| Previous changeset 1:c0e3ae85a40d (2017-09-22) Next changeset 3:42dc8e9e58d8 (2017-11-02) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 1e51bed3a1c10c67ef0404216608e9333db04c64 |
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added:
test-data/201208-378803-cm-filtered.idpDB test-data/201208-378803-cm.idpDB test-data/201208-378803-cm.pep.xml test-data/201208-378803-embeddedGenes.idpDB test-data/201208-378803-embeddedGenesAndQuantitation.idpDB test-data/201208-378803-embeddedGenesAndScanTimes.idpDB test-data/201208-378803-embeddedGenesAndSpectra.idpDB test-data/201208-378803-embeddedGenesAndSpectra2.idpDB test-data/201208-378803-mm-15ppm-fully-tryptic.pepXML test-data/201208-378803-mm-filtered.idpDB test-data/201208-378803-mm.idpDB test-data/201208-378803-mm.pepXML test-data/201208-378803-msgf-filtered.idpDB test-data/201208-378803-msgf.idpDB test-data/201208-378803-msgf.mzid test-data/201208-378803.idpDB test-data/input/201208-378803.mzML test-data/input/cow.protein.PRG2012-subset.fasta |
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removed:
COPYING README.md |
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| diff -r c0e3ae85a40d -r 032c02d10694 COPYING --- a/COPYING Fri Sep 22 10:44:40 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,121 +0,0 @@ -Creative Commons Legal Code - -CC0 1.0 Universal - - CREATIVE COMMONS CORPORATION IS NOT A LAW FIRM AND DOES NOT PROVIDE - LEGAL SERVICES. DISTRIBUTION OF THIS DOCUMENT DOES NOT CREATE AN - ATTORNEY-CLIENT RELATIONSHIP. CREATIVE COMMONS PROVIDES THIS - INFORMATION ON AN "AS-IS" BASIS. CREATIVE COMMONS MAKES NO WARRANTIES - REGARDING THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS - PROVIDED HEREUNDER, AND DISCLAIMS LIABILITY FOR DAMAGES RESULTING FROM - THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS PROVIDED - HEREUNDER. - -Statement of Purpose - -The laws of most jurisdictions throughout the world automatically confer -exclusive Copyright and Related Rights (defined below) upon the creator -and subsequent owner(s) (each and all, an "owner") of an original work of -authorship and/or a database (each, a "Work"). - -Certain owners wish to permanently relinquish those rights to a Work for -the purpose of contributing to a commons of creative, cultural and -scientific works ("Commons") that the public can reliably and without fear -of later claims of infringement build upon, modify, incorporate in other -works, reuse and redistribute as freely as possible in any form whatsoever -and for any purposes, including without limitation commercial purposes. -These owners may contribute to the Commons to promote the ideal of a free -culture and the further production of creative, cultural and scientific -works, or to gain reputation or greater distribution for their Work in -part through the use and efforts of others. - -For these and/or other purposes and motivations, and without any -expectation of additional consideration or compensation, the person -associating CC0 with a Work (the "Affirmer"), to the extent that he or she -is an owner of Copyright and Related Rights in the Work, voluntarily -elects to apply CC0 to the Work and publicly distribute the Work under its -terms, with knowledge of his or her Copyright and Related Rights in the -Work and the meaning and intended legal effect of CC0 on those rights. - -1. 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Copyright and Related Rights include, but are not -limited to, the following: - - i. the right to reproduce, adapt, distribute, perform, display, - communicate, and translate a Work; - ii. moral rights retained by the original author(s) and/or performer(s); -iii. publicity and privacy rights pertaining to a person's image or - likeness depicted in a Work; - iv. rights protecting against unfair competition in regards to a Work, - subject to the limitations in paragraph 4(a), below; - v. rights protecting the extraction, dissemination, use and reuse of data - in a Work; - vi. database rights (such as those arising under Directive 96/9/EC of the - European Parliament and of the Council of 11 March 1996 on the legal - protection of databases, and under any national implementation - thereof, including any amended or successor version of such - directive); and -vii. other similar, equivalent or corresponding rights throughout the - world based on applicable law or treaty, and any national - implementations thereof. - -2. Waiver. To the greatest extent permitted by, but not in contravention -of, applicable law, Affirmer hereby overtly, fully, permanently, -irrevocably and unconditionally waives, abandons, and surrenders all of -Affirmer's Copyright and Related Rights and associated claims and causes -of action, whether now known or unknown (including existing as well as -future claims and causes of action), in the Work (i) in all territories -worldwide, (ii) for the maximum duration provided by applicable law or -treaty (including future time extensions), (iii) in any current or future -medium and for any number of copies, and (iv) for any purpose whatsoever, -including without limitation commercial, advertising or promotional -purposes (the "Waiver"). Affirmer makes the Waiver for the benefit of each -member of the public at large and to the detriment of Affirmer's heirs and -successors, fully intending that such Waiver shall not be subject to -revocation, rescission, cancellation, termination, or any other legal or -equitable action to disrupt the quiet enjoyment of the Work by the public -as