| Previous changeset 3:4a851c02f558 (2022-03-29) Next changeset 5:d6dcd3173bdf (2024-05-11) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" |
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modified:
metanovo.xml |
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added:
test-data/sample_data_1.mgf test-data/sample_data_2.mgf test-data/sample_fasta_collection.fasta test-data/sample_fasta_single.fasta test-data/sample_output_collection.fasta test-data/sample_output_single.fasta |
| b |
| diff -r 4a851c02f558 -r 7a5ff5359b13 metanovo.xml --- a/metanovo.xml Tue Mar 29 20:53:42 2022 +0000 +++ b/metanovo.xml Fri Apr 22 13:31:08 2022 +0000 |
| [ |
| @@ -7,7 +7,7 @@ </requirements> <macros> <token name="@TOOL_VERSION@">1.9.4</token> - <token name="@VERSION_SUFFIX@">3</token> + <token name="@VERSION_SUFFIX@">4</token> <token name="@SUBSTITUTION_RX@">[^\w\-\.]</token> <import>macros_modifications.xml</import> </macros> @@ -31,22 +31,27 @@ ln -s '$input_type.input_mgf' '$mgf_dir/$mgf_name' && #end if - cat $metanovo_config > config.sh && + ## the number of threads should be number of available threads-1 according to the docs + threads=\${GALAXY_SLOTS:-3} && + if [ \$threads -gt 1 ]; then + (( threads-- )); + fi && + echo "THREAD_LIMIT=\$threads" >> config.sh && + metanovo.sh config.sh ]]> </command> <configfiles> - <configfile name="metanovo_config"><![CDATA[#slurp + <configfile filename="config.sh"><![CDATA[#slurp #import re MGF_FOLDER=mgf_files #set fasta_name = re.sub('@SUBSTITUTION_RX@', '_', str($input_fasta.element_identifier)) FASTA_FILE=fasta_file/'$fasta_name' OUTPUT_FOLDER=. CHUNKSIZE=$processing_control.CHUNKSIZE -THREAD_LIMIT=$processing_control.THREAD_LIMIT -JVM_Xmx='$processing_control.JVM_Xmx' -JVM_Xms='$processing_control.JVM_Xms' +JVM_Xmx='10000M' +JVM_Xms='1024M' mn_specificity='$metanovo_parameters.mn_specificity' mn_enzymes='$metanovo_parameters.mn_enzymes' mn_max_missed_cleavages=$metanovo_parameters.mn_max_missed_cleavages @@ -145,9 +150,6 @@ <section name="processing_control" expanded="False" title="Processing Control"> <param name="CHUNKSIZE" label="Size to split fasta for parallel processing" value="100000" type="integer" optional="true"/> - <param name="THREAD_LIMIT" label="How many threads to use per node" value="2" type="integer" optional="true"/> - <param name="JVM_Xmx" label="Maximum memory allocated to each Java thread" value="10000M" type="text" optional="true"/> - <param name="JVM_Xms" label="Minimum memory allocated to each Java thread" value="1024M" type="text" optional="true"/> </section> <section name="metanovo_parameters" expanded="False" title="MetaNovo Parameters"> <param name="mn_specificity" argument="-mn_specificity" label="Enzyme Specificity" type="select"> @@ -302,9 +304,39 @@ </section> </inputs> <outputs> - <data name="output_fasta" format="fasta" from_work_dir="metanovo/metanovo.fasta" label="MetaNovo Output FASTA"/> - <data name="output_csv" format="csv" from_work_dir="metanovo/metanovo.csv" label="MetaNovo Output CSV"/> + <data name="output_fasta" format="fasta" from_work_dir="metanovo/metanovo.fasta" label="${tool.name} on ${on_string}: FASTA"/> + <data name="output_csv" format="csv" from_work_dir="metanovo/metanovo.csv" label="${tool.name} on ${on_string}: CSV"/> </outputs> + <tests> + <test expect_num_outputs="2"> + <param name="input_mgf" value="sample_data_1.mgf" ftype="mgf"/> + <param name="input_fasta" value="sample_fasta_single.fasta" ftype="fasta"/> + <output name="output_csv" ftype="csv"> + <assert_contents> + <!-- Check header. --> + <has_text text=",index,Accession,Record,ID,PeptideCount,Peptides,ScanCount,Scans,Organism,Length,File,Sample sample_data_1 (msms),SAF sample_data_1,NSAF sample_data_1,Summed_NSAF,Protein_Prob,Organism_Prob,MSMS_Percent,Combined_Prob"/> + </assert_contents> + </output> + <output name="output_fasta" ftype="fasta" file="sample_output_single.fasta"/> + </test> + <test expect_num_outputs="2"> + <param name="type" value="collection"/> + <param name="input_mgf_collection"> + <collection type="list"> + <element name="sample_data_1.mgf" value="sample_data_1.mgf" /> + <element name="sample_data_2.mgf" value="sample_data_2.mgf" /> + </collection> + </param> + <param name="input_fasta" value="sample_fasta_collection.fasta" ftype="fasta"/> + <output name="output_csv" ftype="csv"> + <assert_contents> + <!-- Check header. --> + <has_text text=",index,Accession,File,ID,Length,Organism,PeptideCount,Peptides,Record,SAF sample_data_1,SAF sample_data_2,Sample sample_data_1 (msms),Sample sample_data_2 (msms),ScanCount,Scans,NSAF sample_data_1,NSAF sample_data_2,Summed_NSAF,Protein_Prob,Organism_Prob,MSMS_Percent,Combined_Prob"/> + </assert_contents> + </output> + <output name="output_fasta" ftype="fasta" file="sample_output_collection.fasta"/> + </test> + </tests> <help><![CDATA[ **MetaNovo** |
| b |
| diff -r 4a851c02f558 -r 7a5ff5359b13 test-data/sample_data_1.mgf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample_data_1.mgf Fri Apr 22 13:31:08 2022 +0000 |
| [ |
| b'@@ -0,0 +1,9786 @@\n+# \n+# MS.PreferredSpectrumFormat = 0\n+# MS.UncentroidingHalfWidth = 0.2\n+# MS.UncentroidingPointsPerDa = 20\n+# MS.AlwaysUncentroid = 1\n+# MS.RegriddingPointsPerDa = 40\n+# MS.AggregationMethod = 1\n+# MS.MinPeakCount = 1\n+# MS.MinPeakCharge = 1\n+# MS.MaxPeakCharge = 4\n+# MSMS.PreferredSpectrumFormat = 0\n+# MSMS.UncentroidingHalfWidth = 0.2\n+# MSMS.UncentroidingPointsPerDa = 20\n+# MSMS.AlwaysUncentroid = 1\n+# MSMS.RegriddingPointsPerDa = 40\n+# MSMS.AggregationMethod = 2\n+# MSMS.MinPeakCount = 10\n+# MSMS.MinPeakCharge = 1\n+# MSMS.MaxPeakCharge = 2\n+# MSMS.UsePrecursorAsMaxCharge = 0\n+# MSMS.PrecursorChargeSources = 1; 0\n+# MSMS.PrecursorDefaultCharges = 2; 3; 4; 5\n+# MSMS.RedeterminePrecursorMZ = 1\n+# MSMS.PrecursorMZTolerance = 3\n+# MSMS.IgnoreSingleChargedPrecursor = 0\n+# TimeDomain.MinPrecursorMass = 700\n+# TimeDomain.MaxPrecursorMass = 16000\n+# TimeDomain.PrecursorGroupingTolerance = 0.3\n+# TimeDomain.MaxIntermediateTime = 30\n+# TimeDomain.MaxIntermediateScans = 