=CAAX protease self-immunity
accn|NZ_GG692934 HMMER phypat+PGL 187223 188375 5.6999999999999999e-91 + . Parent=HMPREF0556_2438;Name=PF02274;Note=Amidinotransf;Description=Amidinotransferase
18 changes: 18 additions & 0 deletions ...phypat+PGL/feat_gffs/Listeria_grayi_DSM_20601_Alkaline_phosphatase_important_features.gff
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,18 @@
##gff-version 3
accn|NZ_GG692933 HMMER phypat+PGL 67301 67514 9.9999999999999998e-17 + . Parent=HMPREF0556_0159;Name=PF13545;Note=HTH_Crp_2;Description=Crp-like helix-turn-helix domain
accn|NZ_GG692933 HMMER phypat+PGL 269290 269737 3.2e-51 + . Parent=HMPREF0556_0356;Name=PF01262;Note=AlaDh_PNT_C;Description=Alanine dehydrogenase/PNT, C-terminal domain
accn|NZ_GG692933 HMMER phypat+PGL 335050 335260 6.8000000000000001e-14 + . Parent=HMPREF0556_0417;Name=PF08211;Note=dCMP_cyt_deam_2;Description=Cytidine and deoxycytidylate deaminase zinc-binding region
accn|NZ_GG692933 HMMER phypat+PGL 424146 424353 4.9000000000000003e-13 - . Parent=HMPREF0556_0514;Name=PF13545;Note=HTH_Crp_2;Description=Crp-like helix-turn-helix domain
accn|NZ_GG692932 HMMER phypat+PGL 190014 190161 6.2000000000000003e-10 + . Parent=HMPREF0556_1066;Name=PF13545;Note=HTH_Crp_2;Description=Crp-like helix-turn-helix domain
accn|NZ_GG692932 HMMER phypat+PGL 325954 326359 7.200000000000001e-10 - . Parent=HMPREF0556_1221;Name=PF07819;Note=PGAP1;Description=PGAP1-like protein
accn|NZ_GG692932 HMMER phypat+PGL 353497 353719 3.3e-15 + . Parent=HMPREF0556_1254;Name=PF13545;Note=HTH_Crp_2;Description=Crp-like helix-turn-helix domain
accn|NZ_GG692932 HMMER phypat+PGL 364462 364666 8.6999999999999997e-11 + . Parent=HMPREF0556_1263;Name=PF13545;Note=HTH_Crp_2;Description=Crp-like helix-turn-helix domain
accn|NZ_GG692932 HMMER phypat+PGL 499741 499912 1.4999999999999999e-13 + . Parent=HMPREF0556_1397;Name=PF13905;Note=Thioredoxin_8;Description=Thioredoxin-like
accn|NZ_GG692932 HMMER phypat+PGL 581249 581399 7.5999999999999996e-10 + . Parent=HMPREF0556_1483;Name=PF13545;Note=HTH_Crp_2;Description=Crp-like helix-turn-helix domain
accn|NZ_GG692932 HMMER phypat+PGL 799555 799861 1e-10 + . Parent=HMPREF0556_1687;Name=PF03848;Note=TehB;Description=Tellurite resistance protein TehB
accn|NZ_GG692932 HMMER phypat+PGL 985368 985827 5.0999999999999997e-30 + . Parent=HMPREF0556_1869;Name=PF02872;Note=5_nucleotid_C;Description=5'-nucleotidase, C-terminal domain
accn|NZ_GG692937 HMMER phypat+PGL 5726 5999 3.4000000000000002e-13 - . Parent=HMPREF0556_1916;Name=PF12846;Note=AAA_10;Description=AAA-like domain
accn|NZ_GG692937 HMMER phypat+PGL 32369 33386 1.0999999999999999e-53 - . Parent=HMPREF0556_1951;Name=PF12846;Note=AAA_10;Description=AAA-like domain
accn|NZ_GG692935 HMMER phypat+PGL 233709 234093 6.3999999999999992e-14 + . Parent=HMPREF0556_2208;Name=PF02872;Note=5_nucleotid_C;Description=5'-nucleotidase, C-terminal domain
accn|NZ_GG692934 HMMER phypat+PGL 217206 217425 1.4999999999999998e-24 + . Parent=HMPREF0556_2471;Name=PF13545;Note=HTH_Crp_2;Description=Crp-like helix-turn-helix domain
accn|NZ_GG692934 HMMER phypat+PGL 260597 260810 1.5e-16 + . Parent=HMPREF0556_2518;Name=PF13545;Note=HTH_Crp_2;Description=Crp-like helix-turn-helix domain
14 changes: 14 additions & 0 deletions ..._prediction/phypat+PGL/feat_gffs/Listeria_grayi_DSM_20601_Catalase_important_features.gff
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
##gff-version 3
