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Add support for UNMAPPED and taxon identifiers (#11)
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Add support for UNMAPPED and taxon identifiers
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@bebatut
bebatut authored May 2, 2019
2 parents b7db56c + 0ead6a9 commit 1007b9f
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Showing 4 changed files with 125 additions and 118 deletions.
19 changes: 13 additions & 6 deletions src/format_humann2_output.py
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Original file line number Diff line number Diff line change
Expand Up @@ -50,6 +50,7 @@ def extract_go_slim_annotations(args):
def format_humann2_output(args, go_annotations):
with open(args.humann2_output, "r") as humann2_output:
output_files = {}

output_files['molecular_function'] = open(args.molecular_function_output_file,"w")
output_files['molecular_function'].write("GO id\tGO name\tAbundance\n")

Expand All @@ -59,22 +60,28 @@ def format_humann2_output(args, go_annotations):
output_files['cellular_component'] = open(args.cellular_component_output_file,"w")
output_files['cellular_component'].write("GO id\tGO name\tAbundance\n")

for line in humann2_output.readlines()[1:]:
# skip header
next(humann2_output)
for line in humann2_output:
split_line = line[:-1].split('\t')
go_id = split_line[0]
abundance = split_line[1]

if go_id == "UNGROUPED":
extra_id = ''
if '|' in go_id:
go_id, extra_id = go_id.split('|')
extra_id = '|' + extra_id

if go_id == "UNGROUPED" or go_id == "UNMAPPED":
continue

namespace = go_annotations[go_id]["namespace"]

if not go_annotations.has_key(go_id):
if not go_id in go_annotations:
string = go_id + " has not found annotations"
raise ValueError(string)

output_files[namespace].write(go_id + '\t')
output_files[namespace].write(go_annotations[go_id]["name"] + '\t')
output_files[namespace].write(go_id + extra_id + '\t')
output_files[namespace].write(go_annotations[go_id]["name"] + extra_id + '\t')
output_files[namespace].write(abundance + '\n')