contemplated by Affirmer's express Statement of Purpose. - -3. Public License Fallback. Should any part of the Waiver for any reason -be judged legally invalid or ineffective under applicable law, then the -Waiver shall be preserved to the maximum extent permitted taking into -account Affirmer's express Statement of Purpose. In addition, to the -extent the Waiver is so judged Affirmer hereby grants to each affected -person a royalty-free, non transferable, non sublicensable, non exclusive, -irrevocable and unconditional license to exercise Affirmer's Copyright and -Related Rights in the Work (i) in all territories worldwide, (ii) for the -maximum duration provided by applicable law or treaty (including future -time extensions), (iii) in any current or future medium and for any number -of copies, and (iv) for any purpose whatsoever, including without -limitation commercial, advertising or promotional purposes (the -"License"). The License shall be deemed effective as of the date CC0 was -applied by Affirmer to the Work. Should any part of the License for any -reason be judged legally invalid or ineffective under applicable law, such -partial invalidity or ineffectiveness shall not invalidate the remainder -of the License, and in such case Affirmer hereby affirms that he or she -will not (i) exercise any of his or her remaining Copyright and Related -Rights in the Work or (ii) assert any associated claims and causes of -action with respect to the Work, in either case contrary to Affirmer's -express Statement of Purpose. - -4. Limitations and Disclaimers. - - a. No trademark or patent rights held by Affirmer are waived, abandoned, - surrendered, licensed or otherwise affected by this document. - b. Affirmer offers the Work as-is and makes no representations or - warranties of any kind concerning the Work, express, implied, - statutory or otherwise, including without limitation warranties of - title, merchantability, fitness for a particular purpose, non - infringement, or the absence of latent or other defects, accuracy, or - the present or absence of errors, whether or not discoverable, all to - the greatest extent permissible under applicable law. - c. Affirmer disclaims responsibility for clearing rights of other persons - that may apply to the Work or any use thereof, including without - limitation any person's Copyright and Related Rights in the Work. - Further, Affirmer disclaims responsibility for obtaining any necessary - consents, permissions or other rights required for any use of the - Work. - d. Affirmer understands and acknowledges that Creative Commons is not a - party to this document and has no duty or obligation with respect to - this CC0 or use of the Work. |
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| diff -r c0e3ae85a40d -r 032c02d10694 README.md --- a/README.md Fri Sep 22 10:44:40 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,53 +0,0 @@ -GalaxyP - idpQuery -==================== - -* Home: <https://github.com/galaxyproteomics/tools-galaxyp/> -* Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/idpquery> -* Tool ID: `idpquery` - - -Description ------------ - -Bumbershoot idpQuery, a part of Bumbershoot IDPicker. - -See: - -* <http://idpicker.org/> - - -GalaxyP Community ------------------ - -Current governing community policies for [GalaxyP](https://github.com/galaxyproteomics/) and other information can be found at: - -<https://github.com/galaxyproteomics> - - -License -------- - -Copyright (c) 2014 Regents of the University of Minnesota and Authors listed below. - -To the extent possible under law, the author(s) have dedicated all copyright and related and neighboring rights to this software to the public domain worldwide. This software is distributed without any warranty. - -You should have received a copy of the CC0 Public Domain Dedication along with this software. If not, see <https://creativecommons.org/publicdomain/zero/1.0/>. - -You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. - - -Contributing ------------- - -Contributions to this repository are reviewed through pull requests. If you would like your work acknowledged, please also add yourself to the Authors section. If your pull request is accepted, you will also be acknowledged in <https://github.com/galaxyproteomics/tools-galaxyp/> - - -Authors -------- - -Authors and contributors: - -* Matt Chambers <matt.chambers42@gmail.com> - -* John Chilton <jmchilton@gmail.com> - Minnesota Supercomputing Institute, University of Minnesota \ No newline at end of file |
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| diff -r c0e3ae85a40d -r 032c02d10694 test-data/201208-378803-cm.pep.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/201208-378803-cm.pep.xml Fri Oct 06 15:01:05 2017 -0400 |