accn|NZ_GG692936 HMMER phypat+PGL 10543 10681 1.2e-20 + . Parent=HMPREF0556_0012;Name=PF08338;Note=DUF1731;Description=Domain of unknown function (DUF1731)
accn|NZ_GG692936 HMMER phypat+PGL 54764 55613 3.7999999999999992e-119 - . Parent=HMPREF0556_0052;Name=PF04898;Note=Glu_syn_central;Description=Glutamate synthase central domain
accn|NZ_GG692936 HMMER phypat+PGL 55793 56171 1.5999999999999999e-37 - . Parent=HMPREF0556_0052;Name=PF01645;Note=Glu_synthase;Description=Conserved region in glutamate synthase
accn|NZ_GG692933 HMMER phypat+PGL 454293 454800 5.0999999999999995e-53 - . Parent=HMPREF0556_0543;Name=PF04264;Note=YceI;Description=YceI-like domain
accn|NZ_GG692933 HMMER phypat+PGL 464878 465154 6.7000000000000005e-21 + . Parent=HMPREF0556_0552;Name=PF13806;Note=Rieske_2;Description=Rieske-like [2Fe-2S] domain
accn|NZ_GG692933 HMMER phypat+PGL 511717 512557 6.9000000000000001e-61 - . Parent=HMPREF0556_0605;Name=PF02628;Note=COX15-CtaA;Description=Cytochrome oxidase assembly protein
accn|NZ_GG692932 HMMER phypat+PGL 113466 113790 1.0999999999999999e-44 + . Parent=HMPREF0556_0989;Name=PF03960;Note=ArsC;Description=ArsC family
accn|NZ_GG692932 HMMER phypat+PGL 419739 420426 3.4999999999999993e-91 + . Parent=HMPREF0556_1320;Name=PF00198;Note=2-oxoacid_dh;Description=2-oxoacid dehydrogenases acyltransferase (catalytic domain)
accn|NZ_GG692932 HMMER phypat+PGL 921959 922634 1.1e-83 - . Parent=HMPREF0556_1802;Name=PF00198;Note=2-oxoacid_dh;Description=2-oxoacid dehydrogenases acyltransferase (catalytic domain)
accn|NZ_GG692935 HMMER phypat+PGL 3331 3649 6.3999999999999995e-38 + . Parent=HMPREF0556_1995;Name=PF14748;Note=P5CR_dimer;Description=Pyrroline-5-carboxylate reductase dimerisation
accn|NZ_GG692935 HMMER phypat+PGL 199661 199985 6.8000000000000001e-34 + . Parent=HMPREF0556_2180;Name=PF03960;Note=ArsC;Description=ArsC family
accn|NZ_GG692934 HMMER phypat+PGL 137926 139069 1.9999999999999993e-176 - . Parent=HMPREF0556_2392;Name=PF00199;Note=Catalase;Description=Catalase
accn|NZ_GG692934 HMMER phypat+PGL 312658 313243 4.9999999999999999e-13 - . Parent=HMPREF0556_2575;Name=PF02230;Note=Abhydrolase_2;Description=Phospholipase/Carboxylesterase
14 changes: 14 additions & 0 deletions ...e_prediction/phypat+PGL/feat_gffs/Listeria_grayi_DSM_20601_Citrate_important_features.gff
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
##gff-version 3
accn|NZ_GG692936 HMMER phypat+PGL 92888 93122 7.1999999999999993e-33 - . Parent=HMPREF0556_0090;Name=PF10397;Note=ADSL_C;Description=Adenylosuccinate lyase C-terminus
accn|NZ_GG692933 HMMER phypat+PGL 167486 167636 3.7000000000000007e-10 - . Parent=HMPREF0556_0248;Name=PF00135;Note=COesterase;Description=Carboxylesterase family
accn|NZ_GG692933 HMMER phypat+PGL 189027 189177 8.400000000000001e-10 + . Parent=HMPREF0556_0278;Name=PF00135;Note=COesterase;Description=Carboxylesterase family
accn|NZ_GG692933 HMMER phypat+PGL 207893 208181 5.0999999999999999e-29 - . Parent=HMPREF0556_0294;Name=PF02746;Note=MR_MLE_N;Description=Mandelate racemase / muconate lactonizing enzyme, N-terminal domain
accn|NZ_GG692933 HMMER phypat+PGL 400555 400714 1.6000000000000001e-09 + . Parent=HMPREF0556_0492;Name=PF00135;Note=COesterase;Description=Carboxylesterase family
accn|NZ_GG692933 HMMER phypat+PGL 477969 478329 3.4000000000000002e-13 + . Parent=HMPREF0556_0566;Name=PF00135;Note=COesterase;Description=Carboxylesterase family
accn|NZ_GG692933 HMMER phypat+PGL 537965 538256 1.8e-37 + . Parent=HMPREF0556_0635;Name=PF02829;Note=3H;Description=3H domain