output_files['molecular_function'].close()
Expand Down
94 changes: 47 additions & 47 deletions test-data/expected_biological_process_abundance.txt
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Original file line number Diff line number Diff line change
@@ -1,47 +1,47 @@
GO id GO name Abundance
GO:0000160 phosphorelay signal transduction system 1112.3915515778
GO:0000746 conjugation 46.559859807600006
GO:0000902 cell morphogenesis 1.8470267351
GO:0002376 immune system process 23.700662623200003
GO:0005975 carbohydrate metabolic process 2612.6970692966993
GO:0006091 generation of precursor metabolites and energy 943.0642504650992
GO:0006259 DNA metabolic process 2760.3666308885995
GO:0006351 transcription, DNA-templated 0.0615114205
GO:0006412 translation 3280.1516158372006
GO:0006520 cellular amino acid metabolic process 3953.6382689974002
GO:0006629 lipid metabolic process 1380.8390328801004
GO:0006790 sulfur compound metabolic process 1012.3221601218003
GO:0006807 nitrogen compound metabolic process 3915.4792502578994
GO:0006810 transport 1101.0465624405
GO:0006811 ion transport 1276.2633195375001
GO:0006950 response to stress 954.8641672250999
GO:0007154 cell communication 316.8910362473
GO:0007165 signal transduction 45.3316263193
GO:0008150 biological_process 2784.3062048235997
GO:0009056 catabolic process 1728.292233976299
GO:0009058 biosynthetic process 12048.508539055703
GO:0009117 nucleotide metabolic process 2472.3435074350996
GO:0009306 protein secretion 23.141466690899996
GO:0009404 toxin metabolic process 9.095920561400002
GO:0009405 pathogenesis 58.27509464559998
GO:0015979 photosynthesis 44.73480409939999
GO:0016032 viral process 0.7986287266
GO:0016043 cellular component organization 1246.5641915709
GO:0016049 cell growth 4.1997618312
GO:0016070 RNA metabolic process 1855.2220049666994
GO:0016310 phosphorylation 1372.0241480503992
GO:0019538 protein metabolic process 672.0486860101004
GO:0022900 electron transport chain 103.16706894990003
GO:0030031 cell projection assembly 32.495419504000004
GO:0032196 transposition 300.7048225378001
GO:0042592 homeostatic process 306.4798266318999
GO:0043934 sporulation 174.71346946979997
GO:0044281 small molecule metabolic process 4445.203127840403
GO:0045333 cellular respiration 5.518723520100001
GO:0046034 ATP metabolic process 1002.5305430942991
GO:0048870 cell motility 107.9960707376
GO:0051186 cofactor metabolic process 2456.361318531299
GO:0051301 cell division 864.5391215972995
GO:0055114 oxidation-reduction process 215.51031499180004
GO:0071554 cell wall organization or biogenesis 36.7500063207
GO:0071941 nitrogen cycle metabolic process 56.684053508
GO id GO name Abundance
GO:0000160 phosphorelay signal transduction system 1112.392
GO:0000746 conjugation 46.56
GO:0000902 cell morphogenesis 1.847
GO:0002376 immune system process 23.701
GO:0005975 carbohydrate metabolic process 2612.697
GO:0006091 generation of precursor metabolites and energy 943.064
GO:0006259 DNA metabolic process 2760.367
GO:0006351 transcription, DNA-templated 0.062
GO:0006412 translation 3280.152
GO:0006520 cellular amino acid metabolic process 3953.638
GO:0006629 lipid metabolic process 1380.837
GO:0006790 sulfur compound metabolic process 1012.321
GO:0006807 nitrogen compound metabolic process 3915.478
GO:0006810 transport 1101.046
GO:0006811 ion transport 1276.261
GO:0006950 response to stress 954.866
GO:0007154 cell communication 316.891
GO:0007165 signal transduction 45.33
GO:0008150 biological_process 2784.3
GO:0009056 catabolic process 1728.292
GO:0009058 biosynthetic process 12048.505
GO:0009117 nucleotide metabolic process 2472.344
GO:0009306 protein secretion 23.141
GO:0009404 toxin metabolic process 9.096
GO:0009405 pathogenesis 58.275
GO:0015979 photosynthesis 44.735
GO:0016032 viral process 0.799
GO:0016043 cellular component organization 1246.564
GO:0016049 cell growth 4.2
GO:0016070 RNA metabolic process 1855.223
GO:0016310 phosphorylation 1372.024
GO:0019538 protein metabolic process 672.049
GO:0022900 electron transport chain 103.167
GO:0030031 cell projection assembly 32.495
GO:0032196 transposition 300.705
GO:0042592 homeostatic process 306.48
GO:0043934 sporulation 174.713
GO:0044281 small molecule metabolic process 4445.202
GO:0045333 cellular respiration 5.519
GO:0046034 ATP metabolic process 1002.531
GO:0048870 cell motility 107.996
GO:0051186 cofactor metabolic process 2456.361
GO:0051301 cell division 864.539
GO:0055114 oxidation-reduction process 215.51
GO:0071554 cell wall organization or biogenesis 36.75
GO:0071941 nitrogen cycle metabolic process 56.684
50 changes: 25 additions & 25 deletions test-data/expected_cellular_component_abundance.txt
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Original file line number Diff line number Diff line change
@@ -1,25 +1,25 @@
GO id GO name Abundance
GO:0005575 cellular_component 4211.620011669099
GO:0005618 cell wall 101.24244809220001
GO:0005634 nucleus 86.82707381589996
GO:0005694 chromosome 0.0271872006
GO:0005727 extrachromosomal circular DNA 121.82450720269999
GO:0005737 cytoplasm 9919.697399687224
GO:0005739 mitochondrion 193.03667393669969
GO:0005773 vacuole 2.2073187229999993
GO:0005783 endoplasmic reticulum 13.858678920100003
GO:0005794 Golgi apparatus 11.580712904300004
GO:0005840 ribosome 1635.3364950416994
GO:0005856 cytoskeleton 0.1781304753
GO:0005886 plasma membrane 2956.1483673840053
GO:0009295 nucleoid 56.116239729200025
GO:0009579 thylakoid 16.531472969800003