1\n+# TimeDomain.UseIntermediateScanCount = 1\n+# TimeDomain.MinScansInGroup = 1\n+# TimeDomain.CollapseMSn = 0\n+# PeakSelection.FilteringThreshold = 0.7\n+# PeakSelection.MinFilteringPeakMZ = 50\n+# PeakSelection.MaxFilteringPeakMZ = 100000\n+# PeakSelection.FilteringMinSNRatio = 2\n+# PeakSelection.MinPeakWidth = 0.01\n+# PeakSelection.ExpectedPeakWidth = 0.1\n+# PeakSelection.MaxPeakWidth = 1\n+# PeakSelection.MaxIterations = 500\n+# PeakSelection.RejectWidthOutliers = 0\n+# PeakSelection.BaselineCorrection = 0\n+# PeakSelection.BaselineSubtractMethod = 0\n+# PeakSelection.PeakFitMethod = 0\n+# PeakSelection.IsotopeEnvelopeMode = 0\n+# PeakSelection.IsotopePeakIntensities = \n+# PeakSelection.SinglePeakCharge = 1\n+# PeakSelection.SinglePeakWindow = 0\n+# PeakSelection.MinSglPeakWindowMZ = 112.5\n+# PeakSelection.MaxSglPeakWindowMZ = 121.5\n+# \n+BEGIN IONS\n+TITLE=1: Scan 73 (rt=10.7878, f=3, i=1) [F:\\Distiller Data\\Lab212\\Nitrosylation\\YiJu\\100512_SNOCRC\\YJC_100327SNOCRC_B11b372_N01.raw]\n+PEPMASS=505.82405 2454\n+CHARGE=4+\n+SCANS=73\n+RTINSECONDS=647.26702\n+107.96416\t0.008214501\n+147.0613\t0.021948356\n+148.05611\t0.0099355805\n+149.0509\t0.078029332\n+150.04815\t0.038098614\n+156.15725\t0.023002675\n+158.96603\t0.038779182\n+201.21086\t0.040921995\n+203.06206\t0.012839667\n+207.04385\t0.01208611\n+213.203\t0.020010168\n+221.09004\t0.067225969\n+223.08404\t0.02563078\n+241.03739\t0.01437236\n+243.17794\t0.0066413147\n+269.12892\t0.0080031149\n+274.99536\t0.0080549276\n+275.05772\t0.015602645\n+281.05834\t0.37167331\n+282.06013\t0.14600495\n+283.06111\t0.26332671\n+296.8123\t0.016309462\n+310.52827\t0.0077898351\n+317.88734\t0.017119523\n+318.07386\t0.0084859234\n+328.98408\t0.02556185\n+334.9723\t0.0080692825\n+335.5797\t0.0091289706\n+341.0323\t0.08060134\n+346.83724\t0.018052687\n+347.13017\t0.0095990629\n+355.09759\t0.0091404261\n+361.07839\t0.0093124786\n+368.35337\t0.0094136963\n+385.92955\t0.019797847\n+388.30421\t0.0098405343\n+390.90888\t0.0094415404\n+405.23301\t0.0090058497\n+405.53955\t0.0099998252\n+417.03679\t0.16974584\n+424.90928\t0.0097253926\n+439.99781\t0.058045493\n+451.28088\t0.15246399\n+462.53769\t0.17170869\n+462.77944\t0.18360865\n+472.02709\t0.23594209\n+483.29601\t0.96843183\n+483.54294\t0.51592469\n+494.5529\t1.6718735\n+494.80832\t1.1784711\n+505.82176\t1.0849691\n+506.07339\t0.96990712\n+532.03413\t0.010685098\n+534.54729\t0.010973445\n+546.80548\t0.012531089\n+553.60523\t0.011912646\n+561.95864\t0.011705105\n+563.70539\t0.012128502\n+577.26142\t0.016695763\n+590.03015\t0.011721857\n+595.11781\t0.011844949\n+596.97997\t0.012197493\n+603.36429\t0.028159227\n+603.48945\t0.011393642\n+609.3725\t0.011772702\n+610.28118\t0.013662907\n+644.37989\t0.03579512\n+647.46127\t0.012550914\n+651.32724\t0.011750462\n+651.73363\t0.012285533\n+659.07935\t0.041566067\n+660.08337\t0.021793752\n+666.40396\t0.013065374\n+668.01591\t0.012776058\n+674.42448\t0.012278874\n+684.10741\t0.012767173\n+685.4557\t0.013338149\n+696.45698\t0.014555854\n+700.46455\t0.01317609\n+700.88039\t0.01257991\n+711.95658\t0.013326672\n+718.4584\t0.012870441\n+722.27926\t0.013671942\n+735.50666\t0.014013998\n+743.15648\t0.013681685\n+748.43158\t0.0'..b'6\t0.15683295\n+265.12427\t0.11260195\n+268.12263\t0.41470045\n+270.13228\t12.404721\n+272.1363\t0.84899808\n+276.17786\t0.59318206\n+282.13761\t0.25269784\n+286.12838\t4.5838556\n+291.06995\t0.21893158\n+293.15966\t0.28443521\n+298.16186\t0.46487183\n+310.13122\t0.6267722\n+314.16724\t0.56947693\n+316.15181\t0.17391858\n+319.22318\t0.40093494\n+331.19688\t0.41370052\n+332.17024\t3.5536302\n+334.1651\t0.32090586\n+341.22148\t0.6342989\n+343.22409\t0.34637417\n+348.16791\t0.81115052\n+367.21364\t0.31874435\n+375.21259\t7.551698\n+377.20893\t0.53920009\n+387.21398\t1.2521656\n+389.21498\t0.23828831\n+391.20657\t1.0291267\n+395.1801\t0.29772958\n+397.19243\t0.56652209\n+413.18938\t1.0183773\n+415.20932\t9.2750545\n+417.20999\t0.75010756\n+431.20167\t0.59719874\n+444.22575\t0.65390856\n+446.24621\t0.51946912\n+449.19543\t3.7518792\n+451.20137\t0.59666306\n+458.24143\t0.74599662\n+463.22216\t0.76510069\n+471.25357\t1.7631419\n+473.22089\t3.0752377\n+479.23987\t1.5029845\n+480.25802\t4.6425296\n+484.19355\t24.880444\n+486.22818\t4.6941977\n+490.2483\t3.3662453\n+491.24119\t1.5210044\n+500.26579\t0.52193196\n+511.33489\t12.230042\n+515.28614\t0.94836972\n+520.28202\t0.39604466\n+524.27066\t0.36034678\n+527.31386\t0.40903992\n+541.32132\t0.62696902\n+545.32426\t14.245656\n+547.29256\t1.2965384\n+585.31601\t5.8330953\n+628.3569\t1.2885104\n+630.29972\t1.1152766\n+680.34836\t0.43519355\n+690.3978\t4.0316256\n+701.33787\t0.71288493\n+789.40771\t0.68993126\n+END IONS\n+\n+BEGIN IONS\n+TITLE=78: Sum of 2 scans in range 659 (rt=18.5882, f=3, i=28) to 660 (rt=18.6087, f=4, i=27) [F:\\Distiller Data\\Lab212\\Nitrosylation\\YiJu\\100512_SNOCRC\\YJC_100327SNOCRC_B11b372_N01.raw]\n+PEPMASS=741.35107 30940\n+CHARGE=2+\n+SCANS=659-660\n+RTINSECONDS=1115.29-1116.521\n+114.09157\t0.054207427\n+118.03301\t0.090877549\n+126.05851\t0.06625458\n+127.05967\t0.10833462\n+129.102\t0.30632302\n+130.09871\t0.078504025\n+132.05219\t0.21716932\n+136.07596\t0.057137188\n+141.10154\t0.051107188\n+143.1193\t0.17211147\n+147.11718\t0.09216694\n+175.11444\t0.1170387\n+186.09456\t0.10005738\n+188.05531\t0.073870661\n+193.1013\t0.10532433\n+197.10305\t0.052386544\n+201.08968\t0.0708185\n+211.10552\t0.063432726\n+214.12643\t0.32450339\n+223.12477\t0.10806997\n+227.10155\t0.20133165\n+231.1405\t0.08630367\n+234.13635\t0.11001207\n+236.14656\t0.39341033\n+237.10185\t0.05779833\n+243.07903\t0.063179307\n+244.14594\t0.13477826\n+251.0835\t0.07868283\n+258.14197\t0.083279455\n+270.13371\t5.8784204\n+272.13613\t0.55246894\n+276.19533\t0.77336039\n+279.10898\t0.13532779\n+281.05777\t0.14188805\n+284.15496\t0.079048938\n+286.1305\t0.64450647\n+291.08292\t0.11085152\n+298.17566\t0.24568912\n+304.14618\t0.061516681\n+310.12798\t0.31446874\n+313.18587\t0.22011231\n+314.15917\t0.22941904\n+321.13777\t0.10883094\n+332.17203\t2.2925861\n+341.21793\t0.61068205\n+348.16859\t0.19019729\n+350.13872\t0.18768