accn|NZ_GG692932 HMMER phypat+PGL 16371 17031 1.3000000000000002e-60 - . Parent=HMPREF0556_0895;Name=PF11975;Note=Glyco_hydro_4C;Description=Family 4 glycosyl hydrolase C-terminal domain
accn|NZ_GG692932 HMMER phypat+PGL 21522 22185 5.5999999999999989e-48 + . Parent=HMPREF0556_0900;Name=PF11975;Note=Glyco_hydro_4C;Description=Family 4 glycosyl hydrolase C-terminal domain
accn|NZ_GG692932 HMMER phypat+PGL 691105 691612 8.2999999999999998e-11 + . Parent=HMPREF0556_1583;Name=PF06833;Note=MdcE;Description=Malonate decarboxylase gamma subunit (MdcE)
accn|NZ_GG692935 HMMER phypat+PGL 61412 61733 1.2e-15 + . Parent=HMPREF0556_2056;Name=PF02746;Note=MR_MLE_N;Description=Mandelate racemase / muconate lactonizing enzyme, N-terminal domain
accn|NZ_GG692935 HMMER phypat+PGL 239695 240079 1.3000000000000002e-10 - . Parent=HMPREF0556_2217;Name=PF13434;Note=K_oxygenase;Description=L-lysine 6-monooxygenase (NADPH-requiring)
accn|NZ_GG692934 HMMER phypat+PGL 312658 313243 4.9999999999999999e-13 - . Parent=HMPREF0556_2575;Name=PF02230;Note=Abhydrolase_2;Description=Phospholipase/Carboxylesterase
11 changes: 11 additions & 0 deletions ...phypat+PGL/feat_gffs/Listeria_grayi_DSM_20601_Coagulase_production_important_features.gff
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
##gff-version 3
accn|NZ_GG692932 HMMER phypat+PGL 33791 35081 6.4999999999999975e-193 - . Parent=HMPREF0556_0912;Name=PF03051;Note=Peptidase_C1_2;Description=Peptidase C1-like family
accn|NZ_GG692932 HMMER phypat+PGL 88819 89053 1.4000000000000001e-15 - . Parent=HMPREF0556_0964;Name=PF12732;Note=YtxH;Description=YtxH-like protein
accn|NZ_GG692932 HMMER phypat+PGL 504864 505254 1.2999999999999999e-27 + . Parent=HMPREF0556_1402;Name=PF01138;Note=RNase_PH;Description=3' exoribonuclease family, domain 1
accn|NZ_GG692932 HMMER phypat+PGL 505311 505509 4.0999999999999996e-14 + . Parent=HMPREF0556_1402;Name=PF03725;Note=RNase_PH_C;Description=3' exoribonuclease family, domain 2
accn|NZ_GG692932 HMMER phypat+PGL 645391 645682 8.9999999999999995e-24 + . Parent=HMPREF0556_1541;Name=PF12732;Note=YtxH;Description=YtxH-like protein
accn|NZ_GG692932 HMMER phypat+PGL 958093 958189 5.2999999999999996e-12 - . Parent=HMPREF0556_1843;Name=PF13014;Note=KH_3;Description=KH domain
accn|NZ_GG692932 HMMER phypat+PGL 957112 957358 3.5000000000000002e-16 - . Parent=HMPREF0556_1843;Name=PF03726;Note=PNPase;Description=Polyribonucleotide nucleotidyltransferase, RNA binding domain
accn|NZ_GG692932 HMMER phypat+PGL 956434 956821 5.5000000000000006e-24 - . Parent=HMPREF0556_1843;Name=PF01138;Note=RNase_PH;Description=3' exoribonuclease family, domain 1
accn|NZ_GG692932 HMMER phypat+PGL 956830 957019 3.6000000000000001e-19 - . Parent=HMPREF0556_1843;Name=PF03725;Note=RNase_PH_C;Description=3' exoribonuclease family, domain 2
accn|NZ_GG692935 HMMER phypat+PGL 248495 248693 9.9999999999999993e-23 - . Parent=HMPREF0556_2227;Name=PF13244;Note=DUF4040;Description=Domain of unknown function (DUF4040)
2 changes: 2 additions & 0 deletions ...rediction/phypat+PGL/feat_gffs/Listeria_grayi_DSM_20601_D-Mannitol_important_features.gff
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
##gff-version 3
accn|NZ_GG692934 HMMER phypat+PGL 237179 237542 5.5999999999999999e-27 + . Parent=HMPREF0556_2493;Name=PF01232;Note=Mannitol_dh;Description=Mannitol dehydrogenase Rossmann domain
Loading

0 comments on commit bdd39bb

Please sign in to comment.