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| b'@@ -0,0 +1,10303 @@\n+<?xml version="1.0" encoding="UTF-8"?>\n+ <msms_pipeline_analysis date="2014-09-19T11:13:55" xmlns="http://regis-web.systemsbiology.net/pepXML" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/pepXML/pepXML_v117.xsd" summary_xml="C:\\idpicker\\branches\\IDPicker-3\\TestData\\201208-378803.pep.xml">\n+ <msms_run_summary base_name="C:\\idpicker\\branches\\IDPicker-3\\TestData\\201208-378803" msManufacturer="unknown" msModel="unknown" raw_data_type="raw" raw_data=".mzML">\n+ <sample_enzyme name="Trypsin/P">\n+ <specificity cut="KR" no_cut="-" sense="C"/>\n+ </sample_enzyme>\n+ <search_summary base_name="C:\\idpicker\\branches\\IDPicker-3\\TestData\\201208-378803" search_engine="Comet" search_engine_version="2014.02 rev. 0" precursor_mass_type="monoisotopic" fragment_mass_type="monoisotopic" search_id="1">\n+ <search_database local_path="cow.protein.PRG2012-subset.fasta" type="AA"/>\n+ <enzymatic_search_constraint enzyme="Trypsin/P" max_num_internal_cleavages="2" min_number_termini="1"/>\n+ <aminoacid_modification aminoacid="M" massdiff="15.994900" mass="147.035385" variable="Y" symbol="*"/>\n+ <aminoacid_modification aminoacid="Q" massdiff="-17.026000" mass="111.032578" variable="Y" symbol="#"/>\n+ <aminoacid_modification aminoacid="Q" massdiff="0.984016" mass="129.042594" variable="Y" symbol="@"/>\n+ <aminoacid_modification aminoacid="N" massdiff="0.984016" mass="115.026943" variable="Y" symbol="@"/>\n+ <aminoacid_modification aminoacid="C" massdiff="58.005480" mass="161.014665" variable="N"/>\n+ <parameter name="# comet_version " value="2014.02"/>\n+ <parameter name="activation_method" value="ALL"/>\n+ <parameter name="add_A_alanine" value="0.000000"/>\n+ <parameter name="add_B_user_amino_acid" value="0.000000"/>\n+ <parameter name="add_C_cysteine" value="58.005480"/>\n+ <parameter name="add_Cterm_peptide" value="0.000000"/>\n+ <parameter name="add_Cterm_protein" value="0.000000"/>\n+ <parameter name="add_D_aspartic_acid" value="0.000000"/>\n+ <parameter name="add_E_glutamic_acid" value="0.000000"/>\n+ <parameter name="add_F_phenylalanine" value="0.000000"/>\n+ <parameter name="add_G_glycine" value="0.000000"/>\n+ <parameter name="add_H_histidine" value="0.000000"/>\n+ <parameter name="add_I_isoleucine" value="0.000000"/>\n+ <parameter name="add_J_user_amino_acid" value="0.000000"/>\n+ <parameter name="add_K_lysine" value="0.000000"/>\n+ <parameter name="add_L_leucine" value="0.000000"/>\n+ <parameter name="add_M_methionine" value="0.000000"/>\n+ <parameter name="add_N_asparagine" value="0.000000"/>\n+ <parameter name="add_Nterm_peptide" value="0.000000"/>\n+ <parameter name="add_Nterm_protein" value="0.000000"/>\n+ <parameter name="add_O_ornithine" value="0.000000"/>\n+ <parameter name="add_P_proline" value="0.000000"/>\n+ <parameter name="add_Q_glutamine" value="0.000000"/>\n+ <parameter name="add_R_arginine" value="0.000000"/>\n+ <parameter name="add_S_serine" value="0.000000"/>\n+ <parameter name="add_T_threonine" value="0.000000"/>\n+ <parameter name="add_U_user_amino_acid" value="0.000000"/>\n+ <parameter name="add_V_valine" value="0.000000"/>\n+ <parameter name="add_W_tryptophan" value="0.000000"/>\n+ <parameter name="add_X_user_amino_acid" value="0.000000"/>\n+ <parameter name="add_Y_tyrosine" value="0.000000"/>\n+ <parameter name="add_Z_user_amino_acid" value="0.000000"/>\n+ <parameter name="allowed_missed_cleavage" value="2"/>\n+ <parameter name="clear_mz_range" value="0.000000 0.000000"/>\n+ <parameter name="clip_nterm_methionine" value="1"/>\n+ <parameter name="database_name" value="cow.protein.PRG2012-subset.fasta"/>\n+ <parameter name="decoy_prefix" value="XXX_"/>\n+ <parameter name="decoy_search" value="1"/>\n+ <parameter name="digest_mass_range" value="600.000000 5000.000000"/>\n+ <parameter name="fragment_bin_offset" value="0.020000"/>\n+ <parameter name="fragment_bin_tol" value="0.020000"/>\n+ <parameter name="isotope_error" value="1"/>\n'..b'="108" precursor_neutral_mass="1162.515574" assumed_charge="2" index="216" retention_time_sec="1070.9">\n+ <search_result>\n+ <search_hit hit_rank="1" peptide="ISDMNQNIGAT" peptide_prev_aa="K" peptide_next_aa="E" protein="XXX_gi|528944678|ref|XP_005204735.1|" num_tot_proteins="3" num_matched_ions="4" tot_num_ions="20" calc_neutral_pep_mass="1163.512853" massdiff="-0.997279" num_tol_term="1" num_missed_cleavages="0" num_matched_peptides="562">\n+ <modification_info modified_peptide="ISDMN[115]QNIGAT">\n+ <mod_aminoacid_mass position="5" mass="115.026943"/>\n+ </modification_info>\n+ <search_score name="xcorr" value="0.721"/>\n+ <search_score name="deltacn" value="0.290"/>\n+ <search_score name="deltacnstar" value="0.063"/>\n+ <search_score name="spscore" value="28.2"/>\n+ <search_score name="sprank" value="1"/>\n+ <search_score name="expect" value="1.00E+000"/>\n+ </search_hit>\n+ <search_hit hit_rank="2" peptide="ISDMNQNIGAT" peptide_prev_aa="K" peptide_next_aa="E" protein="XXX_gi|528944678|ref|XP_005204735.1|" num_tot_proteins="3" num_matched_ions="4" tot_num_ions="20" calc_neutral_pep_mass="1163.512853" massdiff="-0.997279" num_tol_term="1" num_missed_cleavages="0" num_matched_peptides="562">\n+ <modification_info modified_peptide="ISDMNQ[129]NIGAT">\n+ <mod_aminoacid_mass position="6" mass="129.042594"/>\n+ </modification_info>\n+ <search_score name="xcorr" value="0.675"/>\n+ <search_score name="deltacn" value="0.242"/>\n+ <search_score name="deltacnstar" value="0.000"/>\n+ <search_score name="spscore" value="28.2"/>\n+ <search_score name="sprank" value="1"/>\n+ <search_score name="expect" value="1.00E+000"/>\n+ </search_hit>\n+ <search_hit hit_rank="3" peptide="ISDMNQNIGAT" peptide_prev_aa="K" peptide_next_aa="E" protein="XXX_gi|528944678|ref|XP_005204735.1|" num_tot_proteins="3" num_matched_ions="4" tot_num_ions="20" calc_neutral_pep_mass="1163.512853" massdiff="-0.997279" num_tol_term="1" num_missed_cleavages="0" num_matched_peptides="562">\n+ <modification_info modified_peptide="ISDMNQN[115]IGAT">\n+ <mod_aminoacid_mass position="7" mass="115.026943"/>\n+ </modification_info>\n+ <search_score name="xcorr" value="0.675"/>\n+ <search_score name="deltacn" value="0.242"/>\n+ <search_score name="deltacnstar" value="0.000"/>\n+ <search_score name="spscore" value="28.2"/>\n+ <search_score name="sprank" value="1"/>\n+ <search_score name="expect" value="1.00E+000"/>\n+ </search_hit>\n+ <search_hit hit_rank="4" peptide="VIDEGLMDEK" peptide_prev_aa="E" peptide_next_aa="L" protein="gi|528944676|ref|XP_005204734.1|" num_tot_proteins="1" num_matched_ions="1" tot_num_ions="18" calc_neutral_pep_mass="1163.537991" massdiff="-1.022417" num_tol_term="1" num_missed_cleavages="0" num_matched_peptides="562">\n+ <modification_info modified_peptide="VIDEGLM[147]DEK">\n+ <mod_aminoacid_mass position="7" mass="147.035385"/>\n+ </modification_info>\n+ <search_score name="xcorr" value="0.512"/>\n+ <search_score name="deltacn" value="0.077"/>\n+ <search_score name="deltacnstar" value="0.000"/>\n+ <search_score name="spscore" value="3.7"/>\n+ <search_score name="sprank" value="3"/>\n+ <search_score name="expect" value="2.60E+000"/>\n+ </search_hit>\n+ <search_hit hit_rank="5" peptide="ISDMNQNIGAT" peptide_prev_aa="K" peptide_next_aa="E" protein="XXX_gi|528944678|ref|XP_005204735.1|" num_tot_proteins="3" num_matched_ions="3" tot_num_ions="20" calc_neutral_pep_mass="1162.528837" massdiff="-0.013263" num_tol_term="1" num_missed_cleavages="0" num_matched_peptides="562">\n+ <search_score name="xcorr" value="0.473"/>\n+ <search_score name="deltacn" value="1.000"/>\n+ <search_score name="deltacnstar" value="0.000"/>\n+ <search_score name="spscore" value="15.4"/>\n+ <search_score name="sprank" value="2"/>\n+ <search_score name="expect" value="4.02E+000"/>\n+ </search_hit>\n+ </search_result>\n+ </spectrum_query>\n+ </msms_run_summary>\n+</msms_pipeline_analysis>\n' |
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| diff -r c0e3ae85a40d -r 032c02d10694 test-data/201208-378803-mm-15ppm-fully-tryptic.pepXML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/201208-378803-mm-15ppm-fully-tryptic.pepXML Fri Oct 06 15:01:05 2017 -0400 |
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| b'@@ -0,0 +1,499 @@\n+<?xml version="1.0" encoding="ISO-8859-1"?>\n+<msms_pipeline_analysis date="2015-09-03T17:55:14" summary_xml="201208-378803.pepXML" xmlns="http://regis-web.systemsbiology.net/pepXML" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/pepXML/pepXML_v117.xsd">\n+ <analysis_summary analysis="MyriMatch" version="2.2.8634" time="2015-09-03T17:55:14"/>\n+ <msms_run_summary base_name="201208-378803" raw_data_type="" raw_data="">\n+ <sample_enzyme name="Trypsin" independent="false" fidelity="specific">\n+ <specificity sense="C" cut="KR" no_cut="P" min_spacing="1"/>\n+ </sample_enzyme>\n+ <search_summary base_name="201208-378803" search_engine="MyriMatch" precursor_mass_type="monoisotopic" fragment_mass_type="monoisotopic" out_data_type="" out_data="">\n+ <search_database local_path="cow.protein.PRG2012-subset.fasta" database_name="SDB" type="AA"/>\n+ <enzymatic_search_constraint enzyme="Trypsin" max_num_internal_cleavages="4" min_number_termini="2"/>\n+ <parameter name="Config: AvgPrecursorMzTolerance" value="1.5mz"/>\n+ <parameter name="Config: ClassSizeMultiplier" value="2"/>\n+ <parameter name="Config: CleavageRules" value="Trypsin"/>\n+ <parameter name="Config: ComputeXCorr" value="1"/>\n+ <parameter name="Config: DecoyPrefix" value="XXX_"/>\n+ <parameter name="Config: DynamicMods" value=""/>\n+ <parameter name="Config: EstimateSearchTimeOnly" value="0"/>\n+ <parameter name="Config: FragmentMzTolerance" value="0.5mz"/>\n+ <parameter name="Config: FragmentationAutoRule" value="1"/>\n+ <parameter name="Config: FragmentationRule" value="cid"/>\n+ <parameter name="Config: KeepUnadjustedPrecursorMz" value="0"/>\n+ <parameter name="Config: MaxDynamicMods" value="4"/>\n+ <parameter name="Config: MaxFragmentChargeState" value="0"/>\n+ <parameter name="Config: MaxMissedCleavages" value="4"/>\n+ <parameter name="Config: MaxPeakCount" value="300"/>\n+ <parameter name="Config: MaxPeptideLength" value="75"/>\n+ <parameter name="Config: MaxPeptideMass" value="10000"/>\n+ <parameter name="Config: MaxPeptideVariants" value="1000000"/>\n+ <parameter name="Config: MaxResultRank" value="1"/>\n+ <parameter name="Config: MinMatchedFragments" value="5"/>\n+ <parameter name="Config: MinPeptideLength" value="5"/>\n+ <parameter name="Config: MinPeptideMass" value="0"/>\n+ <parameter name="Config: MinResultScore" value="9.9999999999999995e-08"/>\n+ <parameter name="Config: MinTerminiCleavages" value="2"/>\n+ <parameter name="Config: MonoPrecursorMzTolerance" value="15ppm"/>\n+ <parameter name="Config: MonoisotopeAdjustmentSet" value="[0,0] "/>\n+ <parameter name="Config: NumBatches" value="50"/>\n+ <parameter name="Config: NumChargeStates" value="3"/>\n+ <parameter name="Config: NumIntensityClasses" value="3"/>\n+ <parameter name="Config: NumMzFidelityClasses" value="3"/>\n+ <parameter name="Config: OutputFormat" value="pepXML"/>\n+ <parameter name="Config: OutputSuffix" value=""/>\n+ <parameter name="Config: PrecursorMzToleranceRule" value="mono"/>\n+ <parameter name="Config: PreferIntenseComplements" value="1"/>\n+ <parameter name="Config: ProteinDatabase" value="cow.protein.PRG2012-subset.fasta"/>\n+ <parameter name="Config: ProteinListFilters" value=""/>\n+ <parameter name="Config: ProteinSamplingTime" value="15"/>\n+ <parameter name="Config: ResultsPerBatch" value="200000"/>\n+ <parameter name="Config: SpectrumListFilters" value="peakPicking true 2-"/>\n+ <parameter name="Config: StaticMods" value=""/>\n+ <parameter name="Config: StatusUpdateFrequency" value="5"/>\n+ <parameter name="Config: TicCutoffPercentage" value="0.97999999999999998"/>\n+ <parameter name="Config: UseMultipleProcessors" value="1"/>\n+ <parameter name="Config: UseSmartPlusThreeModel" value="1"/>\n+ '..b'5219930.1|"/>\n+ <alternative_protein protein="gi|528993975|ref|XP_005219931.1|"/>\n+ <search_score name="mvh" value="12.259750257107"/>\n+ <search_score name="mzFidelity" value="34.970325461964"/>\n+ <search_score name="xcorr" value="1.9202226581428345"/>\n+ </search_hit>\n+ <search_hit hit_rank="2" peptide="ISELFDKLDSMSVDK" peptide_prev_aa="R" peptide_next_aa="I" protein="XXX_gi|528968108|ref|XP_005212569.1|" num_tot_proteins="1" calc_neutral_pep_mass="1725.8495025234" massdiff="-0.008717801883" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="11" tot_num_ions="30">\n+ <search_score name="mvh" value="11.323857836871"/>\n+ <search_score name="mzFidelity" value="36.756835575306"/>\n+ <search_score name="xcorr" value="0.93184037338923231"/>\n+ </search_hit>\n+ </search_result>\n+ </spectrum_query>\n+ <spectrum_query spectrum="201208-378803.30.30.3" spectrumNativeID="sample=1 period=1 cycle=1231 experiment=2" start_scan="30" end_scan="30" precursor_neutral_mass="1467.72458061501" assumed_charge="3" index="33" retention_time_sec="839.28400000002">\n+ <search_result num_target_comparisons="8" num_decoy_comparisons="2">\n+ <search_hit hit_rank="1" peptide="GVTEHSNQQQGRK" peptide_prev_aa="R" peptide_next_aa="E" protein="gi|156523214|ref|NP_001096021.1|" num_tot_proteins="3" calc_neutral_pep_mass="1467.7178519195" massdiff="-0.00672869551" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="5" tot_num_ions="25">\n+ <alternative_protein protein="gi|528961840|ref|XP_005211303.1|"/>\n+ <alternative_protein protein="gi|528961845|ref|XP_005211304.1|"/>\n+ <search_score name="mvh" value="6.653798251586"/>\n+ <search_score name="mzFidelity" value="14.932769947598"/>\n+ <search_score name="xcorr" value="0.028206144867315191"/>\n+ </search_hit>\n+ </search_result>\n+ </spectrum_query>\n+ <spectrum_query spectrum="201208-378803.31.31.2" spectrumNativeID="sample=1 period=1 cycle=1234 experiment=2" start_scan="31" end_scan="31" precursor_neutral_mass="1030.473954852586" assumed_charge="2" index="34" retention_time_sec="842.98000000002">\n+ <search_result num_target_comparisons="0" num_decoy_comparisons="3">\n+ <search_hit hit_rank="1" peptide="TFAHQENGK" peptide_prev_aa="R" peptide_next_aa="R" protein="XXX_gi|528921178|ref|XP_592304.7|" num_tot_proteins="3" calc_neutral_pep_mass="1030.4832075229" massdiff="0.009252670314" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="5" tot_num_ions="17">\n+ <alternative_protein protein="XXX_gi|528921180|ref|XP_005195747.1|"/>\n+ <alternative_protein protein="XXX_gi|528995523|ref|XP_002695913.2|"/>\n+ <search_score name="mvh" value="6.979786912131"/>\n+ <search_score name="mzFidelity" value="21.605021401289"/>\n+ <search_score name="xcorr" value="0.49320911207199097"/>\n+ </search_hit>\n+ </search_result>\n+ </spectrum_query>\n+ <spectrum_query spectrum="201208-378803.32.32.3" spectrumNativeID="sample=1 period=1 cycle=1283 experiment=2" start_scan="32" end_scan="32" precursor_neutral_mass="1770.954827198736" assumed_charge="3" index="35" retention_time_sec="883.49500000002">\n+ <search_result num_target_comparisons="1" num_decoy_comparisons="9">\n+ <search_hit hit_rank="1" peptide="TEPHSFQRLSLTEVK" peptide_prev_aa="K" peptide_next_aa="R" protein="XXX_gi|528944676|ref|XP_005204734.1|" num_tot_proteins="1" calc_neutral_pep_mass="1770.9264477115" massdiff="-0.028379487236" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="5" tot_num_ions="30">\n+ <search_score name="mvh" value="6.109846868339"/>\n+ <search_score name="mzFidelity" value="13.900987096911"/>\n+ <search_score name="xcorr" value="0.73578462478668327"/>\n+ </search_hit>\n+ </search_result>\n+ </spectrum_query>\n+ </msms_run_summary>\n+</msms_pipeline_analysis>\n' |
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| diff -r c0e3ae85a40d -r 032c02d10694 test-data/201208-378803-mm.pepXML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/201208-378803-mm.pepXML Fri Oct 06 15:01:05 2017 -0400 |
| [ |
| b'@@ -0,0 +1,20531 @@\n+<?xml version="1.0" encoding="ISO-8859-1"?>\n+<msms_pipeline_analysis date="2015-09-03T15:49:50" summary_xml="201208-378803.pepXML" xmlns="http://regis-web.systemsbiology.net/pepXML" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/pepXML/pepXML_v117.xsd">\n+ <analysis_summary analysis="MyriMatch" version="2.2.8634" time="2015-09-03T15:49:50"/>\n+ <msms_run_summary base_name="201208-378803" raw_data_type="" raw_data="">\n+ <sample_enzyme name="Trypsin/P" independent="false" fidelity="semispecific">\n+ <specificity sense="C" cut="KR" no_cut="" min_spacing="1"/>\n+ </sample_enzyme>\n+ <search_summary base_name="201208-378803" search_engine="MyriMatch" precursor_mass_type="monoisotopic" fragment_mass_type="monoisotopic" out_data_type="" out_data="">\n+ <search_database local_path="cow.protein.PRG2012-subset.fasta" database_name="SDB" type="AA"/>\n+ <enzymatic_search_constraint enzyme="Trypsin/P" max_num_internal_cleavages="2" min_number_termini="1"/>\n+ <aminoacid_modification aminoacid="M" massdiff="15.9949" mass="147.0353846062" variable="Y" description="Oxidation"/>\n+ <aminoacid_modification aminoacid="Q" massdiff="-17.026" mass="111.0325775114" peptide_terminus="n" variable="Y"/>\n+ <aminoacid_modification aminoacid="Q" massdiff="0.984016" mass="129.0425935114" variable="Y" description="Deamidated"/>\n+ <aminoacid_modification aminoacid="N" massdiff="0.984016" mass="115.0269434472" variable="Y" description="Deamidated"/>\n+ <aminoacid_modification aminoacid="C" massdiff="58.00548" mass="161.0146644778" variable="N" description="Carboxymethyl"/>\n+ <parameter name="Config: AvgPrecursorMzTolerance" value="1.5mz"/>\n+ <parameter name="Config: ClassSizeMultiplier" value="2"/>\n+ <parameter name="Config: CleavageRules" value="Trypsin/P"/>\n+ <parameter name="Config: ComputeXCorr" value="1"/>\n+ <parameter name="Config: DecoyPrefix" value="XXX_"/>\n+ <parameter name="Config: DynamicMods" value="M * 15.9949 (Q * -17.026 [QN] * 0.984016"/>\n+ <parameter name="Config: EstimateSearchTimeOnly" value="0"/>\n+ <parameter name="Config: FragmentMzTolerance" value="0.5mz"/>\n+ <parameter name="Config: FragmentationAutoRule" value="1"/>\n+ <parameter name="Config: FragmentationRule" value="cid"/>\n+ <parameter name="Config: KeepUnadjustedPrecursorMz" value="0"/>\n+ <parameter name="Config: MaxDynamicMods" value="2"/>\n+ <parameter name="Config: MaxFragmentChargeState" value="0"/>\n+ <parameter name="Config: MaxMissedCleavages" value="2"/>\n+ <parameter name="Config: MaxPeakCount" value="300"/>\n+ <parameter name="Config: MaxPeptideLength" value="75"/>\n+ <parameter name="Config: MaxPeptideMass" value="10000"/>\n+ <parameter name="Config: MaxPeptideVariants" value="1000000"/>\n+ <parameter name="Config: MaxResultRank" value="3"/>\n+ <parameter name="Config: MinMatchedFragments" value="5"/>\n+ <parameter name="Config: MinPeptideLength" value="5"/>\n+ <parameter name="Config: MinPeptideMass" value="0"/>\n+ <parameter name="Config: MinResultScore" value="9.9999999999999995e-08"/>\n+ <parameter name="Config: MinTerminiCleavages" value="1"/>\n+ <parameter name="Config: MonoPrecursorMzTolerance" value="50ppm"/>\n+ <parameter name="Config: MonoisotopeAdjustmentSet" value="[-1,2] "/>\n+ <parameter name="Config: NumBatches" value="50"/>\n+ <parameter name="Config: NumChargeStates" value="5"/>\n+ <parameter name="Config: NumIntensityClasses" value="3"/>\n+ <parameter name="Config: NumMzFidelityClasses" value="3"/>\n+ <parameter name="Config: OutputFormat" value="pepXML"/>\n+ <parameter name="Config: OutputSuffix" value=""/>\n+ <parameter name="Config: PrecursorMzToleranceRule" value="mono"/>\n+ <parameter name="Config: PreferIntenseComplements" value="1"/>\n+ <parameter name="Config: Pr'..b'="180">\n+ <modification_info>\n+ <mod_aminoacid_mass position="12" mass="147.0353846062"/>\n+ <mod_aminoacid_mass position="14" mass="161.0146644778"/>\n+ <mod_aminoacid_mass position="24" mass="129.0425935114"/>\n+ </modification_info>\n+ <search_score name="mvh" value="21.662729207058"/>\n+ <search_score name="mzFidelity" value="10.946707360696"/>\n+ <search_score name="xcorr" value="2.2375717592793039"/>\n+ </search_hit>\n+ <search_hit hit_rank="2" peptide="EMLIAHSQPAEMSCGKGESEKLSQIE" peptide_prev_aa="K" peptide_next_aa="N" protein="gi|528944676|ref|XP_005204734.1|" num_tot_proteins="1" calc_neutral_pep_mass="2905.3143452141" massdiff="0.03407514139" num_tol_term="1" num_missed_cleavages="2" num_matched_ions="21" tot_num_ions="180">\n+ <modification_info>\n+ <mod_aminoacid_mass position="12" mass="147.0353846062"/>\n+ <mod_aminoacid_mass position="14" mass="161.0146644778"/>\n+ </modification_info>\n+ <search_score name="mvh" value="18.555164806005"/>\n+ <search_score name="mzFidelity" value="9.229647340988"/>\n+ <search_score name="xcorr" value="1.9522110076248838"/>\n+ </search_hit>\n+ <search_hit hit_rank="3" peptide="LLLNTSKRIMDDVETSSLHLDESFK" peptide_prev_aa="T" peptide_next_aa="L" protein="XXX_gi|115497338|ref|NP_001069884.1|" num_tot_proteins="4" calc_neutral_pep_mass="2906.4695232566" massdiff="0.18058826829" num_tol_term="1" num_missed_cleavages="2" num_matched_ions="20" tot_num_ions="171">\n+ <alternative_protein protein="XXX_gi|528968104|ref|XP_005212567.1|"/>\n+ <alternative_protein protein="XXX_gi|528968106|ref|XP_005212568.1|"/>\n+ <alternative_protein protein="XXX_gi|528968108|ref|XP_005212569.1|"/>\n+ <modification_info>\n+ <mod_aminoacid_mass position="10" mass="147.0353846062"/>\n+ </modification_info>\n+ <search_score name="mvh" value="17.95496665471"/>\n+ <search_score name="mzFidelity" value="6.815403335045"/>\n+ <search_score name="xcorr" value="2.564456180282789"/>\n+ </search_hit>\n+ <search_hit hit_rank="4" peptide="QIFVKTLTGKTITLEVEPSDTIENVK" peptide_prev_aa="M" peptide_next_aa="A" protein="gi|115496708|ref|NP_001069831.1|" num_tot_proteins="4" calc_neutral_pep_mass="2904.5583369414" massdiff="0.28673178429" num_tol_term="2" num_missed_cleavages="2" num_matched_ions="20" tot_num_ions="179">\n+ <alternative_protein protein="gi|27807503|ref|NP_777203.1|"/>\n+ <alternative_protein protein="gi|528968221|ref|XP_005212615.1|"/>\n+ <alternative_protein protein="gi|528995063|ref|XP_005220352.1|"/>\n+ <modification_info>\n+ <mod_aminoacid_mass position="1" mass="129.0425935114"/>\n+ <mod_aminoacid_mass position="24" mass="115.0269434472"/>\n+ </modification_info>\n+ <search_score name="mvh" value="16.196711830419"/>\n+ <search_score name="mzFidelity" value="8.384634792566"/>\n+ <search_score name="xcorr" value="1.9797285930138711"/>\n+ </search_hit>\n+ <search_hit hit_rank="5" peptide="ELNGSLQEMQGESSGVSTVWDLLADIK" peptide_prev_aa="K" peptide_next_aa="R" protein="XXX_gi|528944678|ref|XP_005204735.1|" num_tot_proteins="1" calc_neutral_pep_mass="2907.369549893" massdiff="0.07194998909" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="18" tot_num_ions="188">\n+ <modification_info>\n+ <mod_aminoacid_mass position="7" mass="129.0425935114"/>\n+ <mod_aminoacid_mass position="10" mass="129.0425935114"/>\n+ </modification_info>\n+ <search_score name="mvh" value="13.019234366281"/>\n+ <search_score name="mzFidelity" value="6.610442990057"/>\n+ <search_score name="xcorr" value="1.709385507643441"/>\n+ </search_hit>\n+ </search_result>\n+ </spectrum_query>\n+ </msms_run_summary>\n+</msms_pipeline_analysis>\n' |
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| diff -r c0e3ae85a40d -r 032c02d10694 test-data/201208-378803-msgf.mzid --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/201208-378803-msgf.mzid Fri Oct 06 15:01:05 2017 -0400 |
| [ |
| b'@@ -0,0 +1,4631 @@\n+<?xml version="1.0" encoding="UTF-8"?>\n+<MzIdentML id="MS-GF+" version="1.1.0" xmlns="http://psidev.info/psi/pi/mzIdentML/1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.1 http://www.psidev.info/files/mzIdentML1.1.0.xsd" creationDate="2014-09-05T13:19:45" >\n+<cvList xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">\n+ <cv id="PSI-MS" uri="http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo" version="3.30.0" fullName="PSI-MS"/>\n+ <cv id="UNIMOD" uri="http://www.unimod.org/obo/unimod.obo" fullName="UNIMOD"/>\n+ <cv id="UO" uri="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo" fullName="UNIT-ONTOLOGY"/>\n+</cvList>\n+<AnalysisSoftwareList xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">\n+ <AnalysisSoftware version="Beta (v10072)" name="MS-GF+" id="ID_software">\n+ <SoftwareName>\n+ <cvParam 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name="StdevRelErrorTop7"/>\n+ </SpectrumIdentificationItem>\n+ </SpectrumIdentificationResult>\n+ </SpectrumIdentificationList>\n+ </AnalysisData>\n+</DataCollection>\n+</MzIdentML>\n' |
| b |
| diff -r c0e3ae85a40d -r 032c02d10694 test-data/201208-378803.idpDB |
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| Binary file test-data/201208-378803.idpDB has changed |
| b |
| diff -r c0e3ae85a40d -r 032c02d10694 test-data/input/201208-378803.mzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input/201208-378803.mzML Fri Oct 06 15:01:05 2017 -0400 |
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| b'@@ -0,0 +1,5375 @@\n+<?xml version="1.0" encoding="utf-8"?>\n+<indexedmzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.2_idx.xsd">\n+ <mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" id="201208-378803-ABRR-AUG-1" version="1.1.0">\n+ <cvList count="2">\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="3.65.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n+ <cv id="UO" fullName="Unit Ontology" version="12:10:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>\n+ </cvList>\n+ <fileDescription>\n+ <fileContent>\n+ <cvParam cvRef="MS" accession="MS:1000579" 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| diff -r c0e3ae85a40d -r 032c02d10694 test-data/input/cow.protein.PRG2012-subset.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input/cow.protein.PRG2012-subset.fasta Fri Oct 06 15:01:05 2017 -0400 |
| [ |
| b'@@ -0,0 +1,144 @@\n+>gi|528903801|ref|XP_871686.4| PREDICTED: cationic trypsin isoformX1 [Bos taurus]\n+MKTFIFLALLGAAVAFPVDDDDKIVGGYTCGANTVPYQVSLNSGYHFCGGSLINSQWVVSAAHCYKSGIQVRLGEDNINVVEGNEQFISASKSIVHPSYNSNTLNNDIMLIKLKSAASLNSRVASISLPTSCASAGTQCLISGWGNTKSSGTSYPDVLKCLKAPILSDSSCKSAYPGQITSNMFCAGYLEGGKDSCQGDSGGPVVCSGKLQGIVSWGSGCAQKNKPGVYTKVCNYVSWIKQTIASN\n+>gi|528908802|ref|XP_005199340.1| PREDICTED: zinc finger protein 169 isoform X1 [Bos taurus]\n+MRRVFSRKSTHQTKNMAPGLLTTRDEALMAFRDVAVAFTQKEWKLLSPAQRTLYRDVMLENYSHMVSLGIAFPKPKLIIQLEQGDEPWREESECLLDLCAAEGRKEFQPCLSCPVTFSSPQILHHYMLCGHALQIFPGSSAESHFLLDAPSCLNEKAKDGEREGSGTVFGRLQLSGTSRAFFSSSQGQPVDQGGSSSGRIDQGMISDEADAVLTETNISESGAVICENYRLGFSRKSSLFSLQKHHVCPECGRNFCQKSDLVKHQRTHSGEKPFSCRECGRGFGRRSSLTVHQRKHSGEKPYVCRECGRHFRYTSSLTNHKRIHSGERPFVCQQCGRGFRQKIALILHQRTHLEEKPFVCPECGRGFCQKASLLQHRSSHSGERPFVCLECGRGFRQQSLLLSHQVTHSGEKPYVCAECGHSFRQKVTLIRHQRTHTGEKPYLCSECGRGFSQKVSLMGHQRTHTGEKPYVCSECGRGFGQKVTLIRHQRTHTGEKPFLCPECGRTFGFKSLLTRHKRIHSGEEADVYRVCEQRLGLKIQLTSDQRTHSGEKPCVCDECGRGFGFKSALIRHQRTHSGEKPYVCRDCGRGFSQKSHLHRHRKTKSGHHLLPQELFS\n+>gi|528908804|ref|XP_005199341.1| PREDICTED: zinc finger protein 169 isoform X2 [Bos taurus]\n+MRRVFSRKSTHQTKNMAPGLLTTRDEALMAFRDVAVAFTQKEWKLLSPAQRTLYRDVMLENYSHMVSLGIAFPKPKLIIQLEQGDEPWREESECLLDLCAAEGRKEFQPCLSCPVTFSSPQILHHYMLCGHALQIFPGSSAESHFLLDAPSCLNEKAKDGEREGSGTVFGRLQLSGTSRAFFSSSQGQPVDQGGSSSGRIDQGMISDEADAVLTETNISESGAVICENYRLGFSRKSSLFSLQKHHVCPECGRNFCQKSDLVKHQRTHSGEKPFSCRECGRGFGRRSSLTVHQRKHSGEKPYVCRECGRHFRYTSSLTNHKRIHSGERPFVCQQCGRGFRQKIALILHQRTHLEEKPFVCPECGRGFCQKASLLQHRSSHSGERPFVCLECGRGFRQQSLLLSHQVTHSGEKPYVCAECGHSFRQKVTLIRHQRTHTGEKPYLCSECGRGFSQKVSLMGHQRTHTGEKPYVCSECGRGFGQKVTLIRHQRTHTGEKPFLCPECGRTFGFKSLLTRHKRIHSGEEADVYRVCEQRLGLKIQLTSDQRTHSGEKPCVCDECGRGFGFKSALIRHQRTHSGEKPYVCRDCGRGFSQKSHLHRHRKTKSGHHLLPQELFS\n+>gi|528908806|ref|XP_005199342.1| PREDICTED: zinc finger protein 169 isoform X3 [Bos taurus]\n+MRRVFSRKSTHQTKNMAPGLLTTRDEALMAFRDVAVAFTQKEWKLLSPAQRTLYRDVMLENYSHMVSLGIAFPKPKLIIQLEQGDEPWREESECLLDLCAAEGRKEFQPCLSCPVTFSSPQILHHYMLCGHALQIFPGSSAESHFLLDAPSCLNEKAKDGEREGSGTVFGRLQLSGTSRAFFSSSQGQPVDQGGSSSGRIDQGMISDEADAVLTETNISESGAVICENYRLGFSRKSSLFSLQKHHVCPECGRNFCQKSDLVKHQRTHSGEKPFSCRECGRGFGRRSSLTVHQRKHSGEKPYVCRECGRHFRYTSSLTNHKRIHSGERPFVCQQCGRGFRQKIALILHQRTHLEEKPFVCPECGRGFCQKASLLQHRSSHSGERPFVCLECGRGFRQQSLLLSHQVTHSGEKPYVCAECGHSFRQKVTLIRHQRTHTGEKPYLCSECGRGFSQKVSLMGHQRTHTGEKPYVCSECGRGFGQKVTLIRHQRTHTGEKPFLCPECGRTFGFKSLLTRHKRIHSGEEADVYRVCEQRLGLKIQLTSDQRTHSGEKPCVCDECGRGFGFKSALIRHQRTHSGEKPYVCRDCGRGFSQKSHLHRHRKTKSGHHLLPQELFS\n+>gi|528908808|ref|XP_005199343.1| PREDICTED: zinc finger protein 169 isoform X4 [Bos taurus]\n+MRRVFSRKSTHQTKNMAPGLLTTRDEALMAFRDVAVAFTQKEWKLLSPAQRTLYRDVMLENYSHMVSLGIAFPKPKLIIQLEQGDEPWREESECLLDLCAEGRKEFQPCLSCPVTFSSPQILHHYMLCGHALQIFPGSSAESHFLLDAPSCLNEKAKDGEREGSGTVFGRLQLSGTSRAFFSSSQGQPVDQGGSSSGRIDQGMISDEADAVLTETNISESGAVICENYRLGFSRKSSLFSLQKHHVCPECGRNFCQKSDLVKHQRTHSGEKPFSCRECGRGFGRRSSLTVHQRKHSGEKPYVCRECGRHFRYTSSLTNHKRIHSGERPFVCQQCGRGFRQKIALILHQRTHLEEKPFVCPECGRGFCQKASLLQHRSSHSGERPFVCLECGRGFRQQSLLLSHQVTHSGEKPYVCAECGHSFRQKVTLIRHQRTHTGEKPYLCSECGRGFSQKVSLMGHQRTHTGEKPYVCSECGRGFGQKVTLIRHQRTHTGEKPFLCPECGRTFGFKSLLTRHKRIHSGEEADVYRVCEQRLGLKIQLTSDQRTHSGEKPCVCDECGRGFGFKSALIRHQRTHSGEKPYVCRDCGRGFSQKSHLHRHRKTKSGHHLLPQELFS\n+>gi|528908810|ref|XP_005199344.1| PREDICTED: zinc finger protein 169 isoform X5 [Bos taurus]\n+MSVLDHALMAFRDVAVAFTQKEWKLLSPAQRTLYRDVMLENYSHMVSLGIAFPKPKLIIQLEQGDEPWREESECLLDLCAAEGRKEFQPCLSCPVTFSSPQILHHYMLCGHALQIFPGSSAESHFLLDAPSCLNEKAKDGEREGSGTVFGRLQLSGTSRAFFSSSQGQPVDQGGSSSGRIDQGMISDEADAVLTETNISESGAVICENYRLGFSRKSSLFSLQKHHVCPECGRNFCQKSDLVKHQRTHSGEKPFSCRECGRGFGRRSSLTVHQRKHSGEKPYVCRECGRHFRYTSSLTNHKRIHSGERPFVCQQCGRGFRQKIALILHQRTHLEEKPFVCPECGRGFCQKASLLQHRSSHSGERPFVCLECGRGFRQQSLLLSHQVTHSGEKPYVCAECGHSFRQKVTLIRHQRTHTGEKPYLCSECGRGFSQKVSLMGHQRTHTGEKPYVCSECGRGFGQKVTLIRHQRTHTGEKPFLCPECGRTFGFKSLLTRHKRIHSGEEADVYRVCEQRLGLKIQLTSDQRTHSGEKPCVCDECGRGFGFKSALIRHQRTHSGEKPYVCRDCGRGFSQKSHLHRHRKTKSGHHLLPQELFS\n+>gi|528908812|ref|XP_609847.5| PREDICTED: zinc finger protein 169 isoform X6 [Bos taurus]\n+MAFRDVAVAFTQKEWKLLS'..b'ily 12 member 1 isoform X3 [Bos taurus]\n+MSLNNSSNVFLDSTPSNTNRFQVNVINESHESSAAMNDNADPPHYEETSFGDEGQNRFRISFRPGNQECYDNFLQTGETAKTDASFHAYDSHTNTYYLQTFGHNTVDAVPKIEYYRNTGSVSGPKVNRPSLLDIHEQLAKNVSVAPGSADVVANGEGTPGDEQAENKGEDQAGAVKFGWVKGVLVRCMLNIWGVMLFIRLSWIVGEAGIGLGVIIIGLSVVVTTLTGISMSAICTNGVVRGGGAYYLISRSLGPEFGGSIGLIFAFANAVAVAMYVVGFAETVVDLLKETDSMMVDPTNDIRIIGSITVVILLGISVAGMEWEAKAQVILLIILLIAIANFFIGTVIPSNNEKRARGFFNYQASIFAENFGPSFTKGEGFFSVFAIFFPAATGILAGANISGDLEDPQDAIPKGTMLAIFITTVAYLGVAICVGACVVRDATGSVNDTIISGMNCNGSAACGLGYDFSRCRHEPCQYGLMNNFQVMSMVSGFGPLITAGIFSATLSSALASLVSAPKVFQALCKDNIYKALQFFAKGYGKNNEPLRGYFLTFVIAMAFILIAELNTIAPIISNFFLASYALINFSCFHASYAKSPGWRPAYGIYNMWVSLFGAVLCCAVMFVINWWAAVITYVIEFFLYIYVTYKKPDVNWGSSTQALSYMSALDNALELTTVEDHVKNFRPQCIVLTGGPMTRPALLDITHAFTKNSGLCICCEVFVGPRKLCVKEMNSGMAKKQAWLIKNKIKAFYAAVAADCFRDGVRSLLQASGLGRMKPNTLVIGYKKNWRKAPLTEIENYVGIIHDAFDFEIGVVIVRISQGFDISQVLQVREELEKLEQERLALEATIKDNESEEGNGGIRGLFKKAGKLNITKPTPKKDSSINTIQSMHVGEFNQKLVEASTQFKKKQGKGTIDVWWLFDDGGLILLIPYILTLRKKWKDCKLRIYVGGKINRIEEEKIAMASLLSKFRIKFADIHVIGDINVKPNKESWKVFEEMIEPYCLHESCKDLTTAEKLKRETPWKITDAELEAVKEKSYRQVRLNELLQEHSRAANLIVLSLPVARKGSISDWLYMAWLEILTKNLPPVLLVRGNHKNVLTFYS\n+>gi|297479727|ref|XP_002690982.1| PREDICTED: solute carrier family 12 member 1 isoform X1 [Bos taurus]\n+MSLNNSSNVFLDSTPSNTNRFQVNVINESHESSAAMNDNADPPHYEETSFGDEGQNRFRISFRPGNQECYDNFLQTGETAKTDASFHAYDSHTNTYYLQTFGHNTVDAVPKIEYYRNTGSVSGPKVNRPSLLDIHEQLAKNVSVAPGSADVVANGEGTPGDEQAENKGEDQAGAVKFGWVKGVLVRCMLNIWGVMLFIRLSWIVGEAGIGLGVLIILLSTMVTSITGLSTSAIATNGFVRGGGAYYLISRSLGPEFGGSIGLIFAFANAVAVAMYVVGFAETVVDLLKETDSMMVDPTNDIRIIGSITVVILLGISVAGMEWEAKAQVILLIILLIAIANFFIGTVIPSNNEKRARGFFNYQASIFAENFGPSFTKGEGFFSVFAIFFPAATGILAGANISGDLEDPQDAIPKGTMLAIFITTVAYLGVAICVGACVVRDATGSVNDTIISGMNCNGSAACGLGYDFSRCRHEPCQYGLMNNFQVMSMVSGFGPLITAGIFSATLSSALASLVSAPKVFQALCKDNIYKALQFFAKGYGKNNEPLRGYFLTFVIAMAFILIAELNTIAPIISNFFLASYALINFSCFHASYAKSPGWRPAYGIYNMWVSLFGAVLCCAVMFVINWWAAVITYVIEFFLYIYVTYKKPDVNWGSSTQALSYMSALDNALELTTVEDHVKNFRPQCIVLTGGPMTRPALLDITHAFTKNSGLCICCEVFVGPRKLCVKEMNSGMAKKQAWLIKNKIKAFYAAVAADCFRDGVRSLLQASGLGRMKPNTLVIGYKKNWRKAPLTEIENYVGIIHDAFDFEIGVVIVRISQGFDISQVLQVREELEKLEQERLALEATIKDNESEEGNGGIRGLFKKAGKLNITKPTPKKDSSINTIQSMHVGEFNQKLVEASTQFKKKQGKGTIDVWWLFDDGGLILLIPYILTLRKKWKDCKLRIYVGGKINRIEEEKIAMASLLSKFRIKFADIHVIGDINVKPNKESWKVFEEMIEPYCLHESCKDLTTAEKLKRETPWKITDAELEAVKEKSYRQVRLNELLQEHSRAANLIVLSLPVARKGSISDWLYMAWLEILTKNLPPVLLVRGNHKNVLTFYS\n+>gi|529012038|ref|XP_005226889.1| PREDICTED: pregnancy-associated glycoprotein 2 isoform X1 [Bos taurus]\n+MKWLVLLGLVALSECIVILPLKKMKTLRETLREKNLLNNFLEEQAYRLSKNDSKITIHPLRNYLDTAYVGNITIGTPPQEFRVVFDTGSANLWVPCITCTSPACYTHKTFNPQNSSSFREVGSPITIFYGSGIIQGFLGSDTVRIGNLVSPEQSFGLSLEEYGFDSLPFDGILGLAFPAMGIEDTIPIFDNLWSHGAFSEPVFAFYLNTISMNGTVTACSCGCEALLDTGTSMIYGPTKLVTNIHKLMNARLENSEYVVSCDAVKTLPPVIFNINGIDYPLRPQAYIIKIQNSCRSVFQGGTENSSLNTWILGDIFLRQYFSVFDRKNRRIGLAPAV\n+>gi|156523214|ref|NP_001096021.1| protein KHNYN [Bos taurus]\n+MPTWGAGSPSPDRFAVSAEAEDKVREQLPRVERIFRVGMSVLPKDCPENPHIWLQLEGPKENASRAKEYLKGLCSPELQNEIHYPPKLHCIFLGAQGFFLDCLTWSTSAHLVPGVPGSLMVSGLTEAFVMVQSRVEELVERLSWDFRLGPSPGASQCAGVLREFSALLQARGDAHTEALLQLPQAVQEELLSLVQEASRGQGPQAFPSWGWGGPGPLGAQQQGVRTPLGDGGVSLDTGPTGWQESRGERHAVEKEGTKQGGAREMDLGWKEWPGEEAWERQVAFRPQSGGGEASGGGEAGQAGPPKGKALGKEGVPQERGRLGVQGQPPSTQGPYQRASQLRGASLLQRLHNGEASPPRVPSPPPAPEPPWHCGDRGDRGDRADKQLVVARGRGSPWKRGTRGGNLVTGTQRFQEALQDPFTLCLANVPGKPDLRHIVIDGSNVAMVHGLQHYFSSRGIAIAVQYFWDRGHRDITVFVPQWRFSKDSKVREGHFLHKLYSLSLLSLTPSRVLDGKRISSYDDRFMVKLAEETDGIIVSNDQFRDLAEESEKWMAIIRERLLPFTFVGNLFMVPDDPLGRNGPTLDEFLKKPVRAPGSSKPQQSARGVTEHSNQQQGRKEEEKGNGGIRKTRETERLRRQLLEVFWGQDHKVDFILQREPYCRDINQLSEALLSLNF\n+>gi|28849951|ref|NP_788787.1| pregnancy-associated glycoprotein 2 precursor [Bos taurus]\n+MKWLVLLGLVALSECIVILPLKKMKTLRETLREKNLLNNFLEEQAYRLSKNDSKITIHPLRNYLDTAYVGNITIGTPPQEFRVVFDTGSANLWVPCITCTSPACYTHKTFNPQNSSSFREVGSPITIFYGSGIIQGFLGSDTVRIGNLVSPEQSFGLSLEEYGFDSLPFDGILGLAFPAMGIEDTIPIFDNLWSHGAFSEPVFAFYLNTNKPEGSVVMFGGVDHRYYKGELNWIPVSQTSHWQISMNNISMNGTVTACSCGCEALLDTGTSMIYGPTKLVTNIHKLMNARLENSEYVVSCDAVKTLPPVIFNINGIDYPLRPQAYIIKIQNSCRSVFQGGTENSSLNTWILGDIFLRQYFSVFDRKNRRIGLAPAV\n' |