152\n+372.17482\t0.23347093\n+375.21316\t4.8176829\n+377.19565\t0.30423732\n+381.22082\t0.11400591\n+384.18819\t2.562771\n+386.18513\t0.25764687\n+387.21036\t0.52628716\n+391.20937\t1.1888635\n+397.18601\t0.23525369\n+415.20946\t6.8649415\n+417.21248\t0.53207955\n+427.22895\t0.70834979\n+431.20003\t0.78504883\n+439.20574\t0.14590504\n+449.19857\t3.7724257\n+451.19406\t0.35823472\n+457.2176\t0.40767183\n+463.21624\t2.2914534\n+465.2135\t0.27853386\n+473.21597\t1.1644996\n+480.74068\t0.11843239\n+485.19517\t0.67271967\n+489.20662\t0.36229668\n+511.33208\t3.2271808\n+523.2219\t0.43047419\n+532.24737\t0.26875952\n+545.32356\t3.959459\n+563.32734\t0.26486634\n+585.31511\t1.276507\n+591.28834\t0.1981301\n+619.32474\t10.077923\n+621.33166\t1.1569968\n+640.82668\t0.55706745\n+645.32866\t0.44715239\n+650.33799\t0.6306829\n+653.32438\t1.1852887\n+665.28068\t0.52246455\n+684.33969\t1.2258442\n+693.30977\t2.1345198\n+703.34176\t0.51139416\n+724.3436\t0.9368416\n+732.34288\t1.7416262\n+741.34592\t5.9146828\n+747.3739\t10.642163\n+789.40682\t1.7984723\n+798.38948\t0.818403\n+829.41691\t0.81223459\n+841.3963\t0.81040018\n+845.39538\t0.82999305\n+863.39498\t2.9398456\n+925.53808\t1.6879765\n+937.40207\t0.8035101\n+959.50119\t1.2135053\n+999.51365\t0.90220303\n+1015.5042\t0.84098004\n+1023.602\t1.268502\n+1033.5225\t3.095356\n+1067.5161\t2.0278673\n+1081.5826\t0.73020602\n+1098.5347\t0.731169\n+1107.5053\t1.1552626\n+1181.5956\t0.66496437\n+END IONS\n' |
| b |
| diff -r 4a851c02f558 -r 7a5ff5359b13 test-data/sample_data_2.mgf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample_data_2.mgf Fri Apr 22 13:31:08 2022 +0000 |
| [ |
| b'@@ -0,0 +1,9936 @@\n+# \n+# MS.PreferredSpectrumFormat = 0\n+# MS.UncentroidingHalfWidth = 0.2\n+# MS.UncentroidingPointsPerDa = 20\n+# MS.AlwaysUncentroid = 1\n+# MS.RegriddingPointsPerDa = 40\n+# MS.AggregationMethod = 1\n+# MS.MinPeakCount = 1\n+# MS.MinPeakCharge = 1\n+# MS.MaxPeakCharge = 4\n+# MSMS.PreferredSpectrumFormat = 0\n+# MSMS.UncentroidingHalfWidth = 0.2\n+# MSMS.UncentroidingPointsPerDa = 20\n+# MSMS.AlwaysUncentroid = 1\n+# MSMS.RegriddingPointsPerDa = 40\n+# MSMS.AggregationMethod = 2\n+# MSMS.MinPeakCount = 10\n+# MSMS.MinPeakCharge = 1\n+# MSMS.MaxPeakCharge = 2\n+# MSMS.UsePrecursorAsMaxCharge = 0\n+# MSMS.PrecursorChargeSources = 1; 0\n+# MSMS.PrecursorDefaultCharges = 2; 3; 4; 5\n+# MSMS.RedeterminePrecursorMZ = 1\n+# MSMS.PrecursorMZTolerance = 3\n+# MSMS.IgnoreSingleChargedPrecursor = 0\n+# TimeDomain.MinPrecursorMass = 700\n+# TimeDomain.MaxPrecursorMass = 16000\n+# TimeDomain.PrecursorGroupingTolerance = 0.3\n+# TimeDomain.MaxIntermediateTime = 30\n+# TimeDomain.MaxIntermediateScans = 1\n+# TimeDomain.UseIntermediateScanCount = 1\n+# TimeDomain.MinScansInGroup = 1\n+# TimeDomain.CollapseMSn = 0\n+# PeakSelection.FilteringThreshold = 0.7\n+# PeakSelection.MinFilteringPeakMZ = 50\n+# PeakSelection.MaxFilteringPeakMZ = 100000\n+# PeakSelection.FilteringMinSNRatio = 2\n+# PeakSelection.MinPeakWidth = 0.01\n+# PeakSelection.ExpectedPeakWidth = 0.1\n+# PeakSelection.MaxPeakWidth = 1\n+# PeakSelection.MaxIterations = 500\n+# PeakSelection.RejectWidthOutliers = 0\n+# PeakSelection.BaselineCorrection = 0\n+# PeakSelection.BaselineSubtractMethod = 0\n+# PeakSelection.PeakFitMethod = 0\n+# PeakSelection.IsotopeEnvelopeMode = 0\n+# PeakSelection.IsotopePeakIntensities = \n+# PeakSelection.SinglePeakCharge = 1\n+# PeakSelection.SinglePeakWindow = 0\n+# PeakSelection.MinSglPeakWindowMZ = 112.5\n+# PeakSelection.MaxSglPeakWindowMZ = 121.5\n+# \n+BEGIN IONS\n+TITLE=1: Scan 68 (rt=10.7767, f=2, i=2) [F:\\Distiller Data\\Lab212\\Nitrosylation\\YiJu\\100512_SNOCRC\\YJC_100327SNOCRC_B11b372_N02.raw]\n+PEPMASS=505.57237 2535\n+CHARGE=4+\n+SCANS=68\n+RTINSECONDS=646.6\n+126.68747\t0.0095610886\n+147.07\t0.031638011\n+149.05163\t0.056459291\n+150.05645\t0.019850346\n+156.14706\t0.010908528\n+187.21247\t0.011306827\n+221.09147\t0.070367436\n+223.09152\t0.027119914\n+227.20898\t0.018819948\n+241.01204\t0.016283331\n+258.26071\t0.022885642\n+281.05783\t0.50117416\n+282.06195\t0.28568775\n+283.05827\t0.18865751\n+307.20522\t0.0078820481\n+307.97957\t0.0087505494\n+312.15435\t0.0087667276\n+315.33012\t0.017828172\n+318.07859\t0.0087557308\n+320.90563\t0.0092218301\n+327.60525\t0.0090809066\n+328.97869\t0.033006492\n+329.75461\t0.008363671\n+330.96287\t0.015192568\n+341.0305\t0.027068039\n+343.04191\t0.041163204\n+345.15502\t0.0094837177\n+347.09883\t0.016383096\n+348.95513\t0.0090857161\n+371.17976\t0.0098787316\n+376.96514\t0.017792904\n+383.13001\t0.010277052\n+385.9094\t0.0087485971\n+403.86525\t0.018276962\n+410.3541\t0.010160575\n+415.05061\t0.097539253\n+416.04707\t0.22494341\n+417.03241\t0.073477277\n+418.02843\t0.096222752\n+421.22971\t0.009969807\n+437.0032\t0.010349754\n+443.58075\t0.011309803\n+446.99815\t0.03297217\n+448.25739\t0.010733375\n+451.26385\t0.14218942\n+462.54481\t0.13952749\n+462.7823\t0.090057543\n+483.2923\t1.0037322\n+490.30164\t0.16984175\n+494.55577\t1.5429077\n+505.81801\t1.0423915\n+523.37744\t0.011147173\n+526.83272\t0.010653056\n+528.4805\t0.01102442\n+532.80656\t0.012228581\n+537.49702\t0.011434789\n+540.27914\t0.011334841\n+542.6544\t0.011582118\n+551.23078\t0.0117825\n+564.74321\t0.016460683\n+573.38\t0.023726543\n+579.65574\t0.012794591\n+582.3067\t0.01330619\n+593.31438\t0.01167895\n+648.70847\t0.012333998\n+649.38276\t0.012429187\n+654.07104\t0.012383497\n+666.4844\t0.019424907\n+674.44501\t0.012798413\n+676.25682\t0.013503864\n+677.98046\t0.013470969\n+680.83436\t0.012355375\n+686.9323\t0.014504626\n+689.4341\t0.013786818\n+696.78203\t0.014504726\n+700.68255\t0.013873073\n+712.85442\t0.013560643\n+715.16925\t0.013253655\n+720.37975\t0.01229952\n+729.87161\t0.013317105\n+731.80452\t0.013404254\n+750.35492\t0.014285055\n+756.57992\t0.012560136\n+760.40716\t0.014469825\n+768.77259\t0.013593169\n+775.65624\t0.014633176\n+7'..b'iller Data\\Lab212\\Nitrosylation\\YiJu\\100512_SNOCRC\\YJC_100327SNOCRC_B11b372_N02.raw]\n+PEPMASS=424.20158 53265\n+CHARGE=2+\n+SCANS=665\n+RTINSECONDS=1127.709\n+100.07729\t0.1558093\n+101.07502\t0.43085561\n+105.00269\t0.16568988\n+105.07344\t3.0135903\n+106.08229\t0.18196767\n+107.08054\t0.120152\n+110.0675\t0.17214208\n+111.06277\t0.064457189\n+115.06013\t0.072845439\n+116.02411\t0.055277176\n+118.089\t0.14233321\n+120.08039\t0.0898332\n+122.07786\t0.074103482\n+123.02817\t0.052200488\n+125.07004\t0.058640309\n+127.09393\t0.26915553\n+129.10134\t0.30386529\n+130.09174\t0.17979165\n+131.04368\t0.10764192\n+132.08943\t0.17730959\n+133.06757\t14.426181\n+134.07715\t0.51013616\n+136.07478\t0.14207987\n+138.09585\t0.25161902\n+144.09518\t0.057439959\n+145.09914\t0.051276401\n+147.11316\t0.2879986\n+148.07944\t0.39135021\n+149.10018\t0.37861594\n+150.09539\t0.46903875\n+151.08671\t0.20761638\n+159.11992\t0.055595105\n+161.12975\t0.1060639\n+166.07265\t0.12145793\n+167.07021\t0.10600507\n+172.10214\t0.10183278\n+173.10224\t0.10761055\n+175.10393\t0.60150161\n+176.1072\t3.5655414\n+179.05655\t0.2229085\n+187.10998\t0.08071888\n+189.12642\t0.70410209\n+191.13374\t0.082378145\n+193.10175\t2.2849663\n+199.09771\t0.12898304\n+201.11831\t0.11397523\n+207.0584\t0.27581536\n+209.07899\t0.23349591\n+212.62907\t0.17730852\n+215.14836\t0.16688201\n+217.10886\t0.066776806\n+219.11845\t0.35981651\n+222.05819\t0.1078676\n+225.07789\t0.15996451\n+226.10188\t0.43737219\n+227.09083\t4.1534225\n+229.08387\t0.20978236\n+229.62979\t0.6786514\n+232.05312\t0.062635734\n+232.16702\t0.52199445\n+236.14455\t0.98470218\n+238.15255\t0.36027701\n+239.09538\t0.24619315\n+244.16724\t0.15063198\n+248.15971\t0.11749744\n+249.09664\t0.24376379\n+250.08523\t0.2549226\n+251.16449\t0.27775837\n+252.14116\t0.14043622\n+258.14957\t0.15162764\n+262.15176\t0.067701097\n+265.1714\t0.35393466\n+267.10106\t0.85057873\n+268.09813\t1.3651844\n+270.13198\t16.143967\n+272.1337\t0.82749016\n+278.15812\t0.10885094\n+281.18746\t0.32602316\n+282.16689\t1.0875352\n+284.15011\t0.38536487\n+285.10787\t0.56917778\n+288.1497\t0.15701994\n+289.14618\t0.11331353\n+291.0711\t0.29394395\n+291.17806\t0.14140012\n+294.21209\t0.79552042\n+295.15488\t0.2527163\n+298.18319\t0.7140051\n+299.20984\t0.10084875\n+300.23599\t0.14193341\n+302.1621\t0.18105509\n+303.16945\t0.099154916\n+310.12759\t4.5119152\n+311.10927\t1.2795048\n+314.16519\t0.28306313\n+315.17603\t0.53938733\n+319.23801\t0.28680702\n+328.1415\t3.5706863\n+332.17087\t2.8778462\n+334.16815\t0.22944265\n+337.25291\t0.35196154\n+341.02566\t1.7565269\n+341.22805\t2.0874107\n+343.01595\t0.45803525\n+348.19654\t2.5869161\n+351.20973\t0.78216518\n+353.22749\t0.53996335\n+356.70955\t2.7374174\n+360.21523\t0.24532157\n+364.22321\t0.32026782\n+369.2008\t0.35575485\n+369.69904\t0.66854332\n+372.18827\t0.48144623\n+375.21115\t1.5650839\n+378.21297\t9.4922528\n+381.25618\t0.43890587\n+385.19903\t0.66049303\n+387.21512\t7.5350374\n+389.21191\t0.91110379\n+395.20069\t0.44988949\n+399.21201\t0.17617179\n+402.21096\t0.44984986\n+402.70716\t1.8898907\n+415.20282\t3.6556016\n+416.20758\t0.83412697\n+424.21087\t6.0607854\n+426.23424\t2.9374019\n+427.22685\t1.6236636\n+432.23506\t10.882515\n+433.21885\t1.2391782\n+434.23696\t0.67726435\n+435.21212\t0.88764343\n+443.2148\t0.61466735\n+445.25992\t0.43012922\n+458.25155\t2.7109067\n+460.24394\t0.28258041\n+469.30113\t0.59671559\n+476.25568\t0.25299979\n+486.30728\t2.462957\n+498.25176\t0.54276477\n+502.28765\t0.38201709\n+503.27474\t0.14207263\n+516.26478\t1.0172416\n+520.29006\t20.537414\n+522.28508\t1.4993324\n+529.34214\t1.3091044\n+534.30063\t0.59238635\n+542.25766\t0.14022789\n+546.31991\t0.31720364\n+560.29395\t1.2371416\n+563.32962\t72.287328\n+565.34003\t5.3570294\n+578.30122\t2.4216832\n+585.29868\t0.58826906\n+586.27859\t0.28120219\n+589.31675\t0.88514663\n+593.31637\t0.19804084\n+603.33382\t1.0855487\n+605.34004\t0.23618769\n+621.34542\t1.2870024\n+629.33225\t0.22885198\n+653.32259\t0.19026353\n+659.40324\t0.36668645\n+671.39035\t0.8044115\n+674.37013\t0.097290723\n+683.3839\t0.18641374\n+726.39922\t2.1874026\n+743.43878\t0.19567367\n+787.38687\t0.2694962\n+830.40357\t0.45455343\n+847.4302\t0.23114773\n+1067.5129\t0.22993561\n+1305.608\t9.0237272\n+1327.6133\t0.85352772\n+1631.7532\t9.0132572\n+1643.2581\t1.2007442\n+1740.7503\t2.4738138\n+END IONS\n' |
| b |
| diff -r 4a851c02f558 -r 7a5ff5359b13 test-data/sample_fasta_collection.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample_fasta_collection.fasta Fri Apr 22 13:31:08 2022 +0000 |
| b |
| b'@@ -0,0 +1,3362 @@\n+>sp|P68871|HBB_HUMAN Hemoglobin subunit beta OS=Homo sapiens OX=9606 GN=HBB PE=1 SV=2\n+MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPK\n+VKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFG\n+KEFTPPVQAAYQKVVAGVANALAHKYH\n+>sp|Q9TT34|HBB_PONPY Hemoglobin subunit beta (Fragment) OS=Pongo pygmaeus OX=9600 GN=HBB PE=2 SV=1\n+VCVLAHHFGKEFTPQVQAAYQKVVAGVANALAHKYH\n+>sp|P56385|ATP5I_HUMAN ATP synthase subunit e, mitochondrial OS=Homo sapiens OX=9606 GN=ATP5ME PE=1 SV=2\n+MVPPVQVSPLIKLGRYSALFLGVAYGATRYNYLKPRAEEERRIAAEEKKKQDELKRIARE\n+LAEDDSILK\n+>sp|P12235|ADT1_HUMAN ADP/ATP translocase 1 OS=Homo sapiens OX=9606 GN=SLC25A4 PE=1 SV=4\n+MGDHAWSFLKDFLAGGVAAAVSKTAVAPIERVKLLLQVQHASKQISAEKQYKGIIDCVVR\n+IPKEQGFLSFWRGNLANVIRYFPTQALNFAFKDKYKQLFLGGVDRHKQFWRYFAGNLASG\n+GAAGATSLCFVYPLDFARTRLAADVGKGAAQREFHGLGDCIIKIFKSDGLRGLYQGFNVS\n+VQGIIIYRAAYFGVYDTAKGMLPDPKNVHIFVSWMIAQSVTAVAGLVSYPFDTVRRRMMM\n+QSGRKGADIMYTGTVDCWRKIAKDEGAKAFFKGAWSNVLRGMGGAFVLVLYDEIKKYV\n+>sp|Q9P0U1|TOM7_HUMAN Mitochondrial import receptor subunit TOM7 homolog OS=Homo sapiens OX=9606 GN=TOMM7 PE=1 SV=1\n+MVKLSKEAKQRLQQLFKGSQFAIRWGFIPLVIYLGFKRGADPGMPEPTVLSLLWG\n+>sp|P69905|HBA_HUMAN Hemoglobin subunit alpha OS=Homo sapiens OX=9606 GN=HBA1 PE=1 SV=2\n+MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG\n+KKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTP\n+AVHASLDKFLASVSTVLTSKYR\n+>sp|P05387|RLA2_HUMAN 60S acidic ribosomal protein P2 OS=Homo sapiens OX=9606 GN=RPLP2 PE=1 SV=1\n+MRYVASYLLAALGGNSSPSAKDIKKILDSVGIEADDDRLNKVISELNGKNIEDVIAQGIG\n+KLASVPAGGAVAVSAAPGSAAPAAGSAPAAAEEKKDEKKEESEESDDDMGFGLFD\n+>sp|P02768|ALBU_HUMAN Albumin OS=Homo sapiens OX=9606 GN=ALB PE=1 SV=2\n+MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPF\n+EDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEP\n+ERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLF\n+FAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAV\n+ARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQDSISSKLK\n+ECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYAR\n+RHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQNLIKQNCELFE\n+QLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVV\n+LNQLCVLHEKTPVSDRVTKCCTESLVNRRPCFSALEVDETYVPKEFNAETFTFHADICTL\n+SEKERQIKKQTALVELVKHKPKATKEQLKAVMDDFAAFVEKCCKADDKETCFAEEGKKLV\n+AASQAALGL\n+>sp|Q01995|TAGL_HUMAN Transgelin OS=Homo sapiens OX=9606 GN=TAGLN PE=1 SV=4\n+MANKGPSYGMSREVQSKIEKKYDEELEERLVEWIIVQCGPDVGRPDRGRLGFQVWLKNGV\n+ILSKLVNSLYPDGSKPVKVPENPPSMVFKQMEQVAQFLKAAEDYGVIKTDMFQTVDLFEG\n+KDMAAVQRTLMALGSLAVTKNDGHYRGDPNWFMKKAQEHKREFTESQLQEGKHVIGLQMG\n+SNRGASQAGMTGYGRPRQIIS\n+>sp|P0CG04|IGLC1_HUMAN Immunoglobulin lambda constant 1 OS=Homo sapiens OX=9606 GN=IGLC1 PE=1 SV=1\n+GQPKANPTVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSK\n+QSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS\n+>sp|P56470|LEG4_HUMAN Galectin-4 OS=Homo sapiens OX=9606 GN=LGALS4 PE=1 SV=1\n+MAYVPAPGYQPTYNPTLPYYQPIPGGLNVGMSVYIQGVASEHMKRFFVNFVVGQDPGSDV\n+AFHFNPRFDGWDKVVFNTLQGGKWGSEERKRSMPFKKGAAFELVFIVLAEHYKVVVNGNP\n+FYEYGHRLPLQMVTHLQVDGDLQLQSINFIGGQPLRPQGPPMMPPYPGPGHCHQQLNSLP\n+TMEGPPTFNPPVPYFGRLQGGLTARRTIIIKGYVPPTGKSFAINFKVGSSGDIALHINPR\n+MGNGTVVRNSLLNGSWGSEEKKITHNPFGPGQFFDLSIRCGLDRFKVYANGQHLFDFAHR\n+LSAFQRVDTLEIQGDVTLSYVQI\n+>sp|P69891|HBG1_HUMAN Hemoglobin subunit gamma-1 OS=Homo sapiens OX=9606 GN=HBG1 PE=1 SV=2\n+MGHFTEEDKATITSLWGKVNVEDAGGETLGRLLVVYPWTQRFFDSFGNLSSASAIMGNPK\n+VKAHGKKVLTSLGDAIKHLDDLKGTFAQLSELHCDKLHVDPENFKLLGNVLVTVLAIHFG\n+KEFTPEVQASWQKMVTAVASALSSRYH\n+>sp|O60844|ZG16_HUMAN Zymogen granule membrane protein 16 OS=Homo sapiens OX=9606 GN=ZG16 PE=1 SV=2\n+MLTVALLALLCASASGNAIQARSSSYSGEYGGGGGKRFSHSGNQLDGPITALRVRVNTYY\n+IVGLQVRYGKVWSDYVGGRNGDLEEIFLHPGESVIQVSGKYKWYLKKLLFVTDKGRYLSF\n+GKDSGTSFNAVPLHPNTVLRFISGRSGSLIDAIGLHWDVYPSSCSRC\n+>sp|P01009|A1AT_HUMAN Alpha-1-antitrypsin OS=Homo sapiens OX=9606 GN=SERPINA1 PE=1 SV=3\n+MPSSVSWGILLLAGLCCLVPVSLAEDPQGDAAQKTDTSHHDQDHPTFNKITPNLAEFAFS\n+LYRQLAHQSNSTNIFFSPVSIATAFAMLSLGTKADTHDEILEGLNFNLTEIPEAQIHEGF\n+QELLRTLNQPDSQLQLTTGNGLFLSEGLKLVDKFLEDVKKLYHSEAFTVNFG'..b'TKEVRQVLTRCYDRYIKPFERDSSPSFKSKRSESSTRKIRNTRSSAQQESPI\n+PETSAQSPVQTIQVNGSTSLKRPLIERGEQCEYCGLDKNPETILLCDGCEAAYHTSCLDP\n+PLTSIPKEDWYCDACKFNISDYDPRKGFKWKLSSLKERSAEIFNTLGERNSSSKLTNLTE\n+DDIELFYWSSLAESNSGFAPLELEGLSQAYTSTIQSSLPSKEVFPLEKYSSEPWNLHNLP\n+FENPCLFNYSFSDLSSLTITRLSIGMVFYTHGWTKSSLSTGLLHHHRFGDTVTWYVLPPD\n+ESDAFERYLISSYPQYTMEDLNRSNGLPVIVSPSSLIENGFHPIAIDLRPNEFLVVSPNS\n+YHMGFHQGFSSFESVNFATVNWIKDGLLNSSISVLKSMRIPSSVSYEAVIISMVLSKNPC\n+FSSEWLIKCFEDMIANESASKNEIMKLVPNIQALKLESSVPLEIRCSNCKQPCFLSFMQC\n+HEPKKFICLGDCVKEVSLNATSWMLFYRWDVHELSNLAERFVSLIRGPEEWTNRLRSVLS\n+TSPKPQLKVLKSLLVDAEKAMLTTPETVNLRDFVQNANSWIDSVNECLKVASLKRKKDKK\n+PPLFKAHDHWNNTSNLKDSAVLFKVLQTSRSMAFTCQEIENMKQKAFDLLEFRNRLINSF\n+SGPLDKNTCQRLLTEAELLGFTIPELGIIQKYLIQFEWLDMFYSFETTRTTDSDLERLIT\n+YGVSAGIPEDNDYMIFAKAMKGRAEIWENQVYDTLSKSNISYDKLSLLRDEAMNLCVNKE\n+LFSKVVGILNNAEEIKNKIATLCERSQEKDFALRPSIDEVKEALASAEKLPILSESTVTL\n+QKMYDVVLEWIRRGKRLFGKANAPLEILGQHLDYVEKRNSASLSLNDRPGPPMEPASRET\n+SPDSEGRLTIRKKKGCIFCFCRLPESGVMIECEICHEWYHAKCLKMSKKKLRQDEKFTCP\n+ICDYRVEIPRLSNRPKLEDLQSLYKDVKLLPFQPKETETLRKVVDLASKFRQEMQALAHN\n+PFGLTMAEVPLARFYLRKMEGAEILLVDETNLFRQKLHECVPIAPNPPPIIGESKSTRKP\n+RPTKRQRQIMKQVAEGLLPASAIAPPKSSNEKKSSNNVKAVEAETKSKSEKSPKKNGTNI\n+SDANNKNESHVSLMKNWKLGSPAFVTLVKEKNSSCLCGEEFSPRDSFIDCTICERRFHYD\n+CVGLNNEIADSVSKFTCPICMEQSGGIYPWQLRPRNGMHPDHISGFSKEVETDPKLGSSG\n+YTLNNSKFDKAAVSKTLSAQDVSRLQKVSCGEHLYFGTDVFTPLGDMATSASMFSLDDSS\n+EKTDAFTENFLNV\n+>sp|A4H7G5|JBP2_LEIBR Bifunctional helicase and thymine dioxygenase JBP2 OS=Leishmania braziliensis OX=5660 GN=JBP2 PE=3 SV=1\n+MPSGLMRANTSTELESILDIVQSSGEIAVVFTSPSIGDLETITSETQRRQLRIAGIPRGG\n+YTILPAIPLYDDELLQMCERYTAASEHEKVEIRNSLYMREYPLFAYSMRNQRALFHPADY\n+VSRILQFCFHYVQVPDEDVLSLQDRSPFLHISPVKEICVHLRLIVRGTPAAPDESESPVP\n+EQLHFHAESDAEKLAAERARALSIAASSGGASETEPLSLFTGVAPSALFQKGAVEEVDLD\n+TEETIEDLTGEETVDAVHSFHSEYLTLSGFELVTKASIFYDHEGEGQRVVAVYIPGGVPK\n+ETCRAAAAVLELAVTKKNLRAATNGGLPPDTGIVGYYDYLTNPTQHKCRETEFSRRNWGL\n+FSQSESLLKHLDKLYSQLAPTHHHLQRVAIPSQYQLCGTVFSTITVNRNFRTAVHTDKGD\n+FRSGLGVLSVINGEFEGCHLAIKSLKKAFQLKVGDVLLFDTSLEHGNTEVVHPENHWQRT\n+SIVCYLRTGLMSSVCEMERRKHLNRLILQQLLNTEIRHTTVNINEADSSLPPLFVPTRLA\n+SQLAPVQLAALGFIVERTNKQSGCVVAMTMGLGKTLVALTLCFSHLHLAPQADILILTPK\n+PIISHWVDEKNKWGMYGLHFPHFVASDGLNSLEFEQQLLEYERQKNNEKPKAGHVFVINS\n+EYLAGFLRRFRRFTPFLIIVDEGHRVAAKGNKLTESLDRLRCNLRVVLSGTPLQNDASEL\n+YRLVGWVNKGVSKVLPPKRFQELANSINQFVEGDDGAFYNAVMAQEYIQDWMRGFVFREM\n+ENDLPPLHDYLLVCGSSNVQREYEEKLGLTETAMTALRATEHRPHHLSTHPACYLAFISN\n+CYQSMVSGWTVRAQSNTSRLRTTQLEEIDAMRLEQYAQMIENEQLDAFINVSGKMRVLVD\n+IVLRVQARKEKLIIFSLYVGSQDLIHRTLTALRVCTFTVRGRDSQDRRRRAMHEFSENKD\n+LTVLVLSTKIAAYGLEFTAANHVVLFDSWWNPQADAQAIARAYRRNQRKPVTVYRLISAT\n+ENKFVLRSQTRKIALFKCIFHKRTTRQALPSELEDCSANETDNERRDFWAKLKATHLVGD\n+TRALLNVYRYQESVRESQ\n+>sp|P63978|DPO3A_MYCBO DNA polymerase III subunit alpha OS=Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97) OX=233413 GN=dnaE PE=3 SV=1\n+MSGSSAGSSFVHLHNHTEYSMLDGAAKITPMLAEVERLGMPAVGMTDHGNMFGASEFYNS\n+ATKAGIKPIIGVEAYIAPGSRFDTRRILWGDPSQKADDVSGSGSYTHLTMMAENATGLRN\n+LFKLSSHASFEGQLSKWSRMDAELIAEHAEGIIITTGCPSGEVQTRLRLGQDREALEAAA\n+KWREIVGPDNYFLELMDHGLTIERRVRDGLLEIGRALNIPPLATNDCHYVTRDAAHNHEA\n+LLCVQTGKTLSDPNRFKFDGDGYYLKSAAEMRQIWDDEVPGACDSTLLIAERVQSYADVW\n+TPRDRMPVFPVPDGHDQASWLRHEVDAGLRRRFPAGPPDGYRERAAYEIDVICSKGFPSY\n+FLIVADLISYARSAGIRVGPGRGSAAGSLVAYALGITDIDPIPHGLLFERFLNPERTSMP\n+DIDIDFDDRRRGEMVRYAADKWGHDRVAQVITFGTIKTKAALKDSARIHYGQPGFAIADR\n+ITKALPPAIMAKDIPLSGITDPSHERYKEAAEVRGLIETDPDVRTIYQTARGLEGLIRNA\n+GVHACAVIMSSEPLTEAIPLWKRPQDGAIITGWDYPACEAIGLLKMDFLGLRNLTIIGDA\n+IDNVRANRGIDLDLESVPLDDKATYELLGRGDTLGVFQLDGGPMRDLLRRMQPTGFEDVV\n+AVIALYRPGPMGMNAHNDYADRKNNRQAIKPIHPELEEPLREILAETYGLIVYQEQIMRI\n+AQKVASYSLARADILRKAMGKKKREVLEKEFEGFSDGMQANGFSPAAIKALWDTILPFAD\n+YAFNKSHAAGYGMVSYWTAYLKANYPAEYMAGLLTSVGDDKDKAAVYLADCRKLGITVLP\n+PDVNESGLNFASVGQDIRYGLGAVRNVGANVVGSLLQTRNDKGKFTDFSDYLNKIDISAC\n+NKKVTESLIKAGAFDSLGHARKGLFLVHSDAVDSVLGTKKAEALGQFDLFGSNDDGTGTA\n+DPVFTIKVPDDEWEDKHKLALEREMLGLYVSGHPLNGVAHLLAAQVDTAIPAILDGDVPN\n+DAQVRVGGILASVNRRVNKNGMPWASAQLEDLTGGIEVMFFPHTYSSYGADIVDDAVVLV\n+NAKVAVRDDRIALIANDLTVPDFSNAEVERPLAVSLPTRQCTFDKVSALKQVLARHPGTS\n+QVHLRLISGDRITTLALDQSLRVTPSPALMGDLKELLGPGCLGS\n' |
| b |
| diff -r 4a851c02f558 -r 7a5ff5359b13 test-data/sample_fasta_single.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample_fasta_single.fasta Fri Apr 22 13:31:08 2022 +0000 |
| b |
| b'@@ -0,0 +1,2500 @@\n+>sp|P68871|HBB_HUMAN Hemoglobin subunit beta OS=Homo sapiens OX=9606 GN=HBB PE=1 SV=2\n+MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPK\n+VKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFG\n+KEFTPPVQAAYQKVVAGVANALAHKYH\n+>sp|Q9TT34|HBB_PONPY Hemoglobin subunit beta (Fragment) OS=Pongo pygmaeus OX=9600 GN=HBB PE=2 SV=1\n+VCVLAHHFGKEFTPQVQAAYQKVVAGVANALAHKYH\n+>sp|P56385|ATP5I_HUMAN ATP synthase subunit e, mitochondrial OS=Homo sapiens OX=9606 GN=ATP5ME PE=1 SV=2\n+MVPPVQVSPLIKLGRYSALFLGVAYGATRYNYLKPRAEEERRIAAEEKKKQDELKRIARE\n+LAEDDSILK\n+>sp|P0CG04|IGLC1_HUMAN Immunoglobulin lambda constant 1 OS=Homo sapiens OX=9606 GN=IGLC1 PE=1 SV=1\n+GQPKANPTVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSK\n+QSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS\n+>sp|Q9P0U1|TOM7_HUMAN Mitochondrial import receptor subunit TOM7 homolog OS=Homo sapiens OX=9606 GN=TOMM7 PE=1 SV=1\n+MVKLSKEAKQRLQQLFKGSQFAIRWGFIPLVIYLGFKRGADPGMPEPTVLSLLWG\n+>sp|P02768|ALBU_HUMAN Albumin OS=Homo sapiens OX=9606 GN=ALB PE=1 SV=2\n+MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPF\n+EDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEP\n+ERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLF\n+FAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAV\n+ARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQDSISSKLK\n+ECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYAR\n+RHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQNLIKQNCELFE\n+QLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVV\n+LNQLCVLHEKTPVSDRVTKCCTESLVNRRPCFSALEVDETYVPKEFNAETFTFHADICTL\n+SEKERQIKKQTALVELVKHKPKATKEQLKAVMDDFAAFVEKCCKADDKETCFAEEGKKLV\n+AASQAALGL\n+>sp|P05387|RLA2_HUMAN 60S acidic ribosomal protein P2 OS=Homo sapiens OX=9606 GN=RPLP2 PE=1 SV=1\n+MRYVASYLLAALGGNSSPSAKDIKKILDSVGIEADDDRLNKVISELNGKNIEDVIAQGIG\n+KLASVPAGGAVAVSAAPGSAAPAAGSAPAAAEEKKDEKKEESEESDDDMGFGLFD\n+>sp|P12236|ADT3_HUMAN ADP/ATP translocase 3 OS=Homo sapiens OX=9606 GN=SLC25A6 PE=1 SV=4\n+MTEQAISFAKDFLAGGIAAAISKTAVAPIERVKLLLQVQHASKQIAADKQYKGIVDCIVR\n+IPKEQGVLSFWRGNLANVIRYFPTQALNFAFKDKYKQIFLGGVDKHTQFWRYFAGNLASG\n+GAAGATSLCFVYPLDFARTRLAADVGKSGTEREFRGLGDCLVKITKSDGIRGLYQGFSVS\n+VQGIIIYRAAYFGVYDTAKGMLPDPKNTHIVVSWMIAQTVTAVAGVVSYPFDTVRRRMMM\n+QSGRKGADIMYTGTVDCWRKIFRDEGGKAFFKGAWSNVLRGMGGAFVLVLYDELKKVI\n+>sp|P56470|LEG4_HUMAN Galectin-4 OS=Homo sapiens OX=9606 GN=LGALS4 PE=1 SV=1\n+MAYVPAPGYQPTYNPTLPYYQPIPGGLNVGMSVYIQGVASEHMKRFFVNFVVGQDPGSDV\n+AFHFNPRFDGWDKVVFNTLQGGKWGSEERKRSMPFKKGAAFELVFIVLAEHYKVVVNGNP\n+FYEYGHRLPLQMVTHLQVDGDLQLQSINFIGGQPLRPQGPPMMPPYPGPGHCHQQLNSLP\n+TMEGPPTFNPPVPYFGRLQGGLTARRTIIIKGYVPPTGKSFAINFKVGSSGDIALHINPR\n+MGNGTVVRNSLLNGSWGSEEKKITHNPFGPGQFFDLSIRCGLDRFKVYANGQHLFDFAHR\n+LSAFQRVDTLEIQGDVTLSYVQI\n+>sp|Q01995|TAGL_HUMAN Transgelin OS=Homo sapiens OX=9606 GN=TAGLN PE=1 SV=4\n+MANKGPSYGMSREVQSKIEKKYDEELEERLVEWIIVQCGPDVGRPDRGRLGFQVWLKNGV\n+ILSKLVNSLYPDGSKPVKVPENPPSMVFKQMEQVAQFLKAAEDYGVIKTDMFQTVDLFEG\n+KDMAAVQRTLMALGSLAVTKNDGHYRGDPNWFMKKAQEHKREFTESQLQEGKHVIGLQMG\n+SNRGASQAGMTGYGRPRQIIS\n+>sp|P69905|HBA_HUMAN Hemoglobin subunit alpha OS=Homo sapiens OX=9606 GN=HBA1 PE=1 SV=2\n+MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG\n+KKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTP\n+AVHASLDKFLASVSTVLTSKYR\n+>sp|P02766|TTHY_HUMAN Transthyretin OS=Homo sapiens OX=9606 GN=TTR PE=1 SV=1\n+MASHRLLLLCLAGLVFVSEAGPTGTGESKCPLMVKVLDAVRGSPAINVAVHVFRKAADDT\n+WEPFASGKTSESGELHGLTTEEEFVEGIYKVEIDTKSYWKALGISPFHEHAEVVFTANDS\n+GPRRYTIAALLSPYSYSTTAVVTNPKE\n+>sp|P69891|HBG1_HUMAN Hemoglobin subunit gamma-1 OS=Homo sapiens OX=9606 GN=HBG1 PE=1 SV=2\n+MGHFTEEDKATITSLWGKVNVEDAGGETLGRLLVVYPWTQRFFDSFGNLSSASAIMGNPK\n+VKAHGKKVLTSLGDAIKHLDDLKGTFAQLSELHCDKLHVDPENFKLLGNVLVTVLAIHFG\n+KEFTPEVQASWQKMVTAVASALSSRYH\n+>sp|O60844|ZG16_HUMAN Zymogen granule membrane protein 16 OS=Homo sapiens OX=9606 GN=ZG16 PE=1 SV=2\n+MLTVALLALLCASASGNAIQARSSSYSGEYGGGGGKRFSHSGNQLDGPITALRVRVNTYY\n+IVGLQVRYGKVWSDYVGGRNGDLEEIFLHPGESVIQVSGKYKWYLKKLLFVTDKGRYLSF\n+GKDSGTSFNAVPLHPNTVLRFISGRSGSLIDAIGLHWDVYPSSCSRC\n+>sp|P01009|A1AT_HUMAN Alpha-1-anti'..b'-681) OX=167879 GN=gcvT PE=3 SV=1\n+MTNKTVLHAKHLASGAKMVDFFGWDMPINYGSQIEEHHAVRTDAGMFDVSHMTIVDVQGA\n+DAKAFLRRLVINDVAKLATPGKALYTGMLNEEGGVIDDLIIYFFSDTDYRLVVNSATRVK\n+DLAWMTKQSTGFDITITERPEFGMLAVQGPEAKAKVAKLLTAEQIEAVEGMKPFFGVQVG\n+DLFIATTGYTGEDGYEIIVPNNSAEDFWQKLLDEGVVPCGLGARDTLRLEAGMNLYGLDM\n+DETVSPLAANMAWTISWEPTDRDFIGRDVLTAQKAAGDQPKLVGLVLEAKGVLRSHQVVV\n+TEFGNGEITSGTFSPTLGHSVALARVPRSVKVGDTIEVEMRKKLIKVQVTKPSFVRNGKK\n+VF\n+>sp|P51775|ACT_GIAIN Actin OS=Giardia intestinalis OX=5741 PE=3 SV=1\n+MTDDNPAIVIDNGSGMCKAGFAGDDAPRAVFPTVVGRPKRETVLVGSTHKEEYIGDEALA\n+KRGVLKLSYPIEHGQIKDWDMMEKVWHHCYFNELRAQPSDHAVLLTEAPKNPKANREKIC\n+QIMFETFAVPAFYVQVQAVLALYSSGRTTGIVIDTGDGVTHTVPVYEGYSLPHAVLRSEI\n+AGKELTDFCQINLQENGASFTTSAEFEIVRDIKEKLCFVALDYESVLAASMESANYTKTY\n+ELPDGVVITVNQARFKTPELLFRPELNNSDMDGIHQLCYKTIQKCDIDIRSELYSNVVLS\n+GGSSMFAGLPERLEKELLDLIPAGKRVRISSPEDRKYSAWVGGSVLGSLATFESMWVSSQ\n+EYQENGASIANRKCM\n+>sp|O54762|ALLT_ICTTR Alpha-1-antitrypsin-like protein GS55-LT OS=Ictidomys tridecemlineatus OX=43179 PE=2 SV=1\n+MPSSISWGLLLLAGLSCLATGCLIEDSEKSDAPKHDQENSASHKIAPNLAEFAFSLYRVL\n+AHESNTTNIFFSPVSIATALGSLSLGTKADTHTQIMEGVGFNLTEISEAEIHQGFQHLLQ\n+NLNKSNSQLQLTTGNGLFIDHNMKLLDKFLEDIKNLYHSEAFSTDFTNTEEAKKQINTYV\n+EKGTQGKIVDLVKDLDRDSGLALVNYIFFKGTLEKPFKADHTMEQDFHVDEATTVRVPMM\n+NRLGMFDLHYCPTLSSMVLKMKYLGDITAIFIMPKVGRMEYVEETLTKEFLDKLLKKDYT\n+GKNTVHFPKLSISGTIDLKPVLTRLGITKVFSHEADLSGITEDAPLRVSQALHKAVLTID\n+EKGTEAERHTVKGPMALTLAPEVKFNRPFLVTLYDRSTKSPLFVGRVVNPTLH\n+>sp|O14108|ETA2_SCHPO DNA-binding protein eta2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 GN=eta2 PE=1 SV=1\n+MMLAIDMTINENQGTRSNLESPTLSCSSKGAMQERDVMFTDHNTFNITNNKSRPGSLMKS\n+MKRKDVYEFDEDNEFEFEMGSLIHKPSRAHSLGGTSEPVSDDHKDCMEATRQLLENSPLS\n+SVVVKTCSDHASKRKIARSSSDDSESKVESTNSFNAKKRKDAWTEEHEKWFQARIDELLT\n+IRSISREQMIEILEDEHAGSRLQGFLESVASFLNRKENSLLKYMRAFFQVAGYEKIDIGS\n+LAAEEDSQLNFSLEDAQVIQKVVLSYCNNEGVDLQEFGFRMSSSSLRHTNINFLYNELRE\n+LLPTSISRKGIIRYLKEIYKPLDPKDRNAWEESELKKLYTLVEQEGTRWNSIANKLGTSP\n+AACMSQWRFVVGTSTQETIDRRKLWTNEEEAKLLDLVKSSYRSSFHTKKMTSLFTHNNHT\n+TSNIQREIPASDSIAWHSISKKLGTKSPESCRKQYEKTIASYSSNQRQEEDQGKKRKKRK\n+KKKSKGKRKFYVADSLKLLEHVQRQCGEAISINAIDWKGIVKQMPKWSEEELRAQATNLV\n+ASVRGWKKTRLSESVRIAITDLKSLPPDV\n+>sp|A5K6L0|TRM5_PLAVS tRNA (guanine(37)-N1)-methyltransferase OS=Plasmodium vivax (strain Salvador I) OX=126793 GN=PVX_099140 PE=3 SV=1\n+MRNAVDIKTLADVKEKVKHEKRTHCLVLNKYRVNELLKNKDAKIWFLNIFRFPSVLKFRE\n+YQGCLVETGPYDGEVLRFIHSYVESLGGGEVSGQVSGQVNDQLSCQMTSHANDSQAGTPL\n+ADAPLADCRLIPLNARFNRALHELMQREGKGVLEGVDMRPEEGDERDVAAEGGGVEDVAQ\n+QGAAHQDAPPALEKLLRVIKAEGIQIRTIQLQFGYDNMNTSQVLRKVFPSESEVIHKYEM\n+IGHIAHLNFCERFENHKKVIAEIILDKNKSIRTVINKKDSLKNVHRTFTIELLAGEENYL\n+TMLRENDIKVKLNYELMYWNSKLKKERDRIYSLVENNSIVVDVFAGVGIFSLHLSKKNCL\n+CFSNDINLHAYNFMNVNIKLNKRRSILTYNLDARAFVCMLLRLGIFSRDTSTLAMQLGEQ\n+NWRNVSLDFVNSAGRDVVDAGKGKKRAADCKVDCKEDCKEDCKEDCKEDCKEDCKEDCKE\n+DCKEDCKEDCEVKDCKAGDSHQSNSHQSNPHESNPHESAPRDKKKKLAHGDANGPLGERP\n+PGVAATHGGEEVPPEPTNNEAEQKAEDAPTNETHQVDINLGIYGDVHVLMNLPQTALDFL\n+DVFRELLHMYSAGQKDPQGRCRRDQMRNVFIHCYFFSKPELFYEHAERNIRMQLGGIPRE\n+MKITEIRKVSPSKLMYVVEFNLKDVFSQGDQLG\n+>sp|C0LRA7|EBDG_HYPVI Exo-beta-D-glucosaminidase OS=Hypocrea virens OX=29875 GN=gls1 PE=2 SV=1\n+MIAKAVAALLLGSGLASAAGTPLTSKAGDKVPIPDWDLKSSSEVSKDLKGLSKPGVDTSA\n+WYHAGTSKCTLMACLLNAGIYKDEDLWYSDNLNHFNWGQFSIPWLYRHEFALAPAKGKHF\n+ILQTNGITSKADLFFNGQQIADSEYQAGAYAGRTYDITSLAAKDNAFVVQVHPTDYLYDF\n+ALGYVDWNPYPPDNGTGIWRDITVKETGSVSMGPISVVVDIDVPVESSPAKVTIRAEAQN\n+LENVAVVLDAEAVVSGNSCSGGPLKQTVKLAPGEKKLVEFTKTIAKPKIWWPKQWGDQPL\n+YNAKVTFSVNKAVSDTAQTNFGVRKVTSFVNQYNDTQYSVNGHPFQVVGGGYGADMFLRW\n+DGDRFTRIVEYMLDMHQNTIRLEGKMEHPELYEICDKYGLMVMPGWECCDKWEAWAYNDE\n+LAIFPPPVWDDNDYQTANYSMIHEASMLQPHPSVLTFLVGSDFWPNDEAVVLYVNALKNA\n+GWQTPIIASASKRGFPALLGPGGMKMDGPYDWVPPNYWYDTEPSEDRLGAAFGFGSELGA\n+GVGTPELGSLKRFLSQSDLNDLWKNPNKNLYHMSTNVSSFYNRKIYNQGLFKRYGAPTSL\n+DDYLLKAQMMDYEATRAQYEGFSSLWTASRPATGNIYWMLNNAWPSLHWNQFGYYMHPAG\n+SYFGTKVGSRIEHVAYNYQKKEVWVINHSLDQTGPRKVDIELIDTNGKQIAKQSVNINTK\n+ANSGFKAADISSQIGKLSSVAFLRLILSDSKGNVLSRNVYWVTNSIDKLDWDSSTWYYTQ\n+VTSFVDYTPLNKLSAAQISVTTGSSRRVAGVPGTQTRTVTLENKPSVPAVFIRLTLVDKS\n+GNDVNPVSWTDNYVTLWPKEKLQLEVGGWDASGDSIQVSGRNIAATTVKL\n' |
| b |
| diff -r 4a851c02f558 -r 7a5ff5359b13 test-data/sample_output_collection.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample_output_collection.fasta Fri Apr 22 13:31:08 2022 +0000 |
| b |
| @@ -0,0 +1,85 @@ +>sp|Q61539|ERR2_MOUSE Steroid hormone receptor ERR2 OS=Mus musculus OX=10090 GN=Esrrb PE=1 SV=2 +MSSEDRHLGSSCGSFIKTEPSSPSSGIDALSHHSPSGSSDASGGFGIALSTHANGLDSPP +MFAGAGLGGNPCRKSYEDCTSGIMEDSAIKCEYMLNAIPKRLCLVCGDIASGYHYGVASC +EACKAFFKRTIQGNIEYNCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVRG +GRQKYKRRLDSENSPYLNLPISPPAKKPLTKIVSNLLGVEQDKLYAMPPNDIPEGDIKAL +TTLCELADRELVFLINWAKHIPGFPSLTLGDQMSLLQSAWMEILILGIVYRSLPYDDKLA +YAEDYIMDEEHSRLVGLLDLYRAILQLVRRYKKLKVEKEEFMILKALALANSDSMYIENL +EAVQKLQDLLHEALQDYELSQRHEEPRRAGKLLLTLPLLRQTAAKAVQHFYSVKLQGKVP +MHKLFLEMLEAKV +>sp|O88689|PCDA4_MOUSE Protocadherin alpha-4 OS=Mus musculus OX=10090 GN=Pcdha4 PE=1 SV=1 +MEFSWGSGQESQRLLLSFLLLAIWEAGNSQIHYSIPEEAKHGTFVGRIAQDLGLELTELV +PRLFRVASKDRGDLLEVNLQNGILFVNSRIDREELCGRSAECSIHLEVIVDRPLQVFHVE +VEVRDINDNPPRFPTTQKNLFIAESRPLDTWFPLEGASDADIGINAVLTYRLSPNDYFSL +EKPSNDERVKGLGLVLRKSLDREETPEIILVLTVTDGGKPELTGSVQLLITVLDANDNAP +VFDRSLYTVKLPENVPNGTLVVKVNASDLDEGVNGDIMYSFSTDISPNVKYKFHIDPVSG +EIIVKGYIDFEECKSYEILIEGIDKGQLPLSGHCKVIVQVEDINDNVPELEFKSLSLPIR +ENSPVGTVIALISVSDRDTGVNGQVTCSLTSHVPFKLVSTFKNYYSLVLDSALDRETTAD +YKVVVTARDGGSPSLWATASVSVEVADVNDNAPVFAQPEYTVFVKENNPPGAHIFTVSAM +DADAQENALVSYSLVERRVGERLLSSYVSVHAESGKVFALQPLDHEELELLRFQVSARDA +GVPALGSNVTLQVFVLDENDNAPTLLEPEAGVSGGIVSRLVSRSVGAGHVVAKVRAVDAD +SGYNAWLSYELQSSEGNSRSLFRVGLYTGEISTTRILDEADSPRQRLLVLVKDHGDPAMI +VTATVLVSLVENGPVPKAPSRVSTSVTHSEASLVDVNVYLIIAICAVSSLLVLTLLLYTA +LRCSTVPSESVCGPPKPVMVCSSAVGSWSYSQQRRQRVCSGEYPPKTDLMAFSPSLSDSR +DREDQLQSAEDSSGKPRQPNPDWRYSASLRAGMHSSVHLEEAGILRAGPGGPDQQWPTVS +SATPEPEAGEVSPPVGAGVNSNSWTFKYGPGNPKQSGPGELPDKFIIPGSPAIISIRQEP +ANNQIDKSDFITFGKKEETKKKKKKKKGNKTQEKKEKGNSTTDNSDQ +>sp|Q486J8|GCST_COLP3 Aminomethyltransferase OS=Colwellia psychrerythraea (strain 34H / ATCC BAA-681) OX=167879 GN=gcvT PE=3 SV=1 +MTNKTVLHAKHLASGAKMVDFFGWDMPINYGSQIEEHHAVRTDAGMFDVSHMTIVDVQGA +DAKAFLRRLVINDVAKLATPGKALYTGMLNEEGGVIDDLIIYFFSDTDYRLVVNSATRVK +DLAWMTKQSTGFDITITERPEFGMLAVQGPEAKAKVAKLLTAEQIEAVEGMKPFFGVQVG +DLFIATTGYTGEDGYEIIVPNNSAEDFWQKLLDEGVVPCGLGARDTLRLEAGMNLYGLDM +DETVSPLAANMAWTISWEPTDRDFIGRDVLTAQKAAGDQPKLVGLVLEAKGVLRSHQVVV +TEFGNGEITSGTFSPTLGHSVALARVPRSVKVGDTIEVEMRKKLIKVQVTKPSFVRNGKK +VF +>sp|Q8JGS1|STIL_DANRE SCL-interrupting locus protein homolog OS=Danio rerio OX=7955 GN=stil PE=1 SV=2 +MNRVQVDFKGLPAHILENSIAAESLQNTRSSDNVLTPLTFPKSKVALWDPSANGEVVSLH +FSYYRNPRLFLVEKALRLAHRHARQTNKPRFFCFLLGTLAVDSDEEGVTITLDRFDPGRE +QTGCLGKAPTALLPGDILVPCVFEAQHAASSTVHSSEDLNISFKMLQHFCCSKELLELSK +LLTLRAQLSCSENMDRLTFNLSWAAVTLACTLDAVPIRAVPIIPTALARNLSSPAGVTQN +SKRGFLTMDQTRKLLLILESDPKAYTLPLVGIWLSGVTHIHNPLVWAWCLRYLHSSSLQD +KVLSEGGTFLVVLYSLTHRDPEFYQCKPSTGQQQLSFQLLTSRDSLTLYKNVEPSEGRPL +QFELSSENQNQETVLFEEVLSQSVLTGTTLGAASAAPQNKLSISDHDSGVEDEDLSPRPS +PNPHPVSQQTKRVHPLVPELSMVLDGSFLDGSVVNTQGSTPLSHSQSNVHRRNSSPALQG +LSVLRPLVQGSVTKPPPIRRPLTPILSQPKNKLHPNPSQQTPQHSVSRKSLPSMRRSREG +SSASSVSSSSSSSSTKNASPNGSFHQQRQRLSQGFPNKPQLIYSGPPTSGHSSAKKSSSV +PSQTPVPHPSQHRIFHSTPAVNPCNCCTNHPSVAPLYQNNTWQGTPGYPTAVHSPCVFHC +SPETVPPGDHCLSPSRQSLGCRVSPTKSPVCYHSTPPHYSPSSGPCVPTIISNKGLVEQT +PSCQAQCCQVKGSKEPCLDTPMGLLPADAYRMLIDQERQLKLLQLQIQKLLESQSKVPEV +SSEQNAQQQRPNQVPASPPKRTSVSIAVGTGASLFWSTPQETSTHEASSLEWQTETEPKS +GCQNDSTVTSRDRSESACHYSEEHCPGSPQHPTSPQHNTSSGFGVQMFQSPVLGESASMY +YQSQSQSKDLSENREIDDPRFYHELLGQVQSRLQDSVIVEDKVEQDQQSLLKTQSLSPVV +HQSRKPLTTSSIPQTQKTKQPSSPPNQDRVLSATLKQLQQFGVNIDLDSSQEKTTRATVE +SASTLACINPEAVIPRLALSEPVGASIWGPSGSVDLSLEANAIALKYLSDSQLSRLSLGS +QSSSPHSDPSTILLRRPAVEKSNVALSILSPSNMSLATCKYMKKYGLIEGEISSEEEQED +PIQVDSALGCSVQHETSKTISLGQEREEQNTAVLKNITNKPVVNLHTSPIDSQEQILQDL +RPKMQLLLRGGTNSEKENATKRNLIERRSSLTENQRTQEVVDPQGSVGNFLDLSRLRQLP +KLF +>sp|O14108|ETA2_SCHPO DNA-binding protein eta2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 GN=eta2 PE=1 SV=1 +MMLAIDMTINENQGTRSNLESPTLSCSSKGAMQERDVMFTDHNTFNITNNKSRPGSLMKS +MKRKDVYEFDEDNEFEFEMGSLIHKPSRAHSLGGTSEPVSDDHKDCMEATRQLLENSPLS +SVVVKTCSDHASKRKIARSSSDDSESKVESTNSFNAKKRKDAWTEEHEKWFQARIDELLT +IRSISREQMIEILEDEHAGSRLQGFLESVASFLNRKENSLLKYMRAFFQVAGYEKIDIGS +LAAEEDSQLNFSLEDAQVIQKVVLSYCNNEGVDLQEFGFRMSSSSLRHTNINFLYNELRE +LLPTSISRKGIIRYLKEIYKPLDPKDRNAWEESELKKLYTLVEQEGTRWNSIANKLGTSP +AACMSQWRFVVGTSTQETIDRRKLWTNEEEAKLLDLVKSSYRSSFHTKKMTSLFTHNNHT +TSNIQREIPASDSIAWHSISKKLGTKSPESCRKQYEKTIASYSSNQRQEEDQGKKRKKRK +KKKSKGKRKFYVADSLKLLEHVQRQCGEAISINAIDWKGIVKQMPKWSEEELRAQATNLV +ASVRGWKKTRLSESVRIAITDLKSLPPDV +>sp|Q14934|NFAC4_HUMAN Nuclear factor of activated T-cells, cytoplasmic 4 OS=Homo sapiens OX=9606 GN=NFATC4 PE=1 SV=2 +MGAASCEDEELEFKLVFGEEKEAPPLGAGGLGEELDSEDAPPCCRLALGEPPPYGAAPIG +IPRPPPPRPGMHSPPPRPAPSPGTWESQPARSVRLGGPGGGAGGAGGGRVLECPSIRITS +ISPTPEPPAALEDNPDAWGDGSPRDYPPPEGFGGYREAGGQGGGAFFSPSPGSSSLSSWS +FFSDASDEAALYAACDEVESELNEAASRFGLGSPLPSPRASPRPWTPEDPWSLYGPSPGG +RGPEDSWLLLSAPGPTPASPRPASPCGKRRYSSSGTPSSASPALSRRGSLGEEGSEPPPP +PPLPLARDPGSPGPFDYVGAPPAESIPQKTRRTSSEQAVALPRSEEPASCNGKLPLGAEE +SVAPPGGSRKEVAGMDYLAVPSPLAWSKARIGGHSPIFRTSALPPLDWPLPSQYEQLELR +IEVQPRAHHRAHYETEGSRGAVKAAPGGHPVVKLLGYSEKPLTLQMFIGTADERNLRPHA +FYQVHRITGKMVATASYEAVVSGTKVLEMTLLPENNMAANIDCAGILKLRNSDIELRKGE +TDIGRKNTRVRLVFRVHVPQGGGKVVSVQAASVPIECSQRSAQELPQVEAYSPSACSVRG +GEELVLTGSNFLPDSKVVFIERGPDGKLQWEEEATVNRLQSNEVTLTLTVPEYSNKRVSR +PVQVYFYVSNGRRKRSPTQSFRFLPVICKEEPLPDSSLRGFPSASATPFGTDMDFSPPRP +PYPSYPHEDPACETPYLSEGFGYGMPPLYPQTGPPPSYRPGLRMFPETRGTTGCAQPPAV +SFLPRPFPSDPYGGRGSSFSLGLPFSPPAPFRPPPLPASPPLEGPFPSQSDVHPLPAEGY +NKVGPGYGPGEGAPEQEKSRGGYSSGFRDSVPIQGITLEEVSEIIGRDLSGFPAPPGEEP +PA |
| b |
| diff -r 4a851c02f558 -r 7a5ff5359b13 test-data/sample_output_single.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample_output_single.fasta Fri Apr 22 13:31:08 2022 +0000 |
| b |
| @@ -0,0 +1,62 @@ +>sp|Q61539|ERR2_MOUSE Steroid hormone receptor ERR2 OS=Mus musculus OX=10090 GN=Esrrb PE=1 SV=2 +MSSEDRHLGSSCGSFIKTEPSSPSSGIDALSHHSPSGSSDASGGFGIALSTHANGLDSPP +MFAGAGLGGNPCRKSYEDCTSGIMEDSAIKCEYMLNAIPKRLCLVCGDIASGYHYGVASC +EACKAFFKRTIQGNIEYNCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVRG +GRQKYKRRLDSENSPYLNLPISPPAKKPLTKIVSNLLGVEQDKLYAMPPNDIPEGDIKAL +TTLCELADRELVFLINWAKHIPGFPSLTLGDQMSLLQSAWMEILILGIVYRSLPYDDKLA +YAEDYIMDEEHSRLVGLLDLYRAILQLVRRYKKLKVEKEEFMILKALALANSDSMYIENL +EAVQKLQDLLHEALQDYELSQRHEEPRRAGKLLLTLPLLRQTAAKAVQHFYSVKLQGKVP +MHKLFLEMLEAKV +>sp|Q486J8|GCST_COLP3 Aminomethyltransferase OS=Colwellia psychrerythraea (strain 34H / ATCC BAA-681) OX=167879 GN=gcvT PE=3 SV=1 +MTNKTVLHAKHLASGAKMVDFFGWDMPINYGSQIEEHHAVRTDAGMFDVSHMTIVDVQGA +DAKAFLRRLVINDVAKLATPGKALYTGMLNEEGGVIDDLIIYFFSDTDYRLVVNSATRVK +DLAWMTKQSTGFDITITERPEFGMLAVQGPEAKAKVAKLLTAEQIEAVEGMKPFFGVQVG +DLFIATTGYTGEDGYEIIVPNNSAEDFWQKLLDEGVVPCGLGARDTLRLEAGMNLYGLDM +DETVSPLAANMAWTISWEPTDRDFIGRDVLTAQKAAGDQPKLVGLVLEAKGVLRSHQVVV +TEFGNGEITSGTFSPTLGHSVALARVPRSVKVGDTIEVEMRKKLIKVQVTKPSFVRNGKK +VF +>sp|O88689|PCDA4_MOUSE Protocadherin alpha-4 OS=Mus musculus OX=10090 GN=Pcdha4 PE=1 SV=1 +MEFSWGSGQESQRLLLSFLLLAIWEAGNSQIHYSIPEEAKHGTFVGRIAQDLGLELTELV +PRLFRVASKDRGDLLEVNLQNGILFVNSRIDREELCGRSAECSIHLEVIVDRPLQVFHVE +VEVRDINDNPPRFPTTQKNLFIAESRPLDTWFPLEGASDADIGINAVLTYRLSPNDYFSL +EKPSNDERVKGLGLVLRKSLDREETPEIILVLTVTDGGKPELTGSVQLLITVLDANDNAP +VFDRSLYTVKLPENVPNGTLVVKVNASDLDEGVNGDIMYSFSTDISPNVKYKFHIDPVSG +EIIVKGYIDFEECKSYEILIEGIDKGQLPLSGHCKVIVQVEDINDNVPELEFKSLSLPIR +ENSPVGTVIALISVSDRDTGVNGQVTCSLTSHVPFKLVSTFKNYYSLVLDSALDRETTAD +YKVVVTARDGGSPSLWATASVSVEVADVNDNAPVFAQPEYTVFVKENNPPGAHIFTVSAM +DADAQENALVSYSLVERRVGERLLSSYVSVHAESGKVFALQPLDHEELELLRFQVSARDA +GVPALGSNVTLQVFVLDENDNAPTLLEPEAGVSGGIVSRLVSRSVGAGHVVAKVRAVDAD +SGYNAWLSYELQSSEGNSRSLFRVGLYTGEISTTRILDEADSPRQRLLVLVKDHGDPAMI +VTATVLVSLVENGPVPKAPSRVSTSVTHSEASLVDVNVYLIIAICAVSSLLVLTLLLYTA +LRCSTVPSESVCGPPKPVMVCSSAVGSWSYSQQRRQRVCSGEYPPKTDLMAFSPSLSDSR +DREDQLQSAEDSSGKPRQPNPDWRYSASLRAGMHSSVHLEEAGILRAGPGGPDQQWPTVS +SATPEPEAGEVSPPVGAGVNSNSWTFKYGPGNPKQSGPGELPDKFIIPGSPAIISIRQEP +ANNQIDKSDFITFGKKEETKKKKKKKKGNKTQEKKEKGNSTTDNSDQ +>sp|O14108|ETA2_SCHPO DNA-binding protein eta2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 GN=eta2 PE=1 SV=1 +MMLAIDMTINENQGTRSNLESPTLSCSSKGAMQERDVMFTDHNTFNITNNKSRPGSLMKS +MKRKDVYEFDEDNEFEFEMGSLIHKPSRAHSLGGTSEPVSDDHKDCMEATRQLLENSPLS +SVVVKTCSDHASKRKIARSSSDDSESKVESTNSFNAKKRKDAWTEEHEKWFQARIDELLT +IRSISREQMIEILEDEHAGSRLQGFLESVASFLNRKENSLLKYMRAFFQVAGYEKIDIGS +LAAEEDSQLNFSLEDAQVIQKVVLSYCNNEGVDLQEFGFRMSSSSLRHTNINFLYNELRE +LLPTSISRKGIIRYLKEIYKPLDPKDRNAWEESELKKLYTLVEQEGTRWNSIANKLGTSP +AACMSQWRFVVGTSTQETIDRRKLWTNEEEAKLLDLVKSSYRSSFHTKKMTSLFTHNNHT +TSNIQREIPASDSIAWHSISKKLGTKSPESCRKQYEKTIASYSSNQRQEEDQGKKRKKRK +KKKSKGKRKFYVADSLKLLEHVQRQCGEAISINAIDWKGIVKQMPKWSEEELRAQATNLV +ASVRGWKKTRLSESVRIAITDLKSLPPDV +>sp|Q14934|NFAC4_HUMAN Nuclear factor of activated T-cells, cytoplasmic 4 OS=Homo sapiens OX=9606 GN=NFATC4 PE=1 SV=2 +MGAASCEDEELEFKLVFGEEKEAPPLGAGGLGEELDSEDAPPCCRLALGEPPPYGAAPIG +IPRPPPPRPGMHSPPPRPAPSPGTWESQPARSVRLGGPGGGAGGAGGGRVLECPSIRITS +ISPTPEPPAALEDNPDAWGDGSPRDYPPPEGFGGYREAGGQGGGAFFSPSPGSSSLSSWS +FFSDASDEAALYAACDEVESELNEAASRFGLGSPLPSPRASPRPWTPEDPWSLYGPSPGG +RGPEDSWLLLSAPGPTPASPRPASPCGKRRYSSSGTPSSASPALSRRGSLGEEGSEPPPP +PPLPLARDPGSPGPFDYVGAPPAESIPQKTRRTSSEQAVALPRSEEPASCNGKLPLGAEE +SVAPPGGSRKEVAGMDYLAVPSPLAWSKARIGGHSPIFRTSALPPLDWPLPSQYEQLELR +IEVQPRAHHRAHYETEGSRGAVKAAPGGHPVVKLLGYSEKPLTLQMFIGTADERNLRPHA +FYQVHRITGKMVATASYEAVVSGTKVLEMTLLPENNMAANIDCAGILKLRNSDIELRKGE +TDIGRKNTRVRLVFRVHVPQGGGKVVSVQAASVPIECSQRSAQELPQVEAYSPSACSVRG +GEELVLTGSNFLPDSKVVFIERGPDGKLQWEEEATVNRLQSNEVTLTLTVPEYSNKRVSR +PVQVYFYVSNGRRKRSPTQSFRFLPVICKEEPLPDSSLRGFPSASATPFGTDMDFSPPRP +PYPSYPHEDPACETPYLSEGFGYGMPPLYPQTGPPPSYRPGLRMFPETRGTTGCAQPPAV +SFLPRPFPSDPYGGRGSSFSLGLPFSPPAPFRPPPLPASPPLEGPFPSQSDVHPLPAEGY +NKVGPGYGPGEGAPEQEKSRGGYSSGFRDSVPIQGITLEEVSEIIGRDLSGFPAPPGEEP +PA |