GO:0016020 membrane 76.73590696070002
GO:0019012 virion 0.2407286574
GO:0019867 outer membrane 502.1513331402007
GO:0031012 extracellular matrix 0.5991089999
GO:0031982 vesicle 81.09742051820007
GO:0042575 DNA polymerase complex 65.46696539999999
GO:0042597 periplasmic space 130.1736765559
GO:0043190 ATP-binding cassette (ABC) transporter complex 271.6521785019997
GO:0070469 respiratory chain 2.0447839356
GO id GO name Abundance
GO:0005575 cellular_component 4211.617
GO:0005618 cell wall 101.242
GO:0005634 nucleus 86.827
GO:0005694 chromosome 0.027
GO:0005727 extrachromosomal circular DNA 121.825
GO:0005737 cytoplasm 9919.697
GO:0005739 mitochondrion 193.037
GO:0005773 vacuole 2.207
GO:0005783 endoplasmic reticulum 13.859
GO:0005794 Golgi apparatus 11.581
GO:0005840 ribosome 1635.336
GO:0005856 cytoskeleton 0.178
GO:0005886 plasma membrane 2956.148
GO:0009295 nucleoid 56.116
GO:0009579 thylakoid 16.531
GO:0016020 membrane 76.737
GO:0019012 virion 0.241
GO:0019867 outer membrane 502.152
GO:0031012 extracellular matrix 0.599
GO:0031982 vesicle 81.097
GO:0042575 DNA polymerase complex 65.467
GO:0042597 periplasmic space 130.174
GO:0043190 ATP-binding cassette (ABC) transporter complex 271.652
GO:0070469 respiratory chain 2.045
80 changes: 40 additions & 40 deletions test-data/expected_molecular_function_abundances.txt
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Original file line number Diff line number Diff line change
@@ -1,40 +1,40 @@
GO id GO name Abundance
GO:0000156 phosphorelay response regulator activity 4.4347360838
GO:0000166 nucleotide binding 11436.730254302318
GO:0000988 transcription factor activity, protein binding 673.7839975407998
GO:0003674 molecular_function 4087.6458012782
GO:0003676 nucleic acid binding 3028.700666733601
GO:0003924 GTPase activity 490.16358835940014
GO:0004386 helicase activity 273.26291990489995
GO:0004518 nuclease activity 708.2423017374001
GO:0004672 protein kinase activity 626.4942495674997
GO:0004812 aminoacyl-tRNA ligase activity 234.25362423819996
GO:0004872 receptor activity 626.4846539767997
GO:0005102 receptor binding 1.5301407557
GO:0005215 transporter activity 1762.0709654024004
GO:0008092 cytoskeletal protein binding 7.383357547800001
GO:0008134 transcription factor binding 84.63172726779997
GO:0008233 peptidase activity 1182.3108289962993
GO:0016298 lipase activity 3.6081972003000002
GO:0016301 kinase activity 937.2682550285
GO:0016407 acetyltransferase activity 65.750125095
GO:0016491 oxidoreductase activity 2051.3275224607996
GO:0016740 transferase activity 2598.2115822036
GO:0016746 transferase activity, transferring acyl groups 212.45457835869996
GO:0016757 transferase activity, transferring glycosyl groups 319.0056774039
GO:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups 161.48389564689995
GO:0016787 hydrolase activity 280.95384492459993
GO:0016788 hydrolase activity, acting on ester bonds 549.7984070913
GO:0016791 phosphatase activity 148.29697741039996
GO:0016798 hydrolase activity, acting on glycosyl bonds 650.9218081131
GO:0016810 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds 428.24025912369996
GO:0016829 lyase activity 575.0019956493999
GO:0016853 isomerase activity 1916.3316482209
GO:0016874 ligase activity 675.5332395482
GO:0016887 ATPase activity 965.0511058454001
GO:0030234 enzyme regulator activity 31.695909846600003
GO:0034061 DNA polymerase activity 290.6773463926
GO:0034062 RNA polymerase activity 233.7752678209
GO:0046872 metal ion binding 4116.705081461401
GO:0048037 cofactor binding 2930.3128404498993
GO:0051082 unfolded protein binding 203.18389855299998
GO id GO name Abundance
GO:0000156 phosphorelay response regulator activity 4.435
GO:0000166 nucleotide binding 11436.73
GO:0000988 transcription factor activity, protein binding 673.784
GO:0003674 molecular_function 4087.644
GO:0003676 nucleic acid binding 3028.702
GO:0003924 GTPase activity 490.164
GO:0004386 helicase activity 273.263
GO:0004518 nuclease activity 708.243
GO:0004672 protein kinase activity 626.495
GO:0004812 aminoacyl-tRNA ligase activity 234.254
GO:0004872 receptor activity 626.485
GO:0005102 receptor binding 1.53
GO:0005215 transporter activity 1762.068
GO:0008092 cytoskeletal protein binding 7.383
GO:0008134 transcription factor binding 84.632
GO:0008233 peptidase activity 1182.31
GO:0016298 lipase activity 3.608
GO:0016301 kinase activity 937.268
GO:0016407 acetyltransferase activity 65.75
GO:0016491 oxidoreductase activity 2051.329
GO:0016740 transferase activity 2598.211
GO:0016746 transferase activity, transferring acyl groups 212.455
GO:0016757 transferase activity, transferring glycosyl groups 319.006
GO:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups 161.484
GO:0016787 hydrolase activity 280.954
GO:0016788 hydrolase activity, acting on ester bonds 549.799
GO:0016791 phosphatase activity 148.298
GO:0016798 hydrolase activity, acting on glycosyl bonds 650.921
GO:0016810 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds 428.241
GO:0016829 lyase activity 575.003
GO:0016853 isomerase activity 1916.331
GO:0016874 ligase activity 675.532
GO:0016887 ATPase activity 965.05
GO:0030234 enzyme regulator activity 31.696
GO:0034061 DNA polymerase activity 290.677
GO:0034062 RNA polymerase activity 233.775
GO:0046872 metal ion binding 4116.705
GO:0048037 cofactor binding 2930.313
GO:0051082 unfolded protein binding 203